How should I cite the beta version of a book used for a talk?

The most important thing about referencing any source of information is that your audience can find the source, either now or (if the source hasn't been published yet) in the future. Lots of referencing questions become easier if you stick to this principle.

If there are specific standards in your field – for example if you are doing this presentation as part of the assessment for a taught course – then you should stick to those standards. Many referencing guides have sections on referencing 'forthcoming' or 'in press' material. For example, the US National Library of Medicine has detailed instructions for this. Similarly, the APA Style Blog has advice on citing material that is still being prepared, that has been submitted but not accepted for publication, or that has been accepted but not yet published.

If a search for 'forthcoming material' on the website of your preferred or mandated referencing style doesn't produce any useful results and the presentation is for credit, your university library will probably be able to provide advice. If they can't help you, simply asking your instructor will also probably produce a useful answer.

If there are no particular standards for you to follow (e.g. it's a conference presentation and the organisers don't mandate a particular style), you can stick to the principle of making sure your audience can find a source by simply choosing a referencing style and sticking to it. For example, one of the examples on the NLM instructions page is:

  Posner MI, Rothbart MK. Educating the human brain. Washington: American Psychological Association. Forthcoming 2007.

As long as your audience can find the book, that's what matters most.


Is it considered unusual in the United States for a professor to run a class outside on the grass?

A university courtyard is like a park and students are always hanging around.

There are thousands of colleges and universities in the United States. Some have large campuses with lots of space to hang around. Some are urban campuses with little outdoor space available. Some are entirely contained in one building. Some have mainly residential students, and some have mainly (or only, or some) commuter students who live off-campus. Some serve mostly full-time students, while others cater to students who are doing other things outside of school and don't have much free time to hang around. Some are in boring locations with not much else to do, and some are in fun cities with many events and activities available outside the university. Some are in pleasant climates and some are in places that are very hot or very cold for some or part of the year.

All of the factors above and many more go into determining whether a given university, out of the thousands, is one where students tend to hang around outside.

  He also mentioned that it is not unusual for a professor to gather students and sit on the grass outside and run a class.

It may happen occasionally (see example), but it is very unusual. I have never attended, taught, or seen such a class firsthand.

Here is an article with some more anecdotes.

  He mentioned that the university environment is not limited to formal education (what is the case in Europe more or less).

If a professor decides to teach outside, it's still a formal class, not a social event.


How to include volunteering work in CV (as a PhD)?

Don't claim supervision nor volunteering without an agreement. (I'd consider that lying on your CV.) Your work was conducted as a hobby or as professional development or ..., which don't easily fit on a CV and their presentation will depend on the position you're applying for. E.g., for an academic appointment, you could include this information in a covering letter or in your CV's opening blurb.


How to ask for a letter of recommendation on a tight deadline, from professors I haven't spoken to in years?

This is totally fine, don't worry about it. I wouldn't "apologize for your presumptuous e-mail". You might apologize for the fact that you are asking them to write on short notice; I'd simply explain that you had solicited references from people who had interacted with you more recently, and schools to which you had applied had requested a reference from your undergraduate institution.

Also I think it's fine to ask by e-mail instead of in person.

I'm unclear about what your relationship is to your recommenders -- you say that you finished a bachelor's degree earlier; are you a student or an instructor at this community college? In any case, you want to get letters from the people who can attest to your ability to do demanding academic work in your chosen discipline. It sounds like you might have chosen your recommenders poorly (i.e., you have chosen people who will say in generic terms that you are a "good person and a hard worker", or perhaps you taught you easier classes than you took as an undergrad). I speculate that your file is very positive but lacks credible evidence that you will succeed in a graduate program. If this is the case, then the school that contacted you is doing you a big favor (they could have simply rejected you).

You should ask someone who, in addition to thinking highly of you, will know what it takes to succeed in a Ph.D. program and will be able to communicate this in his or her letter.


What are the conditions for using "Smith et al., unpublished data" in journal articles?

The fact that the data behind a claim is unpublished and unavailable obviously makes it hard to establish the veracity of the factual claim purportedly supported by that data.  However, it does not necessarily mean that you can't confirm that a factual claim was made, and in some cases that may be relevant information for your paper.  The example you give is:

"It has been suggested this figure may be in excess of 800 gazillion dollars..."

In some cases, the fact that a particular estimate of an unknown figure was made might be relevant information for a paper, even if only to give some context for the range of estimates people have come up with for an unknown figure.  That is a weaker claim than if you remove the middle-man and just say that:

"This figure may be in excess of 800 gazillion dollars..."

In the former case, the claim is just saying that someone else made an estimate of an unknown thing; in the latter case, the claim is the estimate of the unknown thing.  To confirm the first statement, you need only show that there is a work that makes this estimate; access to the data is not required.  However, to confirm the second statement the actual data backing the estimate becomes important.

Now, it is probably not good practice to make the second claim above and then cite unpublished data, because it will leave your reader skeptical of the estimate, and they will blame you if it turns out to be baloney.  However, if you just report to them that someone else has made an estimate, but the data purportedly supporting the estimate is not available, you are not weighing in on whether or not it is a good estimate.  The reader will still read the estimate about the 800 gazillion dollars with skepticism, but they will be able to confirm your claim that someone made this estimate.


Is it ever appropriate to cold-email post-docs that have graduate from your program?

Yes, it's fine. High energy theory is a casual, non-hierarchical, small field of ~2,000 people. If you lived in a town of 2,000 people, you shouldn't be afraid of talking to anyone in it, even the mayor. Here that goes doubly so, as they're only a few years older than you and went to the same school.

As an undergraduate I cold emailed plenty of full professors; some of my friends preferred directly knocking on their doors. The best physicist I know started doing this in high school. I never got any negative feedback, besides occasional admonishment to call them by their first name rather than by their title. In the long run, excessive deference to perceived status will hurt you more than any email ever could.


Writing Statement of Purpose after answering prompts in the application that already cover the material

I'm assuming that you're applying to enter a PhD or Masters program. I'm a STEM PhD candidate at a research-intensive US university, and I'm basing my advice off of what professors here have told me, as well as successful applications I've seen of admitted students:

Keep in mind that often a committee will read your statement of purpose before any other statement. Thus, you want the statement of purpose to present yourself in a way that makes them excited about reading the rest of your application. In some places, if they're not hooked there, they might not even keep reading your longer sections. In this vein, it's okay to (briefly!!) mention things you explain at more length elsewhere in the application.

Of course, how to craft a statement that does that depends on the particular individuals reading your application, so disclaimer that this is only one set of advice and you likely want to recruit multiple viewpoints. Common themes in similar writing that has been successful in the work I have seen:

Your motivation. Briefly: Why do you want to be in [program]? (In STEM at least, most graduate programs will care nearly-exclusively about your passion for research.)
Why this program? Why is [program] the best fit for you?
Why you? Why should [program] want you? What do you bring to the table that they want?

Those second and third points can be very hard to get a handle of if you've not been affiliated with or visited the school before. Scouring the website is helpful, but you can also email current graduate students in the program. At least in my program, we'd all be happy to answer questions in an email or talk on the phone with a potentially-applying student.

PS: I apologize for not being able to comment first to clarify some of my assumptions, I don't yet meet the 50 reputation requirement.


Is there any API service to retrieve abstract of a journal article?

For the MEDLINE database, with the E-utilities you can:

Use the esearch function to retrieve the PubMed ID (PMID) of the article that includes the DOI as a term (presumably only one article):

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&WebEnv=1&usehistory=y&term=10.1021/bi902153g
Then, use efetch function to retrieve the abstract among other bibliographic attributes of the article (you need to pass the query_key and WebEnv returned earlier by esearch).

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&retmode=XML&rettype=abstract&query_key=1&WebEnv=something

If you have the PMID, it is one step with efetch:

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=17284678&retmode=XML&rettype=abstract


The majority of papers in pure math have no concluding section.  In fact, such papers most commonly end with the last line of the proof of the last main result (or the last lemma needed for the last main result) of the paper.

I think that I have never seen a pure math paper that has a concluding section in the sense of other academic papers, i.e., whose sole purpose is to summarize what has already happened.  Some math papers have a final section which is more forward-looking.  Your current structure has as a final section "Open Problems".  That is as close to a concluding section as I've ever seen.

In fact though even this much is often not really appreciated or desired (by editors and referees anyway): many of my earlier papers contained a substantial "open problems / further work" section.  Once I got the complaint that it seemed that I was trying to stake out territory (and there was some truth to that, I suppose).  More than once I've been told that including too much speculation can be "embarrassing" when the truth comes to light.  (In one case, I recorded computations that suggested a surprising conjecture.  The referee said that I could keep that in if I wanted, but strongly implied that if I were more experienced I would know not to do this.  I left it in, and a few years later my first student proved a theorem confirming these calculations.)  In general if you include too much material in a math paper which is not directly used to prove the theorems of the paper, then referees start to wonder whether there is enough content in the paper to justify taking up all that valuable journal space: they could after all publish another theorem and proof instead.  (And let's be fair: "they" have a point.)

If you're relatively young and inexperienced and hoping for best results on the rapid publication of your work in strong journals, I would stick pretty mercilessly to the format: (i) strong introduction motivating your work and explaining clearly the value added both in the results themselves and the techniques of proof and (ii) the rest of the paper contains careful proofs of all the results, in a very clear, linear, easy to follow fashion, e.g. "Section A.B: Proof of Lemma C".


Trouble coming up with a title for PhD dissertation - strategies?

Quickly write down a dozen possible titles, in short varied combinations of the key words you'd want someone to use to find your thesis.  Avoid fillers like "developing" and "understanding".
Prune the list and add to it the next day.
Then perhaps look over the list with your advisor.


Resubmission of a manuscript to another journal which has been already published in Arxiv

No, it won't.

Two points:
1) The papers on the arXiv are preprints (in former times this meant "before printed publication"…) and as such, it is normal that they will be eventually published in a journal. Hence, many journals do not have a problem when the receive submission of paper that are already on the arXiv. So, uploading to the arXiv prior to submission to a journal is not plagiarism - it's just the same paper.

2) The first submission of the paper to journal A is not public. Submitted information is confidential for most journals (there are newer concepts of open review processes, but I assume that this was not the case here) and also journal A decided not to publish the paper. Hence, you are free to submit the paper to another journal and again, this is the same paper and no plagiarism.

Both points together imply that your in situation there is no plagiarism. You have one paper, available as a preprint, once rejected, once resubmitted. Totally normal… (I had the same paper available on two different preprint repositories and submitted two times to different journals.)


The university does not want me to include my advisor's name on my PhD dissertation

If your university requires you to list a different person as thesis advisor, then that's what you need to do---rightly or wrongly, your university determines its policy there, and you need to follow it.

You, however, can certainly make the contributions of your former advisor clear in the acknowledgements.  As with many ethical questions, this can be safely navigated by the application of sunshine: if you clearly state your former advisor's contributions in the acknowledgements, along with the reason that they are not listed as your advisor, then you should not have any trouble with people thinking that you unfairly chose to exclude them.

Note also, that if you later make any peer-reviewed publications out of this work, then if it would be appropriate to list your advisor as a co-author, you can and should do that.


Is it ethical to merge a set of relative publications in a single journal without additional content?

What you are describing is one form of review article.  Although review articles more typically describe a more general state of the art on a problem, they can also be used to tie together and summarize a collection of linked papers into one coherent entry point.

Doing this well will require creating quite a lot of new content---it just won't be new technical results.  Rather, the content created in such a paper is the distillation of a much larger body of work into a single coherent picture.  This can be quite valuable for readers, because trying to reconstruct the picture of a body of work that is evolving over time and scattered across papers can be painful and difficult; additional detail about particular points can then be obtained by following the citations to the source articles. Note also that if you write this article well there will be little risk of self-plagiarism, because you'll need to rewrite everything pretty much from scratch to fit into the new and more compressed arrangement of ideas.

So, in summary: it's not only ethical, it is legitimate new work and can be highly valuable, just so long as you make the nature of the article extremely clear and include all of the relevant citations.


Will it be too late to start looking for postdoc positions once I am about to submit my thesis for review?

I absolutely agree with emory's answer: the earlier the better. That being said, I didn't apply for a single postdoc position until the date of my defence (I was looking at that time already, but haven't found anything interesting).

There are several factors that may differ from person to person, so make sure the advice you take fits your situation:

some places, you actually work on your manuscript or thesis presentation until the day of your defence (e.g. France). In some places, there is a big "waiting period" between submitting the manuscript and your viva (e.g. UK)
funding: do you have funding up until the date of your defence, or does it finish earlier?
connections: the people you have met in conferences, through your supervisor, etc. Some people establish strong enough connections during their PhD that their postdoc search simply comes down to contacting those connections. If you have to search "blind", it could take much longer.
location and/or immigration: A perk of looking for a postdoc in a country/locale you are familiar with is probably knowing where to look, understanding the language and familiarity with the system. A perk of looking broader is that you have more options (and a lot of places value mobility during postdoc even if you do return to your country of "PhD origin" afterwards); but depending on your nationality and target country, immigration documentation might take some non-negligible amount of time.
finances after the viva: How easy it will be for you to get along if you have a few months of gap? Do you have enough savings (as a PhD student, likely not); is there a good social support in the country you're in (in France, I could get a very nice unemployment package for some months which allowed me to search in peace); are both you and your parents happy for you to move back in with them for a few months, etc.

So, when you start looking will depend on the above factors. I.e. if you are in a system where months leading to the defence are very work-intensive (no "waiting period"), it might simply be too stressful to look right now. That was my case: I was not sleeping regularly (in the holy trinity of work-rest-social, I opted for work+social and ignored sleep...), under a lot of stress, and my social activities were absolutely essential to keep me going. I think I would've had an easier time if somebody told me: don't feel pressure to look if you are already under too much pressure from finishing.

Some additional advice for looking for postdocs at the end of your PhD:

if you find yourself in a pinch and have a good rapport with your supervisor, talk to them. It is not uncommon for PhD supervisors to "magick out" a short-to-mid-long postdoc for their former PhD students. My supervisor (France) was able to offer me a short 4 months contract, which gave me the "buffer time" I needed for a proper search while I was not stressed about my defence. My current lab (UK) has offered some of the PhD students a 1+ year postdoc after graduation.
a lot of places will happily offer you a postdoc position even before you have a PhD diploma in hand (i.e. as long as you show them you have submitted your manuscript and are just waiting for the defence; in case of "waiting period" type systems), and let you take a few days off for your viva, so this should not be a limiting factor.
almost all institutes everywhere are used to receiving applications from different academic cultures, and therefore are accustomed to different "standard" dates applying elsewhere. This is especially true for postdoc positions which typically have little to no teaching obligations.
almost all advertised postdoc positions typically have a contact e-mail for questions. If unsure about how strict the starting date or any other criteria is, asking can only help. If I was worried about whether the advertised starting date could be a problem, I might send something like:

  Hi, I'm X, currently finishing my PhD on topic Y from University Z, and am very interested in applying to your open postdoc position on topic M. As I see that the advertised starting date is in September, I would like to ask if you can offer any flexibility with the starting date. The reason is that the likely date for my defence is early October, and I was wondering if you would still consider my application under these circumstances if I applied?

some applicants manage to establish a really good relation with their examiners, and I've heard of PhD students obtaining postdocs from them (with the connections established during their defence). I find it a risky option, but it is one.
talk to your supervisor; he could have more specific advice either on where to look, when you can expect the bulk of open positions, stories form older students.


Should I mention in a PhD application statement of purpose that I earn a large income from a business I created?

No, don't mention income here. This just looks smug. But ofc you should mention that you are running a successfull buisness and explain how this can contribute to your Phd (experience, skills,...). The problem I see is that you want to do a microbiology PhD while running your own buisness? This could be a big problem because they don't want to fund people who are not 100% focused on their work here.


You can use the Zotero Style Repository and search for the term "harvard".

You can preview a style by hovering over its name:

Once you've found your style, right click on the "Source" link and click on "Copy Link Address". (e.g. https://www.zotero.org/styles/harvard-cite-them-right?source=1)

Now in Mendeley, go to "View > Citation Style > More Styles... > Get More Styles" and copy/paste the link in the "Download Style" box (and click "Download")

Then go back to the "Installed" tab and select the style you just downloaded and click "Use this Style":

(You may have to restart MS Word)


My professor gave me a bad grade and wouldn't discuss it further, I think some prejudice may be involved. How should a student proceed?

Generally speaking, humans - even professors with a bad reputation - behave the way they do in a way that is sensible in at least some context, even if that context is only in their own mind. Without knowing the situation, this behavior could be anywhere from an indefensible prejudice to a "reasonable person" response that one simply fails to understand or have sufficient information to interpret.

So, let's walk through a couple of reasonable interpretations.

Honest Interpretation

In the first interpretation, the professor responded honestly - she felt fear or discomfort in meeting with you privately. "Why" she felt that way cannot be determined from a simple reading of the narrative presented. She could have a disability (panic/anxiety disorder, post traumatic stress), she could have been threatened in the past, she could have believed you were affiliated with people who had threatened her or wished her ill, or she could have interpreted your tone or body language as being angry or...well, intimidating, and surely other reasons I cannot so easily imagine.

People have a right to feel safe, and to insist they not be put in a position where they are made to be in perceived or real danger. When one can un-self-consciously walk down a dark street alone without fear because of one's skin color, size, gender, or physical training, it is easy to be unaware of the fear that others who are not so fortunate must live in continually - often for all too real reasons. As I have two daughters, I can attest that this is a rather disgusting realization to have to come to - but it is an important one in understanding our place in the world and our relationships to others.

Legally and ethically, the University is almost universally required to provide reasonable accommodations to this end for both students and faculty - both you and your professor.

In all this, this does not require that you did anything wrong, nor that you should receive adverse treatment. If the professor was hard of hearing she could require all advisement to be by email, and this would be a reasonable accommodation. To request an appointment with a chaperon might feel silly when you don't see the need, but it can be a reasonable accommodation none the less.

Unfair Treatment Interpretation

Interpretation Two: you were singled out for unfair treatment. In this interpretation, you were treated explicitly unfairly and the professors attitude and actions culminated in adverse, unwarranted treatment.

As a student and "paying customer", you have the right to receive services you paid for, comparably valued substitute services, or a refund. The University makes certain guarantees of service, and they are obligated to make good on their contract.

The University, along with applicable law, usually provides for how complaints should be handled. Generally, the head/chair of the department is involved, and at times special departments (like an Ombudsman or Student Services) can also seek to find a reasonable resolution.

There is not, however, always a guarantee that a class will be offered by a professor who likes you, or whom you like, or who is even in any way helpful or beyond vaguely useful. It's hard to bar passive-aggressive behavior that's shielded by unethical but hard to disprove veils of personal boundaries or safety.

From your writing, it seems a member of administration offered a number of remedies. You likely had the right to complain to administration, be given an administrative (no cost/fault) withdrawal from the class with potential return of related fees, receive 3rd party grading to remove questions of improper marks, a pass/fail opportunity for credit, etc. While none of these are ideal resolutions, there are often no perfect fixes for problems like this.

Part of this is often what is really sought in remedy is not possible or not stated. If you felt insulted and discriminated against, you might have wanted the professor penalized or to apologize to you - which might have been objectively inappropriate or just impossible. You might have wanted your paper regraded as stated, but there may have been insufficient grounds for this is as it is simply an extraordinary request. If a 3rd party can look at your paper and say "it is not beyond reason that a professor, even if they would be very harsh, would have given this paper a C" then it's just a no go there, too.

So, administration has a duty to find a way to make the best of a bad situation. From the sounds of it, they offered pretty much all the recourse they had to offer to you. You could take it or leave it, but by staying in the class and taking the pass/fail offer and receiving credit (and choosing not to attend lecture - which was certainly understandable but not strictly demanded by the situation) the University upheld their end of the bargain - albeit in a not very satisfying way.

A Word on Feminism

One note of issue: the problem with how this is stated in the post is that feminism isn't actually related. If someone is known to have a militant or unkind attitude, behave in a way that discriminates against certain genders or types of people, or just has a reputation for being a terrible teacher or nasty person, say so.

The problem is when words are used as code words for something else entirely. If the administration was unwilling to give a refund it would be appropriate to say they were playing hard ball or being stingy or greedy - not to say they were known to be of a certain ethnicity renowned for thrift (to be time-insensitive, I am presently aware of three entirely different sets of people who have this notion assigned to them).

So, if a professor has a reputation of being nasty or terrible or discriminatory, please just say so outright. To say "feminist" or "extreme feminist" to imply being a man-hating shrew does a dis-service to yourself, your question, to feminists, to man-hating shrews, and to society as a whole.


Mistook new faculty member to be a student, how big a faux pas is it?

I'm a female professor in my late 20s and I'm pretty sure I look even younger than I am. I've been mistaken for a student a bunch of times and it's always been an honest and totally understandable mistake. I'm often assumed to be a grad student; heck, I discovered in front of my mirror three days ago that wearing the school logo T-shirt I somehow acquired is inadvisable because it makes me look nearly indistinguishable from an undergrad.

I know doing this is embarrassing for the person who messed up, but looking at me and concluding that I'm very likely a grad student is reasonable and something I know is going to happen unless I'm wearing a fancy-schmancy suit. Heh! I've even done it myself. One time when I was meeting a (male) colleague, each of us mistook the other for a grad student; we've been teasing each other about it since. The only circumstances under which this would bug me would be if the person doing it were trying to be patronizing, or covered it up in a way that introduced some creepiness.

But yeah. I'm accustomed to it and I know my status surprises people. When someone asks if I'm a student, I laugh it off and say, "I am a very young faculty member." Most of the time thereafter I forget it happened. You did everything you needed to in order to make amends; I'd say put the guilt aside and move forward with a professional relationship with your colleague.


How to emphasize special issue publications in a CV?

How to present this information may depend on your field.  In mathematics, special issues are uncommon, and they carry no additional prestige.  (A special issue might attract stronger papers than usual, or it might be forced to accept weaker papers due to an insufficient supply of thematically appropriate submissions.)  On the other hand, in computer science particularly strong conference papers are sometimes invited to special issues of journals.

You should emphasize the special issue on your CV only if this is a widely recognized concept in your field and it is generally considered prestigious.
I'd recommend listing papers in special issues together with other papers (but with a special indication if appropriate), rather than in their own section.
If you can give a short but compelling description (e.g., the program committee invited the top 30% of the papers at Conference X to the special issue), that could help people from other fields make sense of the designation.  This can be valuable in both hiring and tenure cases.


Dealing with an advisor who is not interested in publishing

In comments, you say that you have less than a year left until graduation.  Given this fact, it would likely not be easy to get more than a couple of quality publications out during this time in any case, particularly with a perfectionist advisor and little experience in publishing yourself.

As such, I think your big goal (besides graduating) should be to get a good postdoc lined up, where you can solidly advance your career and do a lot of publication.  Having few publications but a respected advisor can be a totally reasonable combination for moving to a good postdoc.  If necessary, you may even do more than one round of postdoc.  Once you establish a solid "upward trajectory" and track record of publications, the fact that you published little in grad school will not be a problem, particularly if your one grad school publication is indeed a very good one.


You don't say if you have legal copies of those films, but since you effectively gave her the contents of your drive you gave her your data...

  "I am still hoping it is safe"?

Safe from what? could she use the material - not sure, this may be a legal issue - how would she reference it? Would this be plagiarism as you effectively gave her your data.

  I did not mind this but later I realised she was having fun at my expense

Perhaps you should contact her and ask her to delete that material...
Good luck.


Public lectures are not generally required, but are one of the well-understood benefits of university education.  For most American universities, lots of interesting speakers come through and are widely advertised.  It's good for the university because it shows it's a place that such speakers find worthy of visiting, and for the faculty by giving them opportunities to interact and collaborate.

As for the students: if world-class speakers are showing up and talking about interesting things, why wouldn't students choose to attend the lectures that interest them?


How will C+ and many B+ during online school affect PhD admissions?

The nature of the question suggests that this is in the US, so I'll assume that.
If your lesser grades are outside your major (math) and you otherwise have a good/great application including stellar letters of recommendation, then I think grades elsewhere will matter very little. Given the pandemic, even less.
Don't worry too much about it, but make sure everything else is first class. You can't do anything about the past in any case.


How can I deal with a professor who refuses to communicate?

Given the reluctance of anyone else to communicate with Prof A, it seems less a case of you not knowing the secret handshake to get in touch with him, but more a case of Prof A simply not communicating. It is unlikely that anyone (including the dean) can make him communicate in a reasonable way.
What you need to do is to make sure that the path-of-least-resistance for your department is something that ends with you graduating very soon. My guess is that the best bet for that would be to get someone else to examine you. The "Vorsitzende(r) des Pruefungsausschuss" should be able to authorize such a thing. Phrase it as "Prof A is unavailable for examinations", not as "I failed to get in touch with him". If they claim that Prof A is available, ask them to demonstrate by telling you the date for the exam. Be polite but persistent.


How important is the choice of a guide/adviser for pursuing PhD in a topic

Working on a PhD in an area where your advisor appears to have little to no expertise in is fraught with danger. A PhD degree is in some sense an apprenticeship - while you need to do the heavy lifting, you also get/need to learn the tricks of the trade from an accomplished master. Every craft has subtler/finer aspects that are not acquired easily. Would you want to rely on someone who himself doesn't appear to know much, even at a high level? I wouldn't do a PhD with such an advisor for the same reasons I wouldn't learn painting from someone who doesn't know it himself/herself.

On a more important side note, it might not be very wise to jump into a doctorate in an area you have such little knowledge/interest in. You do appear to have the right background, but even with that, doctoral level research in Spectral Graph Theory (and applications, if you are interested in them) is not going to be easy to pick up, even with an expert advisor.


What do I do with a write-up of possibly folklore knowledge?

I could speculate here, but I think you need advice from an expert in that particular field. It may well be that there is journal out there that would gladly publish such a paper, but also the converse may be true. It may also be that there is some special issue coming up where such a paper would be a good fit. However, these things are only known to experts in the field and hence, your best bet would be to contact one. These could be people in your department, editors of journals on this topic, plenary speakers at conferences or authors of books in the field. Knowing this person personally prior to asking would probably be better (but not necessarily so).

If you do not know anybody to contact, you could also look for a journal that seems to fit and write an email to the editor (or a suitable associate editor) with the write-up attached and ask if this would be suited for said journal. It is not uncommon to sound things out that way. (Beware, that a positive reply does not tell much about chances of acceptance.)

If publication in a journal is not important to you or you don't want to risk another frustrating rejection, uploading the thing to the arXiv is the way to go. You get some publicity and some people will read it…


How do you get back into teaching after being overseas for 10 years and lacking good computer skills?

Some community colleges have pre-engineering programs in which someone with a Ph.D. in engineering could be an instructor.  The engineering courses offered in these programs are typically very limited.  Courses like thermodynamics are not typically offered at the community college level.

Most community colleges have rules for the required academic background of instructors.  For example, a fairly common rule is that instructors are required to have 15 credit hours of graduate-level coursework in the subject that they are teaching.  These kinds of rules might well prevent your friend from getting a job teaching mathematics, chemistry, etc.

Your friend might also consider applying for a job as a full-time instructor at a four-year college that has an engineering program.


Specialising in a field during a PhD at the expense of forgetting other areas

Is this something that other people experience?

Yes, this is completely normal. Our memories get hazier over time, particularly if we don't make use of them. It is nothing to be worried about. We can't keep everything fresh in our minds at all times - as you learn new things, older topics get pushed to the sidelines and we may lose some of the detail.

However, memory is a complicated phenomenon, and just because you are having trouble accessing a memory doesn't mean that it's been completely overwritten. As @PatricianShanahan hints in a comment, I suspect you would find that if you had to re-learn some of these topics, it would come back to you surprisingly quickly. Partly because the memories are still hidden away somewhere, and partly because you will have been getting better and better at the process of learning itself.

  How do you find time to refresh the knowledge of areas that you 'should' know, even if you have no use for them anymore in your research?

I don't think there is any particular need to force this process. The memories that fade the most are the ones that are being used the least, and there's a good reason for that: they are the ones that are less important to you.

General reading will help to keep memories fresh - it's always useful to read broadly around your subject. If you are worried about forgetting things because they are interesting to you then try to find some enjoyable reading on the subject - perhaps pop-science books, or magazines.


What could my postdoctoral advisor do, now that he knows that I started looking for positions in industry?

My feeling is that most supervisors/PIs are aware of the realities of being a postdoc, having been one themselves at one point. I suspect that he valued your honesty, and understands that most people would like a well paid job with stability.

Unless he's shown some signs of being an awful person, I would assume he was asking you out of personal interest, and so that he organise his grants and find a replacement if possible.


Where are academic jobs (starting from postdoctoral contracts) advertised in France?

Permanent positions ("maître de conférences" and "professeur") almost all are listed on the website called Galaxie. The lists are available on this page. It's a bit empty because most applications are over for this year, but there is still the big spreadsheet with the (now outdated) info, to give you an idea.

(There are also some permanent positions called "PRAG" and "PRCE" listed there but they are unlikely to concern you – you would know if they did.)

Some special postdoc positions called "ATER" (attaché temporaire d'enseignement et de recherche) are also listed there, however be warned that 1. their salaries are low, even lower than a PhD student, 2. the teaching load is high, as much as a faculty member, 3. they are often "reserved" for PhD students who are on the brink of finishing but need an extra semester or two. You probably have to ask someone from the university to know if it is the case (I know people who got an ATER who were not PhD students just finishing, so it's certainly possible).

Galaxie is not very well organized and it is a bit hard to find information. In some fields, volunteers run some field-specific websites presenting the same information in more readable form, e.g. Opération Postes in mathematics. Ask your contacts in French universities to tell you if one exists for your field.

I am not aware of any centralized website for postdoc applications. I have personally never searched for a postdoc in France, but in my understanding, you have to subscribe to mailing lists, go to labs' websites, or just know people who are aware of openings, etc. Good luck. Some things to look out for: if something is called a "fondation" (foundation), they probably have some postdoc grants to offer. Similarly if you come across something called a "Labex" (for "laboratory of excellence", yes, it's a bit pompous), it's not an actual lab, it's a five year big grant with many postdoc grants attached.

I realized that I said something wrong above. Not all permanent positions are listed on Galaxie. Some "Grandes Écoles" ("Great schools"), which are not technically universities, still hire professors who teach and do research. More info on Wikipedia. For these positions, I don't think you can do better than going on their websites when it's application season. The procedure is also different from the centralized one, from what I understand.

PS: yes, all these websites are in French... You will find that being able to read and write administrative French (or having someone who can on call) is a vital skill.

tl;dr There is no such website, basically.


Whether to add co-author who helped in modifying a journal paper based on a peer-review feedback?

You should consider it, I think, but there is too little information here to give a positive recommendation. It would depend on whether the other person contributed to the ideas at the heart of the paper. If they only gave advice on wording or presentation, then probably not.

Note that editors and even reviewers making suggestions don't become co-authors. You have to judge their contribution. But note that they may have an opinion about it that you should take into account as well.

But let me suggest something beyond pure accounting and ethical obligation. While this may not be true in some fields that depend on rigorous bean counting to rate people, I'd suggest a general view that you are generous rather than stingy can serve you well in the long run. If I were the commenter on your paper, I'd suggest that an acknowledgement is enough (or more than enough). If I were the author, I'd be more inclined to include the commentator than not, though the first part of this answer still applies. Over the course of your career it may matter little whether you are the sole or joint author of any given paper. But, having a wide circle of people willing to collaborate with you is a big plus in the long term.

But, if you are at the very beginning of your career and looking for a job, you might need a sole author publication at this moment. That depends on the field, I think. But I'd suggest short term thinking only if truly necessary.


Applying for different PhD position: letters of recommendation

Have you ever tried discussing your concerns with your supervisor? It isn't very clear from your previous post and this one. As you mentioned in your previous post that you are quite indispensable to his lab, hence, communicating your problems might make him want to fix them. I had a friend who was on the verge of a burn-out while doing his PhD. Like you, he was also handling multiple projects at the same time. One day he walked upto his supervisor's office and told her that he would like to leave the lab because of certain issues and would like her to support her PhD applications elsewhere. She thanked him for bringing up the issues and did provide letters of recommendations in a timely manner. At the end he continued working in the same lab but the supervisor was much more accommodating of his requests.

Now this might/might not happen with you but making your supervisor aware of the issues seems to be the best approach in my opinion. Especially when your field is interdisciplinary and it may be difficult to change departments without bumping into one of his acquaintances. It would save you from a lot of headache and mess if you just tell your supervisor that you are considering changing labs and want to explore a different (positive and motivating) environment for your PhD. Make a draft of what/how you want to say it. It will take some time but will be worthwhile in the long-run. And if you think he might say something and change his mind later on, it might be best to communicate via email. This will serve as a reference to explain your situation to your potential supervisor/grad school.

All the best!


In my experience, in CS, it is rare but not unheard of for a professor to be first author.  Usually I think that is really when it is the professor who has taken lead, both in running a project and in writing the text, and typically it is when it is a group project where each student has a moderate contribution but it's the advisor who pulled it together.  This is often the case when the paper is an overview of the project as a whole.

In the case of your project, it certainly sounds like you're getting a raw deal and should push back.  But without seeing the professor's side of the story, it can be hard to tell.  They may have a different view of the relative contribution.

IMHO, even if it's 50-50 or 60-40, the student should get priority.  There's a tipping point where it's more understandable, but from your description, you're nowhere close to it.

Good luck!


For how long is research considered valid for publication?

Research does not have an "expiry date", but what it does have is competition. Journals want to produce cutting edge research, new information that will help others in the field.

If you do some research but don't publish it, then find 20 years later that no one else has done it and your information is still something other researchers would want to know then you can easily publish it. Delaying publication is only a risk in that other people may work on the same topic or have the same idea you had, and publish it before you.

One interesting example is Brian May, guitarist in the band Queen. He was studying for a PhD when the band took off and quit his studies in 1974 to become internationally famous. In 2007 he re-enrolled at university, completed and submitted his PhD on the work he started 30 years before. Luckily for him, his field was a small one and no one else had decided to work on the topic he had studied in the intervening years, so his work was still new, interesting and relevant.


Does publishing a monograph with Springer in computer science have any academic value?

Is there any academic value in publishing a book that is based (approx. three quarters of it) on existing (peer-reviewed) material?

If well done, this seems like a useful book to me. Bringing together various related papers, adding some expository material for readers not yet intimately aware of the field, providing some perspective through use cases ... why not? Remember that in CS, the point of books is almost never to have original material. Books in CS are meant as a collection / introduction to a topic, not as a venue for new research contributions (that's what we have conferences for).

  Also, as I am considering applying for assistant professor positions (I am currently working on contract basis), I would like to ask how is this book monograph viewed at by hiring committees? Is it considered vanity or a plus?

Springer isn't a typical vanity press outlet, so I can't see a hiring committee outright discarding your publication there. I guess it will be a small plus (or a bigger plus, if the book turns out really good and becomes better-known in the field). However, your actual original research will probably be much more significant.


Doing a PhD with significant external time obligations (e.g., marriage)

The people who I've seen with considerable external commitments who have still gotten through in a reasonable amount of time all boil down to one thing: They treat grad-school like a job. From 9 to 5 (or 10 to 6, 11 to 7, whatever works for their schedule) they're working. No, they're not available for the infinitely many distractions of life, any more than someone at an office is. They pack a tremendous amount of productivity into that time, and then when they need to be with their family, they're with their family.

Those at least are the people who got through it sane. I think the other major trait is to recognize that, because you have a life, this might take a little longer, and not burn yourself out trying to hammer things through to the point of exhaustion.


He gives me an assignment and I want to reply 'I will do it right away'.

Then reply: "I will do it right away".

But if you're going to do it right away, you can probably wait replying until you have finished the assignment, if a reply in that case is expected.

  I ask him some questions about the assignment and he replies something. And I want to express 'yes, got it!'

Then reply: "Got it, thanks."

To sum up: as many students, you're overthinking all this.


How to cite a source that has vanished due to link rot?

Before worrying about the citation your colleague needs to gain permission to use the image in her work. She needs to contact the owner of the image and ask them for permission. The image could then be used and the citation could be a "personal communication" or the URL of where the image was taken from with the access date.

Finding the contact details of the image owner will undoubtedly be difficult, especially given that the image is not actually on the forum anymore. But if the forum is still active perhaps a question could be posted on there (with the image) asking if anyone knows who took the photo / how they can be contacted and perhaps she'll get lucky.

Edit: As pointed out by StrongBad if your colleague is not planning on actually reproducing the image in the document then seeking permission for its use is not required. If she just wants to describe the image, I guess the only option would be to cite it using the URL where it was, with the access date. However, given that the reader could not then actually find the image themself and look at what your colleague was describing, it probably wouldn't provide that much useful information to the manuscript.


How to approach professor about potential paper?

I think you're overthinking this.

I can't imagine any professor thinking you are desperate or just want money out of this. In fact, I would expect a professor to be excited to get an email from a student that has taken the initiative to start a project and reaches out to see if they are interested in collaborating.

You really have nothing to lose here. Professors are generally eager to publish. Send an email!


Review claims reference was omitted, but it was not

The manuscript was rejected and I do not plan to resubmit

Then do not respond.

Should I accept this and move on

Yes.  Reviewers make mistakes.  That's normal.
Most people who think they know who the reviewer was are wrong.


As somebody who's actually doing a PhD in France, maybe I can provide some more information.

Firstly, as everybody says, you have to get an equivalent of a Bachelor degree (I think that's "licence" in France), and the a Master degree as well. I didn't do this part of my studies in France, but, some things that I overheard:

of course, nobody is paying while you are doing that, and you most probably have to pay a yearly tuition (probably around 400eur)
I think that there is some programs to get some scholarships that could help you, and you'll probably be eligible to help from CAF for a while
to supplement your income, I'm sure you can teach already in the last year of Master, and possibly (but I'm not sure), even as soon as you finish you Bachelors (aka "licence")
other major expenses are living costs and eating costs: you can usually get a student dormitory (200-300 eur/month is plausible, but it depends on a city) and as a student, you get cheap student lunches (3-4eur/meal)

As I said, I didn't do this Bachelor-Master part of my education in France. But, for the PhD I can offer more information:

a PhD in France is basically a normal work contract lasting for (exactly) 3 years, with a usual possibility of extending it for 3-6 months
to obtain a PhD, you have to obtain a grant. Sometimes, you apply to professors for a subject that is already funded, and sometimes you apply to the professors and then you submit your grant application together (like me)
you still have to pay a yearly tuition (~400eur), but you will be receiving a monthly salary where the amount depends on your grant. It's usually between 1300 and 1600eur
in your first year, you are still possibly eligible for CAF
there's two type of PhD contracts: research, or teaching. The teaching contracts are harder to obtain, but it is usually easier in your second year than your first. If you need/want more income per month, a teaching contract gets you an additional 300eur/month on your salary
other major expenses are again lodging and food: again, sometimes dormitory housing is available, but renting a flat can be acceptable as well (around 300eur/month if your flat-sharing up to 550-600 if you're renting alone). Usually, the lab/university provides some kind of lunch discount tickets as well.

As for some additional information about how to get in to a PhD programme:

in France, it is obligatory to do at least one internship in a research lab or a company during your Masters, but two are possible
if you are planning to stay in France, it is very customary for people to do their PhDs in the same lab where they did their internships, and some even just extend on their internship topics
your Master supervisor and all the contacts you made during your internships will probably be most helpful, as you can ask them for advice, or even if they know of a position / professor that would suit your plans
additionally, if you want to do your PhD outside of France (it always needs a Master degree), it's probably a bit harder to obtain (although your Master contacts can help you). It's a paying job with a salary in a lot of European countries (some examples includ: Germany, Italy, Sweden, Switzerland...)


Software/App for electronic research notebooks

For the last month, I have been using Gitit for this purpose.  That link goes to a live demo where you can try it out.  It satisfies all your requirements:

It's a wiki, so you can easily make links between pages.
It's built on pandoc, which understands TeX and uses MathJax to render it (it technically renders a subset of TeX, but it's a pretty substantial subset)
It's actually a Git repository, so you can upload anything you want to it.  Or just put your figures out on the web (via figshare or a public Dropbox link) and link to them.
Same as 3.
Again, it's Git.
It is open source: https://github.com/jgm/gitit

As a bonus, you can put it out publicly on the web if you want (or just run it locally on your machine).  I run it on an internal server at my University and my students and post-docs use it to.  Thus it's a convenient way to share information as well.


Do reviewers get a deadline for reviewing a Paper, if yes, how much?

In general when journals contact potential reviewers, they do tend to give a time frame they expect those who accept to receive a review back in. The more enlightened ones also give a time limit to accept the review. As has been noted in the comments, the length of these windows varies by subject and by journal, with mathematics journals noted as being at the long end, and some disreputable science and engineering journals at the short end. In practice, these are soft targets, and editors tend to be happy if they get any response at all, even a late one. My experience is that these windows tend to be the same for initial and subsequent reviews, but I definitely won´t claim that is universal.
Note that for resubmissions there is a strong preference to reuse the original reviewers, since they are in the best position to check that their criticisms have been addressed. Having a strict deadline for review would be likely to slow the process further, since new reviewers would have to be found (and given a new block of time to respond in), who might easily raise points ignored under the original review.
One misapprehension in your question is in assuming that these targets are set by the publisher. In general it will be the senior editors making the decision based on the volume of submissions they have available, and the standard of impact they are aiming to maintain. The exceptions are at the predatory end of the market, and no reputable journal is going to publish an article unreviewed, just because all the reviewers were late responding. Modern editional systems have made life a bit easier by automating reminder emails, but these are often treated as spam messages by the recipient. Your principal solace is that many of these systems track review times and quality, and push editors to request reviews from fast, high quality reviewers.
As an author, your most useful data is average time from submission to publication, which many journals now advertise to win custom. Note that tis is a figure which can be manipulated however, by techniques such as forcing revisions to be treated as a new submission, or by giving up of articles which have sat for a long time.


How long is too long to wait for a rejection because of a lack of reviewers?

If anything, my reaction is that two months is too soon to absolutely give up on trying to find an appropriate referee.  Generally (at least in my discipline) people are given a week or two to accept or decline a referee request, so two months probably means that not more than ten or so people were asked.

My understanding of what it means to be an editor is that they should in principle be working harder to find a suitable referee.  However, if the editor is having an especially bad time of it, it may be worth letting the author know: maybe they will choose to resubmit to a different journal or to switch to a different editor at the same journal.  The latter happened to me years ago: the editor that I submitted to asked one person to referee, got referred to a second, and so forth.  He reported failure to me after the loop closed up.  But the failure was conditional failure, and he gave me the option of switching to a different editor at the same journal, which I did.  (Unfortunately after that the paper still was not treated well, but that's not part of the present story.)

Academia is specialized, but it's not that specialized: probably most journal submissions have at least 100 suitable referees in the world, right?  If so, then two months is way too soon to say definitively that a suitable referee could not be found.  In my experience, editors often "sugarcoat" the things that they tell authors -- probably because they didn't like the hate mail they got from their earlier, more forthright approach -- to the extent that if you take literally the reasons given for objection, they often sound rather silly.  In this case I might suspect that "I spent two months and I couldn't find a suitable referee" is meant to be code for "I asked enough people whose opinions I trusted, and while they were not willing to formally referee the paper, they told me that it did not interest them and thus probably did not merit publication."  If the editor is himself making a judgment call about the suitability of the submission, in my opinion that's fine but they should be upfront about it.

Unfortunately the current culture of academic journals makes extracting "the real story" from the editor almost prohibitively difficult.  In practice it is probably in your poster's best interest just to try again at a different journal.


Does it matter how long ago you took a course for graduate school admissions

This depends a lot on what you've been doing in the interim. At one extreme, even if you had a solid coursework background, but have not been exercising it, or anything related, for the last decade, and admissions committee will worry that you're not up-to-speed.

At another extreme, if you did well in coursework and have been doing serious stuff subsequently, more-or-less related to your future goals, that's obviously a plus. That is, the "stale coursework" potential problem is not a problem for you since you've not only maintained, but improved, your chops meanwhile.

True, it's easier to flash a transcript to "prove" some knowledge or expertise, while professional knowledge or expertise is not universally set up to be "documentable".


Applying for internship in the US as a European Student

As has been said, your last sentence hits the mark - a direct comparison is impossible.  I would argue that it isn't necessary, either.

I am a US native.  I am currently working an internship in the United States at a child company of a larger pharmaceutical business.  I know that my company had a "minimum" GPA for the application, but this was never mentioned in the interviewing process.  To me this implies that companies use GPA to see if a candidate meets a satisfactory minimum - it's a way to weed out applicants they know they don't want or need.  I think if you explain that your GPA is good by European standards, if indeed it is, then your application will be strong.

A few of my fellow interns are from Germany.  I don't know them well but I mention this to show that success is possible and that some companies in the United States, at least, have a good grasp of how grading scales work in Europe.  I think it worth mentioning that Europe seems to have a relatively smaller amount of grade inflation as compared to here.  That's an important point - grades are somewhat inflated here, and a 3.5 GPA probably indicates a level of performance that is different than you imagine.  Given this, I would say your chances of getting a job are good, especially if you adopt the normal tactics of applying to many positions and being prepared to take a few rejections.


Should I agree to my supervisor's request to place him as first author of my paper?

This is hard to give good advice about without a lot of context. What is ethical and what is done (in some fields) don't necessarily match up well. In some fields, an advisor is often a co-author - even first author.

If the other person has made no contribution to the paper then, ethically, the request is wrong. But you may need to accede to it just out of personal protection. If the advisor has some influence or control over your future then you may be stuck, no matter the ethics. And you may have no effective way to counter it while preserving your future career.

It isn't really a question of which country, though this sort of thing does vary by field. In situations in which the advisor funds a lab in which work is done it is pretty common.

But, think about why he is asking. Think about whether it is really valid. But think most about how your long term career will be affected if you go along and if you resist.

And note that having another paper on your CV is still a good thing, even if he is first author. And even if it isn't right.


Applying to Ph.D. with 5 years in Bachelors

This sort of thing should be explained in the cover letter. This trend is pretty common; freshmen enter college ready to party, realize halfway through that their grades are actually important, and then buckle down and do good work for the rest. You simply need to state that, despite your initial behavior, you are fully committed to your education. Given a 3.5 GPA at the end, I don't imagine you would have too much trouble.

Do note that this will vary as a function of the universities to which you apply; some may take a harsher view than others. Still, you have a good explanation for the one bad year, so it shouldn't post too much of a problem for you.


If asked to provide separate list of publications in addition to CV, should CV still include list of publications?

Yes, I would say so.  A CV always should list publications.

It may be that for some reason to do with their search process, they find it convenient to have a separate document that only lists publications, rather than digging through the CV to find it.  But that doesn't mean you should remove this list from the CV.


In a literature review, should I focus on how much my work will contribute to the discipline?

You would usually not just review "the literature" (How would you do that anyway as there are thousands of papers coming out everyday in most fields).

I like to see the literature review like building a pyramid: You start broad and then narrow down and come closer and closer to what you actually did. Your thesis/paper should then come as the last stone on the top of the pyramid. Along the lines of "This is what other people did, this is how it all builds up but in the end a very important part was missing (= your thesis!) and here it is! Then you start describing your actual work.

In other words you can see the literature review as something what helps to emphasise how important your work is. Literature review is not something that you have to do but something that you want to do because it makes your own work shine.


Open book exams are actually very easy to design (at least I think so, and I favor them in my own teaching): just design it the same way you would design regular exercises. The goal is to evaluate the students’ understanding and skills, i.e. how they analyze and solve problems, rather than the facts they have memorized. To do so, I usually design exams as problems rather than series of trivia questions.


Indicating work was performed as a student for alumni

assuming I use the gmail address, should I add a footnote to my name saying "Work completed while an MSc student at institution" to justify the affiliation?

No, because you never need to justify right in the paper why your affiliation is indicated the way it is, or why you picked one e-mail address over another.

  I've seen this done for papers published by students about work done during internships at companies, such as "This work was completed while name was at company"

I can imagine the benefit here is to inform readers that company is not a likely place to get in touch with name any more. That can be useful information, but it is most likely not provided just as an explanation of why a particular e-mail address was chosen.


Is the postdoc salary negotiable in Canada?

In my experience, postdocs are grant-funded with a nonnegotiable salary. It doesn't hurt to clarify though.
The department chairs I have known would not have considered this rude. Reimbursement for moving costs is often offered as a sort of signing bonus.
Reimbursement for parking is unheard of in my experience. Again, asking politely shouldn't be a problem, but I wouldn't get my hopes up.


How to refer to descriptive information of variables as exogenous variables

This may depend on the field, but to me the phrase "the descriptive information of main variables and item pool characteristics" is utterly unclear. If you don't want to spell out the full set of descriptive statistical operators you use, consider including something like: "Our exogenous variables encompass [...] summary statistics over the main variables".

However, in the interest of reproducibility, I would personally prefer to spell out the full set. Right now, it is unclear to me how far you stretch up the set {min, max, mean, std}. There are so many things that could be included here: median, interquartile range, skewness, kurtosis, higher-order moments, etcetera. It's best to be explicit about your setup.


Should I lead an applause after introducing colloquium speaker?

"Please welcome our guest ..." and applaud with the crowd.

Presumably you have attended to invited speeches before?


What is a reasonable expectation for privacy of exam and homework grades?

The answers in the comments are correct.  FERPA, the Family Educational Rights and Privacy Act, makes "education records," which include grades, private and protected by law in the United States.  Students can reasonably expect their homework and exam grades to be held private from other students.  (Students acting as TAs can necessarily see such grades, but are bound by FERPA to keep them private.)  A search for FERPA will tell you more than you could ever want to know.


Comparing the scientific outputs of researchers

Normalising across fields is hard, but it's worth attempting. I would recommend reading this PLOS Biology paper as a good introduction.

This proposed measure is not appropriate because papers do not have an impact factor. Journals do, but there is a very wide distribution of papers within a journal - an impact factor can, in some cases, jump an order of magnitude because of a single paper.

"Mean impact factors" also take no account of publication volume. If you have a journal with an IF of 2 and one with an IF of 3, it's tempting to say that the mean is 2.5. But what if the first journal publishes ten times as many papers? It gets complicated quite fast.

The approach of normalising against the field/year makes sense, but ideally what you want to do is compare the actual citations for the researcher's papers in year X against the actual citations for the field as a whole in year X. The hard part here is defining the "field"; most approaches do what you planned to do here, treat all journals in a field as equivalent to the field as a whole. This is the basis of the source-normalized impact per paper (SNIP) and mean [log-]normalized citation score (M[L]NCS) measures; a more complex approach involving defining the field by citation networks is the basis for the relative citation ratio (RCR). All the usual caveats about counting citations apply, and numbers should be assumed to have fairly wide error bars for single-person data, but the results will make a lot more sense than one purely based on journal-level averages.

These approaches are a bit more labour intensive, but should be practical if you have access to a tool like Web of Science or Scopus.

This will effectively normalise for age of the paper and for the different citation practices in different fields. What it won't normalise for is fractional authorship - these measures can give somewhat confusing results if you're comparing someone who's routinely fifteenth author on large collaborative papers with someone who works in fields where single-authored papers are normal - or with someone who's usually the lead author on the large collaborations. Likewise, it will give misleading results if either person works in a field with substantial non-journal activity (eg the humanities).


How should I handle disinterested/unorganized adviser?

Advisors are not expected to be perfect but they are expected to do their job. Yours doesn't, he's endangering your PhD and his institution (probably his career too but that's not the point).

  Is this a typical scenario?

No.

Sure, some researchers are disorganized, have a messy office and/or hard drive, it's quite common. Some advisors are also known to occasionally abuse their role and give their students jobs which aren't related to their PhD, that's frowned upon but often tolerated. But whatever their shortcomings, an advisor must be able to fulfill their professional duties, and your advisor doesn't.

  Am I overreacting?

Not at all.

Contact the head of the department, the institution ombudsman or whoever is in charge. It's not too late but it's time. Don't hesitate to go over the department, your institution has a responsibility to provide you with proper supervision.


Is it acceptable to present the same project at two conferences and list them separately on my CV?

When I give the same talk in multiple venues*, I list the title of the presentation once, then underneath all the places I've presented it. For example:

  On the use of nanofibers in basket weaving

  20th Annual Meeting of the Society for Basket Weavers (July 2016), Department of Basket Weaving Seminar at East South University (August 2016), Workshop on Innovative Use of Nanofibers (October 2016)

If it's a different presentation (e.g. different title), even if part of the same project, I'd list separate entries.

* Only at venues which accept work that has already been presented, of course.


Is there any world-wide ranking of conferences/journals?

In Computer Science, CiteSeerX used to provide a Venue Impact Factor, that included journals and conferences, but it seems they've stopped doing it. As indicated by Gopi, Microsoft academic Research is some kind of global ranking, and JeffE also mentions google.scholar.

That being said, a global ranking, across sub-fields, is not necessarily meaningful. For instance, if one does not work on programming languages, then it's unlikely to submit a paper at POPL (the first venue according to CiteseerX). Hence, I'd say that field-specific rankings matter more, for instance in security: http://faculty.cs.tamu.edu/guofei/sec_conf_stat.htm or https://personal.cis.strath.ac.uk/changyu.dong/ranking.html.


How can I improve my attention and make fewer mistakes?

I was unfortunate enough to grow up in an academic upbringing (almost from pre-school up until university) that is a) purely competitive and b) relies solely on multiple-choice exams.

We were drilled for years to try and avoid such small mistakes, since they prove to be extremely costly when millions of people take the same test.

My only advice to you is to make a habit of checking your work, with a clear set of mind. I know it's not always possible (usually due to lack of time) but it's a very important skill to keep in mind that such mistakes do happen from time to time, and having some time at the end of a test/experiment entirely dedicated to checking your work is "money".

To my knowledge there is no fail-safe way to avoid such mistakes. Humans aren't really designed (from an evolutionary point of view) to stay focused for extended periods of time, especially when implicit calculations occur. Which brings me to a "corollary" advice; make a habit of writing out all your thoughts/calculations explicitly. The benefit with that is that it allows you to immediately spot irregularities in your work when you go back and check your work later prior to the point-of-no-return (i.e. you hand in your exam, or turn on the electricity switch or whatever).


How to react when encountering students who have previously failed my course?

Since you are at a small liberal arts college, I think you should not underestimate how much your own actions contribute to the culture of the college community. The notion of "avoiding" students is not something that you or your college wants to be known for (I imagine)! I think it is always best happily greet students that you know, perhaps ask them how things are going, etc. On some level, this kind of pleasant behavior is a professional obligation.

I don't think you should act any differently towards students who have failed your course (vs. students who did not fail, or haven't taken a course from you, etc.). Be cordial, and if the student wants to avoid you, then let them.

I will add that, while it's possible the student is mad at you, they may also be some combination of embarrassed and mad at themselves for failing. If they are embarrassed, then you avoiding them might make them feel worse, and you engaging with them might help them to get over the embarrassment.


Tell the other student as many times as necessary that you just need the okay directly from the PI and then you'll be happy to forward it.

I would try to steer the PI away from okaying the forward.  It would be different if you already knew and trusted this individual.

The germ of an idea for a project can be very important.  This is your baby and I understand your wanting to protect it.

(You need not explain that to the other student.)


How much is the relevance of a synthetic benchmark?

Having just a synthetic benchmark is generally weaker than having a realistic benchmark, but better than nothing.

There some more considerations to be taken into account.

First, quality considerations: Is the design rationale of the benchmark clearly communicated? Was there any effort made to reflect realistic cases? Was the benchmark designed with input from multiple, independent experts (ideally different authors than the author of the paper, due to researcher bias)? Have independent experts been consulted to validate the benchmark? Is the benchmark publicly available and well-documented?

Second, historical considerations: Has the benchmark recently been used in other research? The more widely a benchmark is used, the better, since it will allow an easy comparison between different works.


Does presenting your work at conferences cause your related publications to be cited more?

Yes, most definitely. The simple reason is that at conference it is relatively easy to pick up on the development of a certain field or ones own interest. And naturally, this leads to a bias towards those studies presented.


How often should I notify referees about my PhD application?

My suggestion would be to get in touch with your referees and tell them you that you will be applying for several PhDs, so they should expect to potentially get multiple requests for references.

You can then tell them that if they receive a request for a reference and would like more information about the PhD, so that their can tailor their references, then you'll be very happy to provide that for them as necessary. It may of course be the case that your referees will not be inclined to tailor references to individual projects.

This way they're only receiving information when they would like it.


The writer of that response has given you a valuable clue.  If, having read the email body, the recipient does not already have an active interest in working with you, the recipient is very unlikely to look at the attachments.

Instead, include a short paragraph about your research interests and a short summary of your CV  in the body of the email and offer to send details if requested.


The analogy you postulated is a good one: the commonwealth Chancellor in such systems is pretty much a figurehead and PR person for the university, if he or she so chooses. He or she may or may not also run the executive council meetings; if not, such a duty devolves to the "pro-Chancellor."


CV formats vary widely between countries. In the US, Canada, the UK, Ireland, the Netherlands* and Sweden CVs should not include photos, as these could reveal personal information (on race, age, perhaps religion) that employers are not allowed to use under local laws (source).

In many European countries, except those mentioned above, it used to be or still is expected to include a photo on your CV. However, in internationalized areas like academia, norms are converging toward the Anglo-American/Nordic model. German universities, for example, no longer expect photos on CVs, but it's not wrong to have them. I didn't put a photo on my application and got a postdoc in Austria.

I'm not sure about China and Japan.

*Another source specifically on the Netherlands is less strict: Employers are reported as being indifferent, unless it's a high-ranking (e.g. international?) position, in which case including a photo is seen as "bad form".


How important is research experience of undergraduates in the application for graduate school?

Evidence showing a research experience is definitely a plus.

However, do not get discouraged if you have none. Show in your application that you know what you want and why, be persistent and proactive and see how you can stand out in a positive sense from the rest of the applicants.


Using a quote to begin a new chapter in a thesis

Epigraphs are generally fine unless otherwise proscribed by university rules or the style guide used in your field. (MLA has specific formatting guidelines for them, I'd imagine others do too)

But first ask yourself if they add something to your paper. For example, a quote from Borges on an section on recursion would go rather nicely, setting up the ideas/theme far faster than a stale introductory paragraph. A quote from a historical leader might establish a link between the past and a chapter on modern day politics or society. But an inspirational quote about hard work probably doesn't belong in methodologies chapter.


Summer Research with Advisor or at National Lab?

One unfortunate by-product of the increasingly specialized nature of doctoral research is the tendency to put on "blinders" when it comes time to work on the dissertation: PhD students tend to forget that there are things to study and learn about outside the field of the dissertation. (For example, I always have a few students who complain in the course evaluation "I'm studying X; I shouldn't have to take this mandatory course!")

However, in spite of this, research is becoming inherently more interdisciplinary and interconnected. So having additional experience—and additional contacts—outside your main field can only help you in the long run, if you're planning to pursue a "knowledge-based" career.

That said, this is definitely a matter you should bring up with your advisor. This early in your career, it's probably not such a big deal to do something else for the summer. But you should still check if there are some important counterarguments (related to funding or project sponsorship).


How much can you 'laymanize' a PhD presentation?

First, it is important to recognize that every scientist is effectively a layman for almost all other science.

For example, I am a computer scientist, and I have only a vague layman-level understanding that when you say "non-local waveform collapse" it's probably about quantum mechanics and Bell's theorem, and the math you put up on a slide will certainly be rather alien and fairly incomprehensible to me.  If I put up a slide on the semantics of field calculus, it would probably be likewise alien to you, and if a biologist of my acquaintance put up a slide on the chemical mechanisms of chromatin remodeling it would be alien to both you and I.  Think of a layman, then, not as some sort of idiot to be condescended to, but as an intelligent and interested person whose expertise happens to be in a different field.

Furthermore, our relative ignorance of one another's work is greatly amplified while listening to a talk: when I am puzzled and need to think about what you've just said, I miss the next things being said and have to try to catch up! In effect, only people who are extremely close to your own work, even within your field, will be able to follow deep technical details in a talk.  Every audience except the smallest and most intimate, then, is effectively composed mostly of laymen---but likely with a few experts as well.

So, how do you give a talk to heterogeneous audiences?  Personally, I find it effective to think of a talk as an advertisement, the goal of which is to make people interested enough and convinced enough by your work that they want talk with you about it afterward or to read the manuscripts that present it fully.  Start with a discussion of the goal of your work, how the work relates to other work and why its goals might be interesting, narrow down to a few key details (which might only be understood in detail by the few experts in the audience), present evidence for why your insights are correct, and widen back out to explain why what you just presented satisfies the goals you laid out in your introduction.   Such a structure can then "laymanize" even the most complex topic, by explaining how it fits into the larger world, while at the same time respecting the intelligence of the audience and not sacrificing communication to experts.

For the details of how to accomplish this effectively, I personally have found Patrick Winston's "How to Speak" lecture to be an excellent resource for heuristics and tips, and recommend it to others as well.


Great question!

Among other challenges, citing this book is not easy because it is part of a series, and the publisher's name is very similar to the series name.

Publisher: Hutchinson & Co.
Series: Hutchinson University Library (Philosophy)
Series editor: H. J. Paton

I prefer the Chicago Manual of Style, 17th ed. (2017) (hereafter, Chicago), Notes and Bibliography format. I consulted Chicago to write the citations below.

I would cite the book in a note (footnote) like this:

  G. E. M. Anscombe, An Introduction to Wittgenstein's Tractatus, 2nd ed. (1963; repr., New York: Harper & Row, 1965), 27–29. Citations refer to the 1965 Harper & Row reprint.

If I were to cite the book a second time, I would use a shortened citation ("short form") like this:

  Anscombe, Introduction to Wittgenstein's Tractatus, 34.

In the bibliography I would cite the book like this:

  Anscombe, G. E. M. [Gertrude Elizabeth Margaret]. An Introduction to Wittgenstein's Tractatus. 2nd ed., repr. New York: Harper & Row, 1965. First published 1963 by Hutchinson (London). Page references are to the 1965 Harper & Row reprint.

Notes

Professor Anscombe preferred initials instead of her lengthy given name, but since her full name appears occasionally, I chose to provide it in the bibliography.
I made up the page numbers for the note citations.
The names of both publishers are not required for the note, but should be included in the bibliography.
Chicago states that "2nd ed." is enough, i.e., "rev." (revised) is not necessary because most readers assume that a 2nd edition includes revisions.
Chicago advises against citing the series name and editor in most instances.

Sources consulted

AbeBooks.com
Google Books
Stanford Encyclopedia of Philosophy
The Chicago Manual of Style Online
WorldCat.org


Can I use the work in my journal/conference publications as chapters in my dissertation?

Supplementing the answer from abatkai:
The rules likely vary by field also. In chemistry, converting previously published papers into a Sandwich Thesis is generally accepted and commonplace. My thesis contained a chapter that was prefaced "Portions of this chapter were previously published as (citation), and have been reproduced with permission. Copyright is held by (publisher of the journal)." This was followed by further copyright information and the statement required by the publisher. My institution also required that I submit paperwork in support of my use of published and copyrighted material.
In addition to consulting your adviser and your institution, you should consult the journals in which you publish. Many have policies in place for this. For example, from the American Chemical Society's copyright faq:

The current ACS Journal Publishing Agreement covers several permitted uses by authors... Permitted uses of all versions include:

Use in theses and collections of your own work


What is the academic job market going to be like in September-November 2020?

At my US large state univ, there is a hiring freeze for this coming year. Yes, this did also happen c. 2008.
One difference is that in the US the trans-economic source of the problem is by no means resolved... and even when/if it is "resolved", I think the "new normal" is very hard to predict. So administrations are being, and I think will continue to be, very very cautious about commitments toward the future.
So, no, no reason to be optimistic, because we don't even see the end of the disaster yet. Sorry.


Are Asian-Americans considered an "underrepresented minority" in academia in the US?

There is no universal definition of "underrepresented" and also no universal definition of Asian-American, so it's impossible to answer this question accurately. A very rough answer is that it depends on the discipline (eg computer science vs anthropology) and also on which ethnicities are considered Asian-American.
Your personal experience notwithstanding, it is likely that Asian-Americans are overrepresented in academia overall, simply because Asian-Americans are overrepresented among Americans with advanced degrees. But this isn't a very useful metric from the point of view of diversity and equity.

Edit:
The NSF has a breakdown by race and discipline of US citizens awarded doctorates in 2016:
https://www.nsf.gov/statistics/2018/nsf18304/report/which-fields-attract-students/minorities.cfm
As for faculty, another reason it's going to be hard to find good data on whether Asian-Americans are underrepresented is that schools love to pretend that their faculty is more diverse than it is, so they often have rather creative definitions of "underrepresented."


Can novel findings be submitted rather than a novel methodology?

The point of a methodology is to be able to produce interesting and significant results. If you've managed to apply some combination of existing methodologies to discover something interesting and new, then that discovery is likely publishable.

What is not clear, however, is whether a community of researchers who are focused on making new methodologies will be interested. Thus, you might not be able to publish in the particular machine learning community that you are interested in. Instead, I would suggest:

Look for "applications" journals, conferences, or tracks associated with the machine learning community.  Many "tool" communities have these associated: for example, in the general AI world, the core conference AAAI is always co-located with the much smaller but still high-significance IAAI applications meeting.
Embrace the application community (it sounds like network security in this case), and publish your results there. They will be less interested in the methodologies and more in what you have done with them.


You can ask for an earlier interview, but they may have already scheduled someone for that time block and may not be able to accommodate the request.

As far as the resources go, it’s definitely an “early bird gets the worm” situation when it comes to faculty hires. Schools that delay their interviews run the risk of losing out on good candidates. So I would proceed on good faith: accept the interview, but let them know ASAP if you receive another offer that you intend to accept.


Is it crass to acknowledge a colleague that passed away in my thesis?

I certainly don't think it's "crass", and I have a hard time seeing who could be disrespected.  In general, you can acknowledge whomever you want in a thesis and the only crass thing would be to say something negative about them.

However, there is possibly a bit of room for misunderstanding here, because the ostensible purpose of the acknowledgments is to recognize people who helped you out in some way.  Based on what you write -- you were not close, and he did not help on your thesis -- it doesn't make sense to thank this person in the acknowledgements.

I might instead suggest going for a dedication or commemoration.  Some ways of wording this are given here.  You could either end the acknowledgments with a dedication, probably in its own separate paragraph (and you can dedicate the thesis to more than one person, if you like), or you could include the dedication on its own page separately in the thesis, e.g. "For X", "In memory of X (19xx - 20xx)", etc.

Speaking personally, I like the look of the latter, and I find it to be the opposite of crass to take time out to remember the departed, whether they had a special relationship with you or not.  You are doing your part to make sure that your fellow student will not be completely forgotten for some time to come.  Good for you.


What are good resources on how to carry oneself on a PhD course?

Have a look at this excellent memoir by a recent CS PhD: The Grind by Philip Guo

Although written from a CS perspective, many of his experiences transcend disciplines.


Master's thesis results used to publish a new research paper?

You should normally be a co-author if you contributed a substantial amount of data (and be invited to at least check the paper before submission), but apparently the authors of the paper decided that your contribution was not big enough. It is hard to judge if they are right without knowing the details of who contributed what exactly.

If you are not co-author, an acknowledgement is perfectly normal: A Master thesis is usually not publicly available so there is no point to cite it. This also answers your first question: yes, it is fine to publish results from an MSc thesis in a paper.


Is it compulsory to have a master's degree in computer science for research jobs?

It is highly unlikely that you'd get a permanent research position in CS with a bachelor's degree. It's also unlikely (though not impossible) that you'd get one with an MS degree (for example, it might be possible to enter an organization after an MS, and then move internally into their research wing). The most common path to getting a research job at an institute is after a Ph.D.


In a scholarship application that asks about "overcoming challenges," does this refer to financial challenges or other kinds?

They're leaving the question open-ended intentionally. They will use your answer to judge whether you're a good fit for the school's culture.

Generally when you see questions like this for things like admissions essays or in interviews, the interviewer wants to give you an honest and complete answer. You can discuss any kinds of challenges here, be they personal, financial, or strictly academic, but only bring the challenge up if the way you responded to it either taught you something or reflects a positive character trait.

The goal for your essay should be to show the reader why you deserve the scholarship or why you are most likely to use that money in a better way than another recipient might be. Because of this, keep in mind the kind of scholarship it is. If it's a minority scholarship, for example, remember that the scholarship is, at its core, designed to help underprivileged kids have the opportunity to go to school, and those kinds of scholarships are especially relevant to bright kids with decent test scores who come from places with limited academic resources or families with low income. That kind of situation might give you all sorts of stuff to talk about, from disrespectful kids and xenophobic teachers to insufficient access to technology and school supplies. If you can show that you faced some or all of these kinds of challenges but still got a 29 on your ACT (because you worked hard and applied yourself, naturally), the Minority Office might be more impressed with your application. Review the mission statement of the department that will be receiving the recommendation before writing it, and always tweak essays for other departments before you send out the letters.


I got into grad school, now I need to retract my commitment

It's never easy to break a commitment but you have to let them know as soon as possible, the earlier the better so they can make proper preparations for themselves, perhaps even extend a last minute offer to another student. Hang in there!


What are refereed and non-refereed journals?

In your original question, "referred journal" is a Freudian slip, perhaps on your part.

Refereed journals/conferences are the ones where the published papers have been peer-reviewed.


Pursuing a Second Master's Degree(Part Time) : pros and cons

Pros... it certainly doesn't do any harm, you will learn something, and there is always the personal development aspect.

Cons... if you are going to make the effort to get a second Masters, why not build on the existing Masters and get a PhD? That is worth a lot more than a second Masters.

MBA... in my opinion, not worth a thing. A con. Not a true Masters by any standard.