text:
How do I appropriately decline an invitation to an appointment lecture ("Probevorlesung") without burning bridges?
I will soon be accepting an offered professorship at a university that is a little further away from where I live.
Now I have received the invitation to an audition (lecture + interview) for a professorship at the local university ("Probevorlesung" as it is called here in Germany).
Actually, I don't really want that specific professorship at the local university, but I also don't want to mess with the local university because it is a potential employer for me. I would not rule out changing universities in a few years if the opportunity of a more suitable professorship at the local university arises.
Problem is: Rumors said that candidates who turn down invitations are never invited again.
Is there any way for me to appropriately decline the invitation without burning bridges?

Yes, that's probably a very literal translation of the German expression "den Ruf annehmen". I have changed my post accordingly.

@Roland The new position is ideal for me, but at the wrong university ;-)

It's unclear to me what "Audition lecture" means here. Are you talking about a job talk? Have you applied for a position at this university? This situation needs some more/better explanations. Even if this is culturally dependent on taking place in Germany your question should still describe the problem in a way that non-Germans can understand.

So the question refers to a Probeverlesung? https://de.wikipedia.org/wiki/Probevorlesung

This question really needs more explanation. As it stands I'd guess the question boils down to "I am no longer interested in an academic position I applied for, how do I tell the search committee even though I already received an invitation for giving a job talk" which already has an answer here https://academia.stackexchange.com/questions/150236/how-to-politely-turn-down-an-on-site-faculty-interview-offer

You should clarify what invitation you got - usually, you would get invited for an interview, which would include interview + talk + possibly a Probevorlesung.

You should communicate clearly (and swiftly) that you are declining the invitation because you are accepting the offer of a professorship at another university. In fact you should not just 'decline the invitation', but completely withdraw your application to your hometown university.
I would not be worrying too much about burning bridges, most likely the view of the hiring committee at your hometown university will be more like 'Shoot! We have lost an excellent candidate to university X. We have to be more attractive/move more quickly/offer better working conditions next time'.
Finally, let me say that this seems like a true luxury problem! Being offered a professorship 'a little further from where you live' and being invited for a Probevorlesung at your hometown university is something that most aspiring researchers would only dream of.

My perspective is the US, not Germany, but here, at least, it should be completely acceptable to say that I was sorry that I couldn't accept the invitation since I have another position already and wouldn't want to waste the time of the inviting institution.
But you could add, supposing that you are willing, that you would be happy to give a lecture, though not as an audition for a position.
Among other things, this puts the onus on the university for making a too-late invitation.

+1 for "happy to give a lecture, though not as an audition"

Actually, you could add "at some future time" to the offer. It is, then, an offer from a colleague to give a lecture, and perhaps open collaboration options.

@Roland It's purely a matter of courtesy. It does not mean that one does not understand the system. And if they really so grossly misconstrue the message of OP or assume bad faith, then OP dodged a bullet anyway and doesn't want to have to do anything with them. Plus, I agree with Buffy that the onus is on them for being late.

@Roland Point taken, fair enough. But I still think it is courteous to offer the talk as regular non-application talk. They may decline it, of course, but this is like saying "thank you" in "No, thank you". Not essential, but polite.

@Roland, can you explain why? I don't have any reason to disagree, but would be interested to hear your perspective on the cultural differences. Is it more than the difference in "formality" between US and Germany, or more than that?

@Roland, thanks. I was thinking more of a lecture to faculty and advanced students on some specialized topic, or even open to the public. A seminar type of thing.

In addition to what @Roland says, the Probevorlesung is a lecture (as in teaching undergrad students) on a topic that is specified by the commission, it is not a presentation on OP's research.

The best thing you can do is to immediately turn down the invitation, and withdraw your application, especially if you are potentially interested to moving back to that university at a later time. It would be much worse to continue with the application process. Imagine you would end up receiving an offer, and then you would turn it down: If you decline the offer at that point, this would have cost everyone significantly more time and energy, it would have delayed the entire process, it would have taken someone else's spot on the shortlist (potentially risking to end up without a candidate accepting, also due to the delay), and it would probably not even help you to negotiate at your future university.
So unless you are 100% sure that you won't receive the offer, withdraw now, otherwise you risk to truly burn bridges. (And even if you are sure you won't get the offer, you should withdraw now - the university will learn that you had accepted an offer somewhere else (unless you manage to delay this until you are out) and people will get the impression you weren't taking the application seriously.)


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How do I properly reference?
I’m writing an essay, and have been asked to use Harvard Referencing.
From what I know this type of referencing uses citations similar to (my brain, 2016).
And then contains a bibliography like:
Bibliography  — or — References
My Brain (18 Dec. 2016) - “Title of article, or something” available from my skull
...
I've seen referencing done with [number's] instead of (author / publisher, date) in a few papers and - probably most famously -  wikipedia.
Is this not classed as Harvard referencing?
I find it so much neater and easier to follow, especially if I'm going to refer to multiple peices of work by the same author/publisher.
Also, I've noticed some papers placing mini bibliographies at the end of every page, containing all the references for that page.
Is this not harvard referencing?
I'd like to do this as it removes the pain of having to go all the way to the bibliography to check a citation.

"From what I know this type of referencing uses citations similar to (my brain, 2016)" I'd suggest try not to operate on what you know; better to have a concrete guide. Meet with a librarian at your institute for some comprehensive resources and stick to them. (Secondary, if librarians are busy, Google "harvard reference filetype:pdf" gets some good sources as well.) Should you wish to modify it or use another variation, confirm with the organization/person that will receive and evaluate your work.

The Harvard citation system does not use reference numbers.  It uses, as you describe, the author's last name and publication year.  (This is similar to the APA citation style.)
The reference lists should be at the end of the document, not listed as footnotes.  So your understanding of the Harvard style seems to be basically correct.  Some more details about the Harvard citation style are given here: http://www.citethisforme.com/harvard-referencing
Personally, I too prefer referencing by number rather than author, but if you are supposed to use the Harvard style, then you just have to use it.

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Do large number of attended conferences favour application to postdoctoral or tenured positions?

Situation: I started my PhD (Pure Maths) in January 2018. My research interest lies on functional analysis but not on applied side.
  If possible, I would like to stay at academia as a Maths researcher or lecturer (or even better, professor).

Recently I came across a few conferences that I would like to attend. However, due to my scholarship terms and conditions, I am able to obtain financial assistance from the school only once per year.
However, some of my peers attended more than one conference per year due to their prestigious scholarship.

Question: Would a Phd student with few conference attendances be at a disadvantage when applying for postdoctoral / tenured track position?

By conference attendance, I mean attend AND give a talk at conference.

Do any of the conferences you're interested in have problem sessions or research workshops where attendees can set up new research collaborations about specific problems posed at the conference? My perception is that many math conferences have those, and fairly uniquely relative to other fields? This may be a factor that doesn't come up in more generic advice.

The purpose of attending conferences when you are at the PhD level and post-doc level is not for padding your CV, although people still want to see you have presented at some international recognized conferences. The main purpose is to advertise yourself and your research and to network for what could be your next position. In fact it is possible to walk out of a conference with some kind of contact or verbal agreement that sets you up for your future job.
For professorship application I don't think just attending conferences will help you, rather they will want to see that you have been keynote or plenary.

OP is not asking about professorship applications - but about tenure-track (assistant professor in the US) positions.

@Dawn I don't see anywhere that OP mentions the US, isn't professorship a position to be professor?

You don't state your country.  My experience in the US and Canada in Pure Math is that financing from your program for a conference once per year is on the generous side of standard; I believe when I was a graduate student, we would receive such funding from my program once for the entire term of your Ph.D.   However, I went to many more conferences than that as a student, thanks to funding from the conferences and from my advisor.  If you are giving a talk at a conference, then it would be a bit unusual for the organizers to not provide you with funding (though every rule has its exceptions).  Certainly when I've done conference organization, funding speakers has been my #1 priority for any money we have.
My experience is that going to conferences can be valuable, and I recommend that you do it when possible, but as other answers have said, they are not an important consideration for hiring committees.  Certainly, it's quite normal for me to see postdoc applications with only one or two (or even zero) conference talks on them; I don't see that as a big issue. Focus on doing good research and when you see a relevant conference, request funding from the organizers or your advisor; self-funding is also a possibility, but I would only do it when the conference is really significant or the amount of money required is small.

In my field, it is relatively rare to receive funding from conference organizers even if you are presenting. The exception would be very small and specialized conferences.

@Dawn Yes, what Ben Webster describes sounds standard for pure math (conferences are often funded by grants that include registration and housing and maybe travel for attendees), but it is the exact opposite of, say, expensive conferences in Computer Science.

@cactus_pardner Right - I am making this comment to ensure/emphasize that people who are not in pure math and look at this question realize that this may vary in their field.

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Have there been studies about the effect of idle time vs time pressure in learning?
There is a discussion in our institute about how much of their time students should spend on lectures and homework.
My own experience has been that idle time and wandering of the mind is necessary for seeing the big picture, but I understand that this depends on personality, context etc.
Are you aware of any papers which discuss this issue? What are the keywords for this topic?

I don't know about studies that directly address what you're asking about, but I do know of studies (reported in a book What's the Use of Lectures?) showing that time spent actively studying lecture material is vastly more effective the sooner it comes after the lecture.  That is, do the homework first, then let your mind wander.

There is an article on college students under pressure. It details on the effects and the health related issues involved.

Amy Novotney, "Students under pressure," American Psychological Association, Vol 45, No. 8, pp. 36 September 2014.

Although it doesn't explicitly account on idle time, you should be able to draw conclusions from the content provided.


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Including a non-relevant work experience in Statement of Purpose for higher studies abroad
After completing my undergraduate studies in Biotechnology, I switched to a career in Banking services where I have worked for a year. But now I would like to pursue higher studies abroad in biological sciences and I don't know how exactly I am supposed to include my work experience in my SOP. Since, my work experience is not related to my program of interest, how should I approach this issue?

I'd suggest including in your SOP just as much about banking as you've included in your question here. That is, give it about half a sentence and then move on to relevant things.

Related: http://academia.stackexchange.com/questions/58440/should-you-list-irrelevant-work-experience-on-graduate-school-applications

Just a blank stretch in your time line does look bad.

Juat describe things as they are - there is no way around it.

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What is the best way to explain the change of my research interest in my Statement of Purpose for a PhD application?
I've been an research assistant in a lab of my department for a while. I've gained some research experience and skills but I've developed some new research interests during my internship and I found them more interesting to pursue in my graduate study. However, I have no related research experience. How do I address that in my SOP for the Ph.D application?

How about explaining just along the same lines within your statement of purpose, as you do in your question, in a more developed way?
If you have a strong line of argument to underpin your change of research interests, and you can demonstrate you are committed to go further with this line of enquiry, and how your previous research can help with what is to come, and/or demonstrate how the knowledge and skills you've acquired and developed so far will support your future research efforts, that would be a good way to address this change in your application.


text:
Assistant professor position in the USA. Can any leftover startup money for equipment be used to pay students or my summer salary?
I got an offer for a tenure-track assistant professor position in USA, Department of Engineering. The university national ranking is between 35th and 65th at the US News website. if I will have any left start-up money for equipment, could it be used to pay PhD students or my summer salary? Or are they two different accounts? Does it maybe depend from University and University?

Yes, it depends on the university and what you negotiate.

No one here can answer that, you need to ask the people who made you the offer.

This varies not only from university to university but from department to department. In some places it wouldn't be a problem, and in others it may even be impossible.
I recommend you get in touch with whoever your point of contact is (whoever extended you the offer) and ask them directly. It is important that they know you want to do this as this will naturally affect how much startup funds you are liable to need.

In addition to what rturnbull suggested, have whatever is promised in writing. Administrators change and verbal promises can be easily forgotten.


text:
Startup package, for assistant professor in USA: should I ask for a an extra PhD or an extra post-doc?
I got an offer for a tenure-track assistant professor position in USA, Department of Engineering. The university national ranking is between 35th and 65th at the US News website. I was offered a single PhD, fully supported for 2 years (partial support for the remaining 3 years) and then I was asked how much I need for equipment. I have two questions:

Should I ask for a second PhD or a post-doc (I think for 1 year)? Some people told me to get a PhD since supervising a post-doc does not really count much for getting Tenure, while it matters a lot if one is mentoring PhDs. Other people say: get a Post-doc, he/she will be much more productive and he/she will get you papers out fast, and your mentoring effort will be on the PhD. What is your suggestion?
I am actually also debating if I should also try to ask for a third person (in that case surely a PhD) since I am not asking too much money as for equipment (just computing cores in the supercomputer). And I need workforce since I have various good research ideas. Would I sound too greedy?

So basically, should I ask for a total of 3 persons (2 PhDs + 1 post-doc or rather 3 PhDs?) or 2 persons (2PhDs or rather 1 Phd + 1 Post-Doc?)?

Get the postdoc.  The postdoc is what will lower your stress.  You know the phrase popular among women in grad school?  "I need a wife"?  Researchers needs a postdoc.  (I don't mean to say it's not a symbiotic relationship between professor and postdoc.)

(Jokingly) How much money do you want to save?

Mmm what do you mean with " How much money do you want to save?"  I dont get the joke...

@Lupocci - I would guess CMosychuk meant that a postdoc gets a higher salary than a PhD student.  But if you really want an answer, you have to get the person's attention as follows:

@CMosychuk - Did I get your idea right?

@aparente001 I wasn't getting notifications on these replies. You're right that a Ph.D. student will cost you less in the long run

There are a number of factors to consider.
PhD students take an indeterminate amount of time to finish. Committing yourself to getting funding to cover the last "few" years for 2 or 3 PhD students is a stress you may not want your first year.
The cost to a department of a PhD student and Post doc can be vastly different. In some cases a PhD student means allocating a student from a general pool directly to you, such that there is no change in the schools budget. In other cases the stipend, tutuion, and fees all show up on the school budget. In other cases the number of PhD students may be limited (e.g., the department may not attract lots of good students) in which case a PhD student is way more "expensive" then a post doc. You ideally want to ask for whatever is cheapest (which includes money and political capital), for the department.
Another thing to consider is what is typical for a startup package. Also what can you justify. Often startup package negotiations are between the department chair and the dean. While it may seem like you are negotiatin with the chair, you are often equipping them with the information to battle the dean on your behalf.

The info you shared looks helpful.  But there's a big advantage to a postdoc, see my answer.

The advantage of a postdoc is that s/he is more independent, so you invest less and gain more.  Also a postdoc can help you set up a lab, if you are going to have a lab.  If there are experiments that require having someone in the lab at odd hours, you can take turns covering -- that can be a big plus.  And you may publish some papers together -- that will help you both build your careers.
If you had asked, one postdoc or one (or two) PhD students, that would be trickier to advise on, without a lot more information.  But in your situation, you get the fun of a PhD student regardless of which scenario you go with.

Thanks. Is it true that mentoring post-doc does not matter for tenure?

You should ask the department chair.  As StrongBad said, the department chair will want to negotiate with administration to bring as many resources as possible into the department.  The chair can help you figure out what resources you can get.  The chair can also tell you about the importance of PhD supervision to your tenure case.
Random people on the internet do not know your institution's goals and funding situation.  The department chair does know.


text:
Should I cite my supervisor in a thesis?
I am currently writing up a thesis and was wondering if one should cite the PhD supervisors on insights that were solely their idea?
As an example I have a sentence in the thesis that looks something like this in the outlook section at the end of the thesis:

We noticed {cool new phenomenon}, which we suspect to be a result of {awesome effect/explanation}. The details are currently under investigation.

Now my supervisor and I discovered this phenomenon together, but she came up with the explanation without my input. One could say that "we" means "my supervisor and I" in a thesis, but then the author of the document is just me.
I was wondering what proper citation practice is on something like this?
Options:

Maybe I can put a reference to "superviorName, date, private communication"? Is that enough though
Explicitly putting their name into the formulation, e.g.

My supervisor {supervisor name} and I noticed {cool new phenomenon}. {supervisor name} found this to be a result of {awesome effect/explanation}. The details are currently under investigation.

I cited one of my advisors in my thesis - but this was because my paper explicitly used papers she had published. I didn't cite either of my two advisors just for the ideas they gave me.

Since this is a concrete item (rather than some generic advice) and someone else (meaning "not you") came up with it, you need to cite it.
A personal communication reference would be in order. Your first text sample seems fine to me though (once the reference is added): I assume that you do share the suspicion of your supervisor, so the text is not misleading.
Asking your supervisor about this is definitely a good idea, though.

thanks for your answer! I also feel like I need to cite it, there is only one problem I see with it: realistically all the projects in the thesis are to a large extent crafted by the supervisor and many of the main ideas come from them, even though it might not be such a concrete item as my example. But if I cite my concrete example doesnt it seem foolish considering that I never cited any of the other non-concrete stuff? It may almost seem like I intended to indicate that this was the only thing the surpervisor did, which is really the opposite of what I want to express with the citation.

I think it is common and well-known that the supervisor sometimes helps the PhD student. In fact, the main work of the supervisor is giving ideas that they come up with due to their experience and knowledge. In many cases, this ideas will not work, in some cases they may. It is up to the PhD student to work out the details and see what comes out in the end.
Thus, I don't think that you should cite your supervisor at every idea she came up with. It should of course be clear in the document who supervised you and you might want to add an acknowledgement.
Two small points to finish:

If the result is important enough for a stand alone publication, i.e. if you are writing a paper out of it, your supervisor deserves to be one of the authors (then again, this should be rather common for most papers written by a PhD student...).
If you are in doubt, ask your supervisor about it. She will know how to write it and you can be sure that she agrees with your choice.

I do think it is best practise though if the student is clear about which ideas they got from their supervisor and which ones they came up with on their own. In this case it is not even clear to me that this is an observation the supervisor intends to "give" to the student.

@Arno I think it depends on how elaborated the idea is. Something general like "this paper I read recently might help you" might need a different treatment than "I worked out this theory and I proved that it solves your problem, here you have my five pages of notes". Thus, asking the supervisor might be the best choice here.

Many years after my PhD thesis with Andy Gleason I wrote this in a tribute:

The central mechanism for  producing  examples  and  counterexamples
  showing  the  theorem  was  sharp  came  later  that  spring.
  Moreover, I think the idea was his, although I didn’t give him due
  credit then. (http://www.ams.org/notices/200910/rtx091001236p.pdf)

He didn't say a word when he read the thesis.
I don't think you need to thank her for this particular idea. But you should ask.

During my diploma thesis, my supervisor indeed insisted in having ideas stemming from him properly cited. The reason he gave was so that I could not make any claims when he made use of them.


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Whether to exclude standard deviation in plot of outcomes of a series of experiments?
I have performed 21 different experiments, which I have repeated 3 times in total (63 samples gathered).
I plan to compare data using a bar plot. For bar plotting, I initially decided that I will calculate the mean over every 3 samples, and I will graph this value. However, along with the mean an important thing to state is also the standard deviation. I really do not want to include standard deviation on my graph as it will blur the results to the reader.
Of course, I can just put standard deviation into table, but this will be completely useless to regular reader.
Seeing other papers I sometimes spot that researchers do not really state how the values was gathered. Should I then assume they have conducted measurement only once?
Would it be ethical to not inform the reader that I plot the mean on my graphs? Any other suggestions are welcome.

Standard deviations do not "blur the results to the reader"; they inform the reader about important information about the variability in your data.

I think you're vastly underestimating your readers by assuming that the standard deviation is useless information to them. It's probably some of the most crucial information you could include.

@JackAidley ChrisHayes I can't disagree with you. See my current barplot (http://ibin.co/2V6lTIjnvPsb) Imagine it combined with the SDs. To make the madness even higher, please be aware I have four such graphs currently. I hope you can now see my point of view - IMO this would look terrible. Maybe dotchart as proposed by StephanKolassa is a way to go.

@KWubbufetowicz: It would look a lot less terrible than it looks without them. Also take the exact numbers off the chart. You don't need them and they needlessly clutter the data.

Put the exact numbers into a table in the supplementary online material. Switch the order of the legend so the colors in the legend are the same as the data. The y axis is unclear, can you make it more informative? And yes, use a dotchart! (I'll never use ggplot2 because of the ghastly grey background, but lots of people seem to be happy with it. I'd recommend looking at this.)

You should also ask yourself if you want to list SD or SEM. This depends on what you are attempting to show with the plot, specifically if you wish to show technical variation, then you should show the SD. However, if you want to figure to portray an effect in your actual sample (biological/chemical or what not) then SEM might be better.

Don't do this.
Here is some random data with 21 experiments A-U, each one repeated 3 times. In both cases, the experimentwise means (indicated using red crosses) are identical, but the within-experiment standard deviations are very different (1.0 in the top graph and 0.2 in the bottom one). R code is below.

Just seeing the experimentwise means is very misleading. In the bottom case, the experiments seem to be pretty different, and you could start interpreting the differences between them. In the top case, it's rather obvious that the difference between experiments is dominated by the variance within experiments. Put differently: the proportion of variance explained by the experiments is very different between the two cases.
This is a crucial piece of information. Do not leave it out. Leaving the variability out does not "blur the results to the reader" - the variability may be more important than the means.
In particular, remember that most readers will only look at your graphics, and even if they do read the text, the main thing they will remember will be the graphic. If you only put the means there, readers will remember the means. They won't remember whether the standard deviations were large or small compared to the differences in means.
So: look for a way to visualize both means and variability. For starters, don't use bar plots. Use, for example, dotcharts as I did. With your small dataset, you can without problems plot all your data, plus means.
If you want to emphasize the means, you can do all kinds of things involving colors, shapes or sizes. For instance, I used smaller grey dots for the observations so the means (larger red crosses) stood out more. And I used vertical lines to indicate experiments, and these lines are a lighter shade of grey than the dots.
Note that the human brain is better at interpreting positions (as in a dot chart) than lengths (as in a barplot). Nor should you use so-called "dynamite plots", that is, bar plot with "whiskers" that indicate standard deviations (or standard errors of estimated means - one problem with dynamite plots is that it is not always indicated whether whiskers give SDs or SEMs, and these are very different things).
See here and here for more on dynamite plots. This earlier answer of mine gives a few more options for visualizing data.

R code:
experiments <- LETTERS[1:21]
set.seed(1); means <- runif(21)
obs <- list()
set.seed(1); obs[[1]] <- matrix(rnorm(63,0,1),ncol=3,byrow=FALSE)
set.seed(1); obs[[2]] <- matrix(rnorm(63,0,0.2),ncol=3,byrow=FALSE)

opar <- par(mfrow=c(2,1),mai=c(.8,.8,.1,.1))
    for ( ii in 1:2 ) {
        obs[[ii]] <- obs[[ii]]+means-rowMeans(obs[[ii]])
        plot(c(1,21),range(unlist(obs)),type="n",xlab="Experiment",ylab="Observation",xaxt="n")
        abline(v=1:21,col="lightgrey")
        points(rep(1:21,3),as.vector(obs[[ii]]),pch=19,col="darkgrey",cex=0.8)
        points(1:21,rowMeans(obs[[ii]]),pch="+",col="red",cex=1.5,font=2)
        axis(1,1:21,experiments)
    }
par(opar)

Good answer; but I think the problem is not intrinsic to dynamite or whiskers plots, but to the person plotting them not specifying what they mean.

@Davidmh: if the plotter (pun intended) does not specify whether whiskers indicate SDs or SEMs, that is indeed one problem. However, dynamite plots inherently compress information, which is a problem all by itself for small $n$, quite independently of the author's annotating them or not.

+1 for explaining what (not) to do and why, as well as answering the question (including code).

Adding to @StephanKolassa 's excellent points, another reason to show all the data is that there could easily be outliers that might be very interesting. (Also, note that Stephen's plot does not include the SD because it does not need to.  It shows all the data without being cluttered).

@StephanKolassa, thank you for the directions. Your answer is very useful and informative. I have been looking for a suitable way to represent my data, but as the R noobie I have ultimately fallen back to barplots. The dotchart proposal seems to be well suited to my problem - I will give it a try. BTW, thanks for the R code!

I have run into exactly the same situation, where I wished to plot means but not standard deviations, in order to show the data in a less cluttered manner.  How I dealt with this problem was:

In the main text, put the plot that I felt most communicative, i.e., with only the means.
Attach the more cluttered plot that included the standard deviations as supplementary material, so that all the information was available to the reader if they want it, and it's clear I wasn't hiding anything.
When discussing the figure in the main text, explain exactly what I did and give a pointer, something like "Only means are shown here, for clarity; full information is in Supplementary Figure XX."

In short: you can present things as clearly as you like, and also should not try to hide anything.

Although, the community seems to value the other answer much more - I am also satisfied with yours. I will see how my data will present with dotchart as Stephan Kolassa proposes. If this will be looking poorly I will fall back to into your suggestion. Anyway - thanks!

@KWubbufetowicz The dot chart is a good way of dealing with moderate density datasets.  For very high visual density (e.g., the data in Supp.Fig 5-12 of this supplementary, in which the means already pretty much fill the graph, a dot chart would not be sufficient.  For your case, where you've got only 21 bars, the dot chart will probably work well, though.


text:
Authorship;first,second,co
I am finishing my first paper. I am unaware of how I should treat a certain situation, and have come  here for advice.
The paper is about 30 pages long. I have written 26 of those pages. On the pages I wrote, the other person helped with how thoughts are to be expressed, but all the theorems and proofs were done by me. The ideas of the paper are mine, and their execution.
How is the authorship to be divided in such an example? Should I be the first author or the corresponding author? Both? Should he be the second author, or the co-author?
I read this answer here, saying in math and computer science all authors are considered to have contributed equally. How should the ranking be notated than?
EDIT:
Question in partially answered in the linking answer (duplicate), at the comments bellow.

First author, second author, corresponding author: They're all authors.
Whenever there is more than one author, all authors are co-authors in relation to each other. Corresponding author is one author and can be assigned to any authorial position. The LaTeX issue is a minor technical issue that has no relationship with the fundamental question of (a) who should be corresponding author? (b) What should the order of authorship be? I feel like you may want to edit your question to focus probably on the basic questions of author order and who goes corresponding author.

I have edited the title and the body. Thank you for your comment. Might you offer an insight on ordering? I think you cleared up the corresponding author issue already.

I took out LaTex tag because it is no longer relevant.

If you mean that you are in either math or CS (by the last sentence), then the authors should be listed alphabetically. Who should be corresponding author is just deciding who wishes to deal with the journal.

@TobiasKildetoft Yes, I am. How is first, second authorship notated than? Or is it the case, that is is not.

The order of authors is the order in which they are listed on the publication (reading from left to right as always). In math and theoretical CS, nobody cares which place in the order you are (since as I said, it is alphabetical rather than by contribution).

Thank you, your comments, and the possible duplicate answered my question.

Please specify your field in your question. The authorship is very much field dependent.

 Simply, you should be the first author.
A corresponding author will be responsible for replying to the queries come from the research community and help them to a better understanding as well as gain more citations. There are other things can you find them in the link below.
Finally, If the other author can do this task, make him the corresponding author and you can help him when needs.
This post talk about The difference between Corresponding author and First author.

Simply, this might be incorrect depending on the field of the OP.

@TobiasKildetoft can you provide an example?

This was covered in the comments to the question. The OP is in a subject where authors are listed alphabetically, so they should only be first author if their name comes first alphabetically.


text:
Factors determining a feasible research field
It was discussed in prospect of PhD research proposal previously, but this question is for all ages of researchers.

What factors should one take into consideration before selecting a research field?

This related q. deals with professors: http://academia.stackexchange.com/questions/1449/how-do-professors-usually-discover-new-research-interests

Are you passionate about it?
Are you good at it?
Will people pay you to do it?

Everything else is noise.

Being paid helps but is not a necessary condition for feasibility. I am doing 20 hours a week of research that is uncompensated because I satisfy the first condition so well.

But if you want to do it as a career, it would be nice to get some remuneration for it.

I think the most important is the first one, You should passionate you going to investigate. The research field must like you.

Some points for STEM:

What are worldwide current emerging technologies? Which topics become attention by scholars, industry and funding institutions in journals.
Funding: What topics (like green energy in Germany) are on the local research agenda of your country for the next decades?
Fundamental research: where are contradictions of widely-accepted but incomplete theories in a field. Are the major paradigms consistent? (e.g. bringing together general relativity and particle physics). See my answer here on open problems
Meterology improvement/measurement methodology. Often very tricky, time- and cost-intensive engineering problems, but often making falsification/discovering of new phenomenons possible at all, opportunity to develop patents
Are there enough possible and qualified students, scholars for collaboration in a special (new) research field you can hire/attract? Of course, someone has to make the first step, but in STEM money and manpower is often the crucial factor to compete with other research groups, otherwise it's easy to waste a lot of money and time while someone already published the results you are still trying to measure. Without good students and a well-equipped lab it will be hard to attract money, students and scholars. In Germany you see this in form of "clustering" of several research institutions interested in semiconductors and chip-technology in German silicon valley near the city of Dresden.
Can you and your group dive easily into a new or related research topic? Do you have the infrastructure, is the gap of knowledge too big? How big is the risk, if you fail in this topic or it becomes suddenly un-trendy/unimportant. That's why research groups often do some diversification of research interests. Don't put all your money on a single stock.
a really good nose, overview and knowledge of current state of the art and knowledge.

Typo. Too small to change with my rep. "phyiscs" should be "physics".


text:
How to evaluate an open access journal?

Possible Duplicate:
How do you judge the quality of a journal?

How to evaluate the genuineness/authenticity, impact, significance & reputation of an open access journal? The prestigious journals have Impact factor & various indices, What about open access journals?
EDIT: Although a previously asked question has garnered many responses, this question is only toward open access publishing.

this question is explicitly for open access.

I'm with @JukkaSuomela. There shouldn't be a difference.

@bobthejoe but there is a difference.

The economics are different for open vs. closed.  This means the "human physics" are nearly entirely incompatible with a non-open-access journal.  Look at communism/socialism vs. market economy.  The level and pervasiveness of tyranny is nearly asymptotically maximized in the former.  That is "different physics" for reviewers of the papers.

In the same way you evaluate quality of a non-open access journal: who are the people on the editorial board, what kind of papers do they publish, etc.

Yep.  The quality of a journal is completely orthogonal to its business model.

I think this question has more merit than it is being given credit for.  Most of the journals that I currently have experience with are not open access but I can judge them based on extensive experience both as an author and a reader.  However as I become more interested in supporting and furthering open access, I am faced with having to evaluate journals that I have essentially no experience with (and neither do my peers).  This means that I can wait until I have acquired years of experience before I begin to publish in OA journals or look to use a different approach.

@DQdIM, I think that the correct question is how do you evaluate a new journal, not necessarily an OA journal. For instance, eLife is a brand new journal and there is no IF to measure or past experience, but from merely looking at their list of editors, you know it is going to be legit.


text:
Error discovered in an accepted conference paper but not yet presented
I'm a CS student, and I discovered two code bugs that change some numerical values on a table of a paper that got accepted and will be presented at a conference very soon. The changes is very small (think 0.1), and they don't affect the main conclusions of the paper at all.
I haven't talked to my coauthors yet but I don't know how to go about this. On the one hand I'm scared if I contact the organizers they might retract it for not being super accurate or something like that (conclusions don't get affected at all), but on the other hand I don't want to publish buggy code on GitHub and get caught there. What is the best way to go about this? Will the retract the paper if I contact the organizers?

Have you submitted a camera-ready paper yet? If not, then just modify the paper before you do.

Talk to your co-authors of course. But also talk to the conference committee and provide, or offer to provide, corrected copy. They may be able to help or not. But for the presentation, give the latest, most correct, version and note, if necessary, that the printed version has small errors not affecting the conclusions.
Some CS conferences will print proceedings and some of them will have a version ready before the conference. It may be possible that a second version, for general distribution, can differ a bit in details, but that is up to the conference and to the publication board of the organization sponsoring the conference.
But letting everyone know immediately is the best overall strategy.

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


text:
Why is it necessary to have a master’s in Europe to apply for PhD?
When I look for a PhD position, they always write that they need a master’s degree. However, most of the times I see that I have all the experience they are looking for. PhD is a lab-based work, so what they will do with the degree? Shouldn’t they take someone who is more good at lab work?

A PhD degree should indicate that you are ready to do research in your field. That requires a combination of skills, including understanding of your research area and related areas, not just lab work.
Typically, in the USA the PhD program includes coursework to build and demonstrate that understanding. An alternative, which makes the PhD program itself shorter, is to require a related master's degree.

For example, most US PhD programs which start after a bachelor's degree are planned for 5 years, while in most cases, a German PhD is planned for 3 years but requires a 2 year master's degree, so in the end the times are comparable.

A PhD is degree you receive for research. There are formal prerequisites that you have to meet, depending on the law of the country and the university regulations. Usually, the PhD advisor cannot alter these requirements. In some cases though, there might be room for lowering formal prerequisites if a committee approves this.
In some countries (including Germany), a masters degree is the usual "proof" that you reached the scientific level to work on a PhD.


text:
How to nail a Ph.D. interview?
I have been asked for an selection interview by a Professor in Australia for Ph.D. position (cancer research group). This position is really important for me so I want to give my best. Can anyone suggest some tips or share his experience of success or failure so that I can get an idea how to prepare myself.
Thanks a lot.

Read a few of their papers, listen to them and ask interesting questions that show you can think critically ("hmm, that's interesting, but wouldn't Y happen if you did X?").

Let me pretend I'm the professor. Things I will want to know:

What drives you? What is important in your professional life?
What is it about cancer research that appeals to you? The raw science? Helping humanity? Glory?
How big is your curiosity?
Why do you want to do this degree at this university?
Can you work hard? Where is the evidence?
What have you done in your previous situation that will help/hinder  you in this one?
Can you write? Evidence?
Do you follow the evidence wherever it leads?
Do you work well with others? How comfortable am I making you part of my group? Note that you may get to meet some of the others as part of this.
Have you any experience with this sort of research? If not, how fast can I predict you will catch on?
Do you have ideas for research for a dissertation? (Not a deal breaker if no, but possibly useful if you do.)
What sort of questions did you ask me in the interview? What do they say about you?
Other things I can't think of now but that may come up in the interview.

Take a pen and notebook so you can take quick notes if needed. Nothing elaborate or electronic. I suggest a pencil and a few index cards actually.
Note that some of these are hard to express and hard to evaluate. Some are impossible to just ask and answer. It is even counterproductive to try to directly express some of them. Showing is better than telling. Some are more important than others, but the next person has a different ranking.
I may have read your CV before the interview, but I'm pretty busy. I may want to talk to a former professor afterwards (unlikely).
But more important than all of that is to be yourself and just be comfortable with it. Don't try to force it.

Contrary to stereotypes, "Do you like beer?" probably won't be a consideration. Tea is acceptable.

@Dukhiatma, I forgot. Take a pen and notebook so you can take quick notes if needed. Nothing elaborate or electronic.  Good luck.


text:
Is It appropriate to put code in slides for a technical presentation?
I am doing a technical presentation on Minimizing Real-Time Data Stream Latency:  Node.js and Asynchronous Operations. I've done some thorough research on the topic and I want to add some code blocks to a few slides to visually show Asynch Programming in Node.js as well as to visually show pros and cons.
The presentation is for 30–40 minutes.   I want to keep it to about 10–12 slides.
Questions

Is it appropriate to add code blocks to some slides?
If it is appropriate, how many slides is too much?

I use the pseudo-code (LaTeX style) which goes into my papers. I felt that the audience finds it easier to grasp.

This was cross-posted in Workplace... please don't do that, users frequent both areas. Thanks!

If it is a technical talk on a particular library then yes, code is appropriate, and in some cases - even recommended (as opposed to hand waving).
But:

keep it readable (big font, syntax highlighting, reasonable variable names),
keep it short (examples as minimal as possible),
give enough time to read and understand it.

Some examples how it is being done: this slide or for async JS: this presentation.

It may or may not be appropriate, depending on your audience (I also feel this way about equations). A couple things to keep in mind:

If you have non-technical people in your audience, you'll likely lose them for these slides, and there's a risk you'll lose them entirely.
Even if people are technically-inclined, they now need to read your code block, interpret it in their mind, and think about it long enough to see your point. And they'll have the distraction of you talking to them at the time. That's a pretty steep thing to ask your audience to do.

Generally, I think you'll likely be better served talking about these issues conceptually, rather than with code, which will require people to wade through it. If you must include code blocks, make sure they are clear, in a very recognizable style (no personal quirks or idioms, clear variable names, etc.) and clearly annotated as you walk through it.
But honestly, I don't think I've ever seen a talk with code-as-content (beyond "These 2 lines instead of these 15!") that I thought was aided by having it there.

This audience is extremely technical...The majority are engineering doctors I believe if that makes a difference.  The job interview is for an entry position software applications developer at a very reputable organization if that makes a diff.

I suggest testing your slide, using colleagues with similar skills to the target audience. As Fomite pointed out in a prior answer, listening to a speaker and reading code can be difficult to do at the same time.
One option would be to allow time for the code reading: "Please examine this code block" followed by a pause. You can find out how long a pause is needed by observing your test audience. If you cannot afford to allow enough time to read and understand the code, get rid of it.

Complicated concepts are often best explained with a figures. Try representing synchronous & asynchronous data-stream packets as boxes traveling along a line. Coupling this with a few lines of pseudo-code, might allow you to explain your algorithm's superiority.
-0-0-0-0----0----0----0----0----0-0-0-0----0----0----0----0-0-0-0----0----0----0
--0-0--0-0-0--0--0-0-0--0---0-0--0-0-0--0-0--0-0--0----0-0-0-0-0--0-0--0-0-0--
This demonstration of your knowledge / problem solving skills goes along way towards recommending you for a job. And remember, it is all about clear communication -- not about trying to impress (or confuse) anyone.

It is almost never appropriate to put code in your slides, psudo-code or not.  This has nothing to do with the level of technical finesse of your slides, and everything to do with whether or not it is a good presentation that your audience can follow.  Most of the time, you will want to represent your ideas graphically, not textually.
A slide-based presentation is a visual medium, supplemented by what you have to say about each slide.  The content should largely be bold-print headers and visual representations of your concept - not large chunks of text that your audience is not likely to read in the time it is on the screen anyway.
One case in which you could justify the inclusion of code is if you plan to go over each step of the code line-by-line, or as a side-by-side comparison, and then only if you are willing to guide your audience through every single step, preferably with a laser pointer or other type of pointer to indicate how each part of the code is relevant.
Even then, I would not recommend including more than a few lines of code - text is very difficult to focus on during a presentation when the presenter is speaking, unless they are explaining the text to the viewer.  The larger the block of text, the more explanation will be required, and the less interest your viewers will have.
As a technical presentation, if it is strictly necessary to include an example, then there is no question - you will have to include it, and find a way to explain it within your allotted presentation time.  But if you have the option, a visual representation with a flowchart or some other graphic medium would be better suited to a slide-presentation style.
(Note: If it is not actually a 'presentation' and is meant to be a handout to others, disregard this and include some examples, but do not go over them too much during the actual presentation unless absolutely required.)


text:
Is it appropriate to express concerns to a professor about a new exam format?
I'm taking a math class at community college. The class has three regular exams (25% of grade) and a final (25%). Normally, the professor generously grades the fifteen-question exams with partial credit, but because of the COVID-19 crisis, we have had to move everything online.
I received excellent scores on the first two exams, but the third exam we had to take online. In the new, twenty-question format, she obviously could not offer partial credit because a computer scored it. Going into the exam, I didn't feel unprepared, but I ended up getting a terrible 62%. But then, the professor announced that the entire class had performed poorly on the exam, and she gave us another day to retake it. I had already spent an entire day studying and working on the exam, and I knew it would be dropped anyway, so I declined. I still don't think that there was much that would have changed if I took it a second time without being able to see what I got wrong. When I did get it back, I found that several of my mistakes had nothing to do with math and were a result of failing to correctly enter my results into the computer.
I don't know how the rest of the class performed on the exam compared to me, but the professor was concerned enough to give an extra day, so I'm willing to bet it was around the same. Needless to say, I strongly suspect that our collective failure is a result of the new exam format. I think that our grades depended on the partial-credit scoring. And now, the final, worth 25% of my grade, is coming up on May 18th.
I have a 98% in the class. If I get a 60% on the final, it will completely destroy my grade. And what's most disturbing to me is that so far, there has been no correspondence on what the final will look like. In terms of format, I don't know what I'm studying for, exactly. If it is going to be similar to the third exam, then I'm very likely doomed. With my two AP exams also around the corner, in the same week, it is causing an undue amount of stress.
I really appreciate the professor, and I naturally want to remain respectful and stay on good terms with her. Is it appropriate for me to voice my concerns? What kind of language should I use, and which parts of what I have disclosed here are appropriate to include? And what reasonably should I request?

Changing the rules shouldn't disadvantage anyone. But perhaps if everyone suffered then she will make allowances. But yes, express any concerns.

"I have a 98% in the class. If I get a 60% on the final, it will completely destroy my grade."  If you have a 98% before the exam and get 0% on the exam, you will still pass the class.  If this is an introductory class, I would guess you would have an above average grade, too.  I think you are worrying too much about your grade.  Learning is more important than grades.

If you do send a message, I suggest you acknowledge that the professor has already put in extra effort to help students by putting the exam online allowing retakes.

What do you mean by “Several mistakes were a result of failing to correctly enter my results into the computer.”?

@AnonymousPhysicist I am a high schooler taking this through dual enrollment. My goal cannot simply be to pass--GPA is important in high school.

@AnonymousPhysicist That is excellent advice--I will be sure to acknowledge that.

@Damila By that I just mean that I did the work correctly and got the right answer, but when I put it into the computer I made some mistake. So for instance, x^10y^10 became x^10y10

Ahh. Thank her for taking the time to make an online class but explain that you believe that some correct answers were marked incorrect due to computer formatting. Ask if it is possible to regrade by hand.

Not sure how community colleges handle this but "real" universities usually have systems in place where students can voice their concerns. At TU Delft we even had an entire student committee for the single purpose of discussing course quality with the professors. That is, voicing concerns is very much encouraged. Hence it's absolutely appropriate. It's also cool to voice your concerns in an e-mail.

It’s totally appropriate to point out to your professor that your grade is suffering for technical reasons having to do with the online format of the exam. If your professor is reasonable she will not be in the least bit offended by this.
By the way, we are pretty much all dealing with issues of this sort nowadays. I experienced something similar just a few days ago when I gave an online quiz. One of the problems required entering the answer to a question in decimal notation, and this was automatically graded by the testing platform. The correct answer was 15/64=0.234375, but some students assumed it was okay to round off the answer and entered 0.234 or 0.23, only to have that marked off as incorrect. When they emailed me to point out the issue, I gave them the points for the question.
To summarize, let your professor know. Be polite and explain the technical issues in entering the answers that caused your answers to be marked as incorrect. If you explain it clearly and convincingly enough, not only will the professor be in a better position to design a fairer format for the final exam, she may actually give you back some of the points that were marked off in the current exam.

BTW, if teacher is minimally tech-savy, he could hash the answers and give the hashes to students. Hence, if you know the answer is 15/64, you can test "15/64", "0.23", "0.234375" and other variations and tell if you've got the right answer or not. While it partially informs the student if he's got a wrong answer (no variation is working) it gives absolutely no clue as to what the correct answer should be.

Many teachers new to online exams don't realize that the computer grading is very intolerant to formating issues. There is often a partial credit or re-grading possible. I am very happy to have my students point out that I missed another grave misspelling or extra blank or rounding error on an online exam. As Dan said, be polite. We are all stressed out.

Thank you for the wisdom, and for sharing your experience. Is it hard to believe that I had never even really considered trying to get the points back for the other exam? I guess I have a phobia of asking for things--I'd rather quietly chug along and turn out good work. I think I need to be more aware of how this crisis is effecting my professors as well as myself--it's a bit of a revelation to me that a professor would be happy and even relieved to receive this kind of feedback. I will take your council.

It is perfectly acceptable to give your professor negative feedback on the exam format.  You can either do this by email, or you could do it anonymously with an unsigned letter in her pigeonhole on campus (once it is open).  Since the exam format was necessitated by the remote learning circumstances due to COVID-19, it is likely that your professor already knows that this format is sub-optimal, and your negative feedback will probably just confirm what she already knows.  Once you are back to face-to-face classes, it is likely that she will change back to her previously preferred format.
If you decide it is worth giving negative feedback on the exam format, I suggest you write this with some context that recognises that the professor is operating under remote learning restrictions.  Make sure you are polite and appreciative of her work, and frame your feedback as something to give her the experience from the point of view of a student.  Generally speaking, professors do not mind negative feedback from students so long as it is constructive and polite.

Thank you for the advice--I will be sure to include context acknowledging the steps that my professor has already taken.

TL;DR:
Your professor probably does not care about these issues as much as you do. That is a non-problem. Just reach out to your professor and do not sweat over it. Focus on whatever is more important than these grades. Family, sports, opposite/same sex, this does not worth your time.
Longer answer:
If you have a concern about something that affects your life (grades do, unfortunately) why shouldn't you be able to reach out to your professor?
Academics, in general (or at least in theory) are devoted to science and justice. There are some oddballs, yes but that is the kernel of their profession. Why would you spend all your life behind a desk/in a lab if you don't have such passion -even only for the first few years of your profession? Money? That falls under oddballs category. Prestige? Do academics have any prestige in this world at all? Nothing. Dealing with problems is my passion and that case is yours is another problem to be solved.
Don't tell everyone but there is a trick: If you can pose any problem in a brain-tingling way you can lure any academics to pursue any problem. What to do with this information is up to you though. I will not give away all our secrets out of nowhere.
Don't be confrontational, because in that case their first instinct would be to destroy you with facts -that is how academy works: the way of hard science. That is most probably not personal. I said instinct, because in most cases it can't be controlled and maybe even noticed.
Of course this is my experience and my way of interacting with students, and not everyone has to be like this. Yet even if they unwelcoming, what would you lose? Your grade you already lost? Your grade which will be even lower? Latter is why there are boards and ethical committees. They will say some bad words and hurt your feelings? Don't be a special snowflake. There are idiots posing as academics, deal with it. You will not see them next year or the year after but I have to deal with them almost daily.
Just... Just don't be disrespectful and don't be confrontational if you are not ready to play that way. I can tolerate (and even enjoy in a sinister way) confrontation but disrespect is some another level. I can hurt your feelings, and you would brush them off by tomorrow.

Your knowledge of the academic world seems extremely limited and you make some very sweeping generalisations, as if they are hard fact, that I don't think are accurate at all.

That was an "insider info" to a person who was overly stressing about minor things, and was intended to be an eye-opener. If 10+ years is "extremely limited", then it is, sure. My academic circle, as far as I know, see things more or less like I stated. Of course it would vary from academics to academics, department to department, etc but I stand by what I have stated. Those being said, thank you for taking your time to write a comment. At least I can now understand why I am downvoted.

@H.Green My comment above seemed dismissive. Let me say I give credit to "as if they are hard fact" part of your comment. (oops I can't edit a comment after 5 minutes)

This seems like a pretty good answer to me, but the TL;DR seems to be saying the opposite of what the rest of the answer is saying. By "just do it" do you mean, just contact the professor? When I first read that phrase, I assumed you meant "just move on, don't worry about your grade". But I think you mean, just contact the professor and stop stressing about it; is that correct? To summarize, good answer but it could use a bit of an edit to make it a bit more clear, and I'd definitely remove the last line. I think it's a joke, but can come across poorly in a medium like this unfortunately.

@bob I meant "Just contact and forget, there are more important things to worry about" Edited. Feel free to edit further as you see fit, because I am probably bad at wording and you seem to get the gist. Thanks a lot.

No problem, happy to help!


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How to effectively respond to harsh suggestions from the faculty of review committee?
As generally expected the doctoral review committee has to evaluate the PhD student by asking questions, by debating etc.,
Faculty in doctoral review committee can give soft suggestions and are capable to provide grade for student for that particular semester and can even fail the student.
All the above are not insulting since all are dependent on performance of student.
But how to respond to the intimidating comments by faculty in the committee that are harsh and targeting personally, which are not deserved for a doctoral student?

Example for harsh suggestions includes follows:
1) Don't roam outside too much, sit and do work silently;
2) Better to eat less and work more;
3) It is not worth for you to do this degree;
4) Can't you understand the content that bachelor degree students can
  understand?
5) The work done by you in this semester can be done by masters
  student in a week.
etc..,

So what suggestions ?

Getting 3), 4) and 5) means you may not be equipped to do a PhD degree.

Have you actually received these comments or suggestions?

@Anyon Not personally, but watching those scenarios.

So, how do you get these scenarios? From a dream? Or were you present at someone else's review? Or repeated to you by other students (who could by winding you up...)

@SolarMike  Second and third ... I heard them directly when I attended for reviews, I heard them from underwent students.

1-2 are inappropriate, it is nobody's business how much one eats or spends outside, as long as officially required hours (if there is a requirement, which I personally find unproductive) are put in; or results are obtained. Possibly, if the latter is found wanting, remarks 3-5 may reflect reality or not; we do not know. But they are very rude, in any case. To something like that, the response needs to be - "What is it concretely that you expect me to improve?"

I think we need more information here. What culture is this (allegedly) happening in?  Does the student deserve these comments? #2 in particular seems so egregious that I can imagine a professor being disciplined for it.

are you looking for retorts here or some kind of advice on ending bullying?

I don't know what is the norm in your institution, but I would characterize comments 1-3 as highly inappropriate and unprofessional. The committee should not comment on a student's work and social habits, their eating habits (this would be considered taboo in many places), or offer dismal views on their prospects after a PhD. In my department, making comments like this towards a student will, at the very least, be cause for a very unpleasant talk with the department head, and will require a written apology to the student.
Criticism on your progress or your understanding is definitely acceptable, but can be conveyed in a more conducive manner (e.g. by not comparing your understanding to that of undergraduates - offensive to both you and to undergrads).
That said, if you receive these kinds of comments, you should speak with your advisor and see what you can do to make things work better. Comments 4-5 are simply a rude way of saying that you aren't making sufficient progress.
If you feel comfortable with your advisor, and assuming a culture of abuse is not prevalent in your department, you may raise this issue with them. I for one would be furious to hear this and would probably confront the offending committee member myself. If not - try to contact student affairs.
Abuse towards students should not be tolerated.

Avoid getting spun up into a fight.  Or saying poor me.  Or conceding global negatives about yourself.  Just ignore the gratitous observations on you. Concentrate on the content.
Fix any issues with your work (or your response to questions).  Get corrections done.  If a re-exam is done, make sure you can cover questions that were a problem last time.
[Even if the observations were to be "right" (and they may not be), it's not like you can flip a switch and radically change your capabilities at this stage.  Concentrate on the objective which is passing.]

Sometimes simple and direct (but very polite) answers are the best.

1) Don't roam outside too much, sit and do work silently

I find it easier to concentrate when I roam outside in my spare time.

2) Better to eat less and work more

I unfortunately cannot work more if I am hungry.

3) It is not worth for you to do this degree.

That is sad to hear, but I find it pretty amusing to pursue a PhD and I will continue to do so.

4) Can't you understand the content that bachelor degree students can
  understand?

I might have a lack of knowledge or practice, but I am pretty sure I will learn what I have to, and fulfill the requirements soon enough.

5) The work done by you in this semester can be done by masters
  student in a week.

I really wish I was as talented as one of the masters students that you know. I will try harder, though.
It should also be noted that these comments are merely subjective and have no weigh unless backed up with concrete proof.
The proof is usually an evaluation of the student through comparison between the duties (or promises) and the achievements.


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How to cope with the abuse of notation in the literature?
In mathematics or (mostly) computer science, there is a gap between the literature and the standard textbooks.
Many good research papers are also abusing the notations either with or without mentioning them explicitly.
Is there any standardised mechanism or authoritative body that deals with this issue? If not, how to deal with it?

In which sense are they abusing notation? Can you make any concrete example?

NO.  There is no authoritative body that enforces mathematical terminology.  For example, when a physicist says "delta function" and a mathematician answers "it is not a function", there is no referee to decide which is right.

Not an answer: 1) Abusing notation often helps understanding at an advanced level. 2) There is much more abuse of notation than you may be aware of, even in first year textbooks.

What is notation? It's really just a way to say things, in much the same way as we use words to express concepts in sentences.
Now, think about how we use language. Charley Owens said "Say it ain't so" to Shoeless Joe Jackson, which is not correct English but everyone understands what he was saying. Jaz-Z says "And I ain't tryin' to see no highway chase" and gets told "Well, you was doing 55 in a 54", neither of which is correct Oxford English. But everyone knows what he's tellin' us!
Notation is the same way: We use it to communicate, but it is not necessary to stick to a rigid use of it to make ourselves clear to our readers. What is necessary is that every educated reader understands what we're saying, but this allows for some "abuse" of notation, which is really typically just a convenient way of expressing things without having to go into great formal detail that does not actually illuminate anything.

I am not sure if you are really looking for a way to cope with varying notations, but mostly these are necessary to name all the values involved in a document. Often, different topics deal with different sizes, all of which need a unique identifier.
The best way to cope with this is to adapt to it. In my field it is common to introduce every variable explicitely before using it, so when I fully read a document, I just need to make sure to not miss these introductions.
If you have trouble remembering, it may help to write them down for each publication etc. you are considering.
I had a problem where an author used M and N the other way round than I would have. I failed to reproduce some results, only to realize I had not properly read the paper.
This was my fault though, the author is free to define their own notation as long as they tell the reader.


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Are communicability and verifiability the only reasons to prohibit other true results?
In order to publish a research paper in a particular domain, or the domain itself must satisfy the above two requirements: Communicable to and verifiable by other people. Isn't it?
In this context, I got a doubt that the content of research papers are limited by objectivity and results that cannot be either uncommunicable or unverifiable are considered off topic and are never encouraged in the either academic or the scientific community.
Isn't it limiting the scientific development that can reach such truths also?

Can you specify what you mean by 'subjective truth'? How would any scientific field benefit from publishing what a single individual believes to be true, without presenting any proof?

Subjective truth I m referring are subjective experienced such as life review, out of body experience etc..,

There are other formats of non-fiction texts, which might be better suitable than a research article in such cases. For example biographies, reports or a critical analysis of a topic. Research papers have strict purpose and thus also defined rules

So, in your model, would you say that the subjective experience of mass psychosis would qualify as a research result?

@Captain Emacs No, I'm asking why the scientific community is restricted to communicability and provability although no one can prove that the truths can be objective only.

@hangum There is a school of thought (qv. Karl Popper) which states a result is scientific not if it's provable, but if it can be shown to be invalid (falsifiable). Unfortunately a single person's unrepeatable experiences still wouldn't qualify.

There is something that we consider "grounding". It is the ability to perform experiments, largely independent from where we are and get consistent results. Of course, when that fails (and it can fail, especially if theory is required to validate the experiments and that theory is at the limits of its expressiveness), then there is a problem. But in principle, the rules of semiconductors, lasers, gravity etc. should work equally independently of the experimenter. There is no such transferability for "subjective" experiences - perhaps it will change if we understand the brain better?

Seems very abstract.  Hard to grasp.  Give us a little flavor of a specific example (preferably the one that provoked the question).  We can still generalize afterwards but as written the question is too general and theoretical to engage.

First you need to remember that science is not the only form of research. Second, subjective results come in all sorts of flavors. If I ask one person person if they like A better than B, that is a subjective result. If I ask 1000 people, and do statistics, is that still a successful subjective result? Someone else could ask a new group of subjects the same question and verify my results.
Now consider an objective measure of a one time event (e.g., the amount of snow that fell during a storm). No one can verify the measurement, but it is still objective.


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Is there any difference between theoretical and mathematical?
In computer science, is there any difference in usage of the terms: theoretical, mathematical?
If yes, which is more broader?
Context: If my supervisor says focus on theoretical aspects of the paper  and focus on mathematical aspects of the paper. Should I interpret as same?

The terms are used differently in different contexts. Please include more context.

@lighthousekeeper Is it okay now?

If you provide some details about the paper, then I'll try to improve my answer.

As someone in computer science you shouldn't miss the fourth option with regards to subsets, that neither is included in the other.

@mlk mathematics < computer science < theoretical computer science, maybe...

@hanugm Better but still not enough context. You probably would need to present details from your paper, but then the question is too specific. My recommendation would be to ask your supervisor.

Questions about what you supervisor told you: ask your supervisor.

@user2768 For some definition of the different fields surely. But definitely not in the implicit definition of mathematics that is used when talking about "mathematical aspects of the paper".

This question is relevant to more than just computer science, so here's a take on it from an economist's perspective, that may still be relevant to other fields.

... a growing feeling in the later years of my work at the subject that a good mathematical theorem dealing with economic hypotheses was very unlikely to be good economics: and I went more and more on the rules - (1) Use mathematics as a shorthand language, rather than an engine of inquiry. (2) Keep to them till you have done. (3) Translate into English. (4) Then illustrate by examples that are important in real life. (5) Burn the mathematics. (6) If you can't succeed in (4), burn (3). This last I did often.
Alfred Marshall, 1906

This quote (which is amusing in the light of where modern economics has gone), strongly suggests that theory is some meta level above mathematics, and that mathematics is in fact often used to support theories.  I feel like this generalizes to other fields, even mathematics itself.  After all, if a mathematical theory remains unproven, what is it based on?  Of course, I'm being sloppy with my language here, and I believe conjecture would be a more technically accurate term.  But when your hypothetical advisor says to "focus more on the theoretical aspects" I believe they're probably using the term theory more in a colloquial sense.  I'm not involved in theoretical computer science, but there appears to be similar topics there.
So in short, I feel like theory may include mathematics, or non mathematics, like narrative reasoning or formal logic, and is thus broader.

Theoretical and mathematical: They're different. Mathematical aspects are the mathematical parts, whereas theoretical aspects are the fundamental computer science parts. E.g., computational complexity is theoretical computer science, whereas statistical analysis is mathematical.
That said, it may depend on the context. Ask your advisor for clarity.
Ask your advisor for clarity whenever you don't understand, or, at least, mention that you don't understand and that you'll look into the details later, possibly asking for direction on where to look.

Some years ago, I wrote a proof that a proposed cache coherence protocol would not deadlock. That was applied, not theoretical, computer science. It was also mathematical.

@PatriciaShanahan Surely you proved the result in a theoretical model? (I appreciate that terminology is blurry. I think context generally gives way to distinct usage of terms.)

I expect that your supervisor is using both words fairly loosely, and that you should think about them in the context of what you are working on specifically.
"Theoretical" parts of the paper might refer to some grounding mathematical theory, but also might just be in contrast to an experimental part. For example, if you are writing a paper about computer systems, the theoretical part might be where you explain your model of what is going on abstractly, as opposed to when you do experiments to probe and develop that understanding. In this case it does not necessarily involve mathematics, but probably is a bit abstracted from the concrete cases considered in the experiments.
"Mathematical" parts of the paper might again relate to the abstract theory, but could also mean where you apply statistical analysis to experimental data.
So you should take these comments in the light of the actual topic and paper at hand. In terms of what your supervisor is trying to communicate, I would check with them to confirm, but it sounds like they are trying to direct your attention towards the chunk of the paper that's to do with the formal setting of the research, and away from thinking (for now) about other aspects of the paper, such as experiments, literature review, formatting, etc.


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Is it bad to not test the capability of the explainability of the student at the graduate level?
Suppose I am the only instructor for a subject.
I need to conduct an exam. I am confused between the following two approaches for designing questions.
Approach I: Questions with single line answers such as boolean answers, multiple-choice questions, etc., note that the answers to these types of questions do not occupy more than one line.
Approach II: Questions that demands explanation, subjective/objective explanations, etc.,
The advantages of approach I is at least trifold
(I) Marking is objective
(II) less evaluation time
(III) No partial marking
But, recently, one of the elder professors of my campus, opined that approach I is a bad way to conduct exams and he told that approach II is needed because of the reason that studies of students should be research-oriented and hence explainability or presentability of the concept is very important for a student and hence approach II is preferred a lot over the approach I.
I am really concerned about the bolded part, I mean, is it really a bad way?
Assume that the subject I'm dealing with has the flexibility to support both types of questions.

What exactly do you want to achieve with the exam? (Often, graduate exams are graded as "everyone gets the best grade and done)

Also, wrong explanations will often tell far more about the misconceptions a student has than 1-line-answers.

It depends on what you want students to learn.  Use open ended questions for learning critical thinking.  Either approach is good if you want students to learn facts.
Nearly always, at the graduate level, you want students learn "critical thinking" from the analyze/evaluate/create parts of the Bloom Taxonomy of learning.  Frequently this is the case at the lower levels of education as well.
Open-ended questions are necessary to demonstrate the ability to create, and can make it easier to tell if students are analyzing and evaluating.
If your goal is for students to remember a list of facts, then multiple choice questions are an efficient (but not necessarily better) way to test that.
"Understand" or "Apply" are often best addressed with open-ended questions, but could be addressed either way.

Put both types of questions in the exam.
So, some students get the highest grades because they can answer both types well,
Other students get lower grades because they answer type 1 well but poorly answer type 2,
This gives a range of grades based on the students performance.
Deliberately not going in to the discussion about whether exams are a suitable test...

I don't think getting a range of grades is a good objective for a test.

@AnonymousPhysicist so all should get 100%?

Grades should not be the objective of a test period.  See: https://cft.vanderbilt.edu/guides-sub-pages/understanding-by-design/#overview (link hopefully fixed)

@AnonymousPhysicist so where do you suggest getting grades from? Coin toss? And is that link categorical for all teaching institutions?

I am not sure what you mean by "categorical."  Backwards design is a very well known approach to pedagogy.  I never said grades should not come from tests, I simply said generating grades is not a good objective for tests.  It is also not the guiding factor in quality test design.

Grades should come from demonstrating an ability to achieve the main objectives of the course, which is usually to achieve some level of competency in the subject matter. The question is asking if testing the ability to expand on ideas is a good grading criterion. What you're describing is how to rig a marking scheme to ensure a distribution of grades based on the variability in learning strategies and test answering abilities of students. Not really the same thing.


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Contribution of the supervisors in publishing paper from thesis
I did my M.Sc. recently and we have agreed to publish it in a journal with my supervisors.
I have got once comments from the first supervisor but it is almost two months I couldn't got the final comments. I have followed up it and the supervisor mentioned he would give comments shortly. I am worry he may want to refuse from contributing, and he couldn't mention it, directly. He may have any convincing reason for him self for refusing from authorship but I am pretty sure the quality is good enough and it can be published in a journal.
How can I politely ask his decision?
Should those papers that are derived from thesis include supervisors name?

How can I politely ask his decision? — I suggest "What is your decision?"

Authorship: Strictly speaking authorships should be determined by the academic intellectiual contribution. It is rare that a thesis topic is solely invented by a student on their own so it is most likely that an advisor regardless of input during, say, writing stages will be an obvious co-author (if that is how authorships are determined in the specific field). There may of course be more co-authors and the order is not necessarily clear due to differences in traditions and cultures.
Response: Not getting response is unfortunately quite common and very unfortunate. I think you have to keep asking for a response but also add that you are interested in submitting the paper soon. If you are through with your education, you might be moving and it seems reasonable to get a paper in before leaving for other work/equivalent. So the answer is to simply politely ask and maybe massage your advisors ego by saying how much you would appreciate/need his/her comments to complete the joint paper. Just keep your cool and avoid nagging. At some point you will simnply have to provide a firm deadline due to whatever circumstances may exist. If you have some other faculty to whom you can confide then asking for advice may be a good point as well.

If I ask someone from other university to give comments I have to add his name in the paper, subsequently. Shall I inform my co-authors before asking comments or help from someone else in my case?

I don't think you need to add someone as a co-author unless that person's comments significantly added to the content of the paper.  For example, if someone simply helped polish the language or provided other editorial feedback, I wouldn't consider that a "significant technical contribution".  In such cases it would be enough to mention their contributions in an Acknowledgements section at the end of the paper.

Providing feedback to a manuscript is not generally enough to warrant co-authorship. The contribution should be more significant and affect the conclusions in such a case.


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How to handle a subawardee that is not performing?
I work at a small for profit company.  We won a Fed grant based on some of our previous work, and included in it a university researcher as a subawardee.
The university researcher has done next to nothing.  He has been very busy with other engagements and essentially handed off the entire work to a grad student, who has no background in this area and is unable to produce.
For several months, I've tried to right the situation.  First I raised the problem.  I got a mediocre response, basically telling me that the work is fine, that he doesn't have time to be more involved, that it's taking him away from other responsibilities and lucrative consulting, and that the funding agency is too clueless to know or care anyway, and that my expectations are too high... At one point, he suggested he just cancel his award and refund the money, but that was said in jest.  In short, I got no results or even expression of concern.
I then tried to remedy the situation by setting concrete milestones, a project plan, and written goals.  The researcher received this well but continued to do next to nothing.  The grad student has tried but not been able to do the work.  He delivered something which is incomplete, unintelligible, and downright flimsy, certainly nothing we could use in the work or for publication.  At this point, I really have nothing to show from their involvement, and am giving up hope that they'll produce anything.
My questions is: How do I handle this? If the contract was with a small business, I'd simply not pay them, and state "You haven't done the job."  We'd probably reach some type of agreement and move on.  But I imagine that, with a university, its a lot more complicated.  The professor can't exactly tell his university "yes, I ended up not having the time to do the work, please cancel it" - I imagine that would get him in a lot of trouble.  The university likewise is unlikely to accept my claim and instead, I imagine, would always back their own people.  I don't want to make an enemy of the researcher, or to cause him problems at his university, or to get into a protracted lawsuit with the university.  But I can't justify handing over the cash to the university when I know they've done nothing.  Not to mention that, legally and ethically, I'm responsible to be a good custodian of the funding agency's money.
Given that I've essentially despaired of getting anything from the university researcher, how can I bring this to a controlled landing? Ideally, I'd like to find a way to reach a settlement, giving him a path to back out of the subaward without causing him problems with the university, and avoiding a fight between myself and the university, or myself and the researcher, while reaching a settlement where I don't hand over (most of) the funding.
Handing over the funding would be a real shame, not only because they're not producing anything with it, but, being that their end has not been done, the project will remain incomplete.
(The situation is complicated because the university has already paid him extra summer salary, and I doubt there's a mechanism for him to return it, and, even if there were, I doubt he'd be willing to admit any wrongdoing.  In short, I think the conflict and the admission of guilt are greater concerns than the funding itself.)

UPDATES:

Several hundred hours were budgeted for the professor
The professor provided next to no deliverables; except for a few emails, all deliverables were provided by the student only
The work provided by the student was clearly flimsy and not suitable; any person qualified in the field would reach that conclusion
The researcher has done good work in other things; he made no real attempt to hide that, in this case, he basically just handed things off to the student.  I've seen his work in other cases, and, if he would even do 25% of his budgeted hours, he could get the job done.
The student seems to be aware of all of the above; he seems to realize that he's unable to do it by himself, and that the researcher really isn't too involved; he's made gentle statements of such
I've made many attempts over the course of the work to bring this to the researcher's attention or to help correct the problems; none have brought results.  I think he simply doesn't have the time and doesn't want to take time away from more important activities (he's practically said as much)

Thank you for the great answers.  Some recommended just paying.  My question on that is: doesn't that subject me to liability vis-a-vis the funding agency?
Some recommended trying to have gentle conversations, emphathize, etc.  I've done that several times now with nothing to show.
Some recommend reporting it to the ethics agency.  I certainly don't want a war.  I don't want to harm the researcher.  I'm not even sure that not doing work you are supposed to do is unethical.  I am sure that the university would not want to make their own faculty look bad (it looks bad on them) and would fight any ethics charges tooth and nail.

How much time do you still have before the project deadline?

Please see this procedure for merging your accounts so that you will be able to edit your post.

Out of curiosity, would you have gotten the grant if the university wasn't on board? Your situation sounds like a university/SME public/private partnership for meeting the grant requirements. If so, this can work very well, but it also can be an unequal relationship. Any disputes over the grant will likely be a major issue for the SME, while the university won't really be affected, plus funding agencies can be fickle. Writing off the university's share as procurement costs is probably the safest bet.

I'd like to find a way to reach a settlement, giving him a path to back out of the subaward without causing him problems with the university, and avoiding a fight between myself and the university, or myself and the researcher, while reaching a settlement where I don't hand over (most of) the funding.

This is a noble, but likely unrealistic goal. Your two subgoals "don't give them most of the money" and "avoiding a fight" are very much in conflict by now. Based on what you explain, most (all?) of the money has already been spent by the university (on summer salary, on grad student stipends, etc.). Hence, there is no graceful way out for the researcher anymore, as every potential way out will lead to substantial losses for the university. Further, I would expect having to fight the university the legal way for the not-paid-out money, as it seems highly unlikely that they will agree to your viewpoint that they did not deliver except in the utmost extreme cases (basically, the only case I can imagine is when the team of the researcher delivered absolutely nothing, no code, no papers, no study, verifiably did not attend the meetings or teleconferences ...). This does not seem to be the case - shoddy work is a very distinctly different beast than no work, especially to an outside observer who is likely not an expert in your field.
To me, as an outsider, there remains a bit of doubt based on your description whether the work they delivered was indeed bad, or whether you just had a misconception of what you can expect from a university as a partner. Even in this case the researcher may easily be at fault, as (my impression) universities often unreasonably upsell the quality of the work they will be able to produce with the resources they have before entering industrial collaborations. However, funding agencies will typically not agree to withholding money for a reasonable job done by the researcher, even if you expected much more and even if more was (usually somewhat hedgily) promised in the grant proposal.

My questions is: How do I handle this? If the contract was with a small business, I'd simply not pay them, and state "You haven't done the job."

Firstly, think about this not as a contract with a small business, but as a contract with a division of a large enterprise. In this case you would also not "simply not pay them", at least not without reasonable expectation of not having to fight over a law suite.
Secondly, how I have seen underperforming partners being handled is usually in a proactive way. For instance, in a 3-year EU project, we had a partner who delivered very bad work in the first reporting period (i.e., the first year). After a stern discussion with the coordinator, the agreement was reached that this partner's resources (and tasks) for the second and third year were substantially reduced, and a new partner was taken on board to take them over. The money for the first year was paid out in full. As this money was already spent (even if it was spent badly), there was simply no graceful way to take it back again.
I understand that your project is already at its completion, so this isn't an option for you anymore. I am afraid, in this case you can really only choose between fighting over the money (and, honestly, this is a fight you could easily lose) or hand over the money in full and learn from the experience. One thing to learn is that (even, or especially) university projects need management and proactive progress monitoring. A second thing to take away may be that the input that is to be expected from the university needs to be defined orally and in writing in much clearer terms. For instance, it should not have come to you as a surprise that the researcher delegated most of the actual work to a grad student.

Thanks.  I'll add that I did try to handle it proactively, raising my concerns in writing from early on when I saw no work was done.  Also, the budget requires him to spend several hundred hours, which were clearly not done - he made no attempt to hide this (but, again, I'm sure if pressed by the university, he'll say "Sure, I worked on this for 10 hours a week" - not that he'll have any records of either his work or any output coming from such).

Also, if I do just pay it, even though I know they didn't do the work, doesn't that make me liable to the funding agency?

@SRobertJames Usually time sheets are used to provide "proof" of hours worked. As for liability - this I do not know about, but I would consider the practical risk for you personally very low.

Additionally to the perfectly fine answer by @xLeitix, I would like to suggest to try to arrange that the grad student physically is located in your office (preferably full-time, but if that is not possible, then at least three days per week) for the remainder of the project. Then have regular progress meetings (once per day, or at least a few times per week).
That will make the communication much easier, and allows you to give much more direct feedback. Unrealistic or unintelligible plans can be identified straight away, and not only after spending days or weeks on them.
Do not expect a lot from the professor. It is clear that your project is at the bottom of his priority list. I doubt that there is much that you can do to change this.
Lessons for next time (with a different institute/professor, I would assume):

When negotiating the collaboration: make it explicit who will be doing the hundreds of hours of work: a grad student? a post-doc? somebody else?
Especially when the work is of great importance to you: try to be part of the interviewing committee in case the student still has to be contracted.
Also make the guidance explicit: how many hours, and by whom (post-doc, overworked professor?).
make the deliverables as tangible as possible. In case of code, think also of unit tests, code reviews, etc.
Before starting the project: agree on regular progress meetings (which frequency?), and in which form (face-to-face, telephone, ...)