text:
How should I ask my PhD advisor to let me work remotely...permanently?
My wife plans to graduate in a few months. I have 1-2 years left before I defend and graduate. I'd like to move away with my wife so we can stay together.
My work is entirely on a computer, so working remotely is entirely feasible. I have my own funding, so I do not need to stay in order to TA for pay.
I typically meet once every 1-2 weeks with my primary advisor and "secondary advisor" (a research scientist who also mentors me and who frequently works more closely with me than my advisor). When I first began working with my primary advisor, I mentioned that I may need to work remotely for my final year. He said he didn't like the idea in general, but that he understands that life happens, and that we'd figure it out when the time came.
The time has come, though I wouldn't move away for another two months.
How should I breach the topic with my advisor(s)?
This question is extremely relevant, but differs in that it asks this question for "extensive periods", whereas I'm asking about working remotely permanently. Several answers for that question involve staying away for progressively longer periods of time, but I'd prefer to not pay two rents.

I'm not sure what kind of answer you are looking for other than to ask him directly at your next meeting.

This reminds me of a comment I saw on Workplace.SE where a remote worker who was supposed to come in every once and while wasn't coming in so they called him and asked him when he was coming back, and he said "Never, I live in Idaho now." (The office was in DC.) Dunno how it turned out for him, but you could always trying moving cities, then telling your advisor.

@Azor-Ahai: funny anecdote, but  I don't think that is a good idea at all. :-) How would it improve advisor-advisee relations? I want to continue building his trust and respect, not tear it down. I need him to graduate, and I expect him to be my primary job reference when I enter the job market.

Oh it's not a good idea! That's why it's a comment.

@AustinHenley: Quite unfortunately, it needs to be via email. My wife was offered a position and has one week to respond. Meanwhile, my advisor is gone for almost the whole week. What I'm looking for is how to prepare for this conversation: developing a plan and presenting it in a way that would give my advisor(s) little reason to not agree.

@jvriesem It is a little concerning that you put yourself into this situation (your wife looking for a job, presumably interviewing, and getting an offer all before you had this conversation with your advisor). At this point it sounds like you are in the situation to inform your advisor that you are moving (not ask permission). I'd suggest emailing and asking to have an urgent phone call.

@AustinHenley Why? Should the advisor demand that the OPs wife declines a job offer? A third party made a decison, and that's that.

@Karl I think you are misinterpreting something in my comment. I said it is too late to ask for permission since the OP has already gone down this rabbit hole and it is instead time to inform his advisor. However, the "third party" is of no interest to the advisor (he works with students, not a student's spouse) and he can reasonably tell the OP that he is not willing to work with a student remotely. It would be no different in any other employment situation. You can't force your employer to be willing to let you move while retaining employment.

@AustinHenley The prof can still say yes or no in a week. And he practically has already said he'd be OK with it. I guess he feels that you cannot expect that s.o. makes job decisions depending on his or her's spouse's prof's feelings.

(Large companies, the size of universities, have policies on working remotely. If it's reasonable, you usually can. Of course, reasonable by the companies standards, not your own. ;-) )

@Karl His spouse can certainly make job decisions. This one potentially ends his however. I would never force my employer into this situation unless I was 100% prepared to quit (especially on such short notice!!!). I would have definitely discussed this with my advisor before my wife went on the job market. Communication works wonders.

@Karl In regards to "usually can" work remotely, do you have a reference for that? I know several large tech companies that explicitly forbid it. Some companies allow it. Some don't. Some managers allow it. Some don't. Again, I would have figured out this policy long before my wife starts looking for a job.

@ all: As mentioned in my question, I have already discussed the possibility with my advisor (~3 yrs earlier). He said we'd talk about it again when the time neared—which is now. I should have reminded him about this possibility 2-4 months ago when my wife was looking for jobs. I'd like to stay with my wife, but I am open to staying local for a semester (maybe two) if need be. For this reason, I don't think it's appropriate or genuine to inform my advisor that I'm moving. As Karl and AustinHenley have discussed, I think I do need to ask permission...in some sense.

Be prepared to live with a compromise. As other people have already mentioned, your best idea would have to bring this up before it is a fact, to figure out the best compromise for both parties. Now it is up to you to give in to non-optimal solutions. That means you might have to come back very regularly and also even for extended times (not just a day, more like a week) or even stay for some more months until your work is in a state that can be finished remotely. This is not that much about what you prefer any more. Your wife and your advisor might also prefer things and not get them.

Bring this up directly and immediately.
You mentioned in the comments that your advisor is out of town for a week but your wife must respond to the offer in a week. This doesn't leave you much choice, so email him immediately and ask to have an urgent phone call.
Tell him openly about the situation and get his feedback. It is up to you whether to frame it as asking for permission or informing him of your decision.
However, you have to be prepared that he will not be willing to work with you remotely. You are putting your advisor in a potentially difficult position without much time to discuss it and basically giving him an ultimatum. I would have had an involved discussion about this before my spouse went on the job market (informing him that your spouse will be looking for a job and that you will be moving away if she gets an offer).

Would you mention the topic of the conversation in the email, or be vague in the email?


text:
When should I cite, if using code from Stack Overflow?
I already found a question handling the case if you got some information from Stack Exchange for my thesis. Unfortunately I did not find anything about the case that I get a solution (not necessarily from stackexchange) for a specific problem.
For example, if I have a problem with a specific part in my code, or if I have to design a circuit, and I run into a problem: What is the threshold of information, i.e. when should I cite the answer in my thesis? Should I always cite Stack Overflow (or the other web page), even if its just for two lines? Where is the threshold?
And how should I do this in my code? Should I rather make a comment block around the specific part of the code, redirecting to SO, or should I simply cite it in my thesis?

Your question on attributing help from Stack Overflow in your code rather feels like something for Programmers SE.

This question is poorly written.  The grammar and sentence structure is poor. If you want good answers, then you would do well to spend time to write your questions well.

@MrMeritology: Can you give me some suggestions to improve the question, for example which sentences are bad, and why?

@arc_lupus: The opening sentence is hard to understand. It should be something like "I have already found a question which handles the case of using information from Stack Exchange for my thesis."

@arc_lupus I suggest the following: Your first sentence should be a question, ending with a question mark. For example: "In academic Computer Science, what is the best method for citing social media sources such as Stack Exchange?"  Then write one or two questions giving specifics of your context. Close with what alternatives you are considering.

The important distinction to make here is between:

Intellectual contributions to the actual research/science.
Technical help.

Contributions of the first kind are – roughly speaking – what warrants authorship or, if the contribution is already published, a citation. With other words: If the contribution would warrant authorship if unpublished, it has to be cited. As already stated, this is somewhat simplified and distinguishing between when to cite and when to include as an author can sometimes be tricky, but it should give you a rough idea, as to what you have to cite. Also note that there are other reasons for citing, such as context embedding, which do not apply here, however.
Two lines of code (to take this example) almost always fall under contributions of the second kind: They help you with the tools you need to use for your research but not with the actual subject of your research. It’s roughly comparable to the contribution of somebody fixing the microscope you need for some biological research. Of course, it might be a very helpful contribution that saved you months of work (in which case you should consider mentioning it in the acknowledgments), but it’s not a scientific contribution.
However, the decision may not always be that easy. Apart from the aformentioned authorship criterion (also note the authorship tag on this site for this), asking yourself the following questions might help to solve the question:

Is the kind of contribution to your work fundamentally different from:

designing the programming language you used,
designing or building your CPU,
designing or building your microscope?

If yes, consider citing.
Does the contribution affect the results of your research or is it necessary for others to reproduce your research? By results I here mean something like:

The 666th digit of π is 6.
  The proposed algorithm outperforms the current standard method.

and not:

I managed to compute the results before the deadline.
  Unfortunately, the results do not make any sense, probably due to some bug.

If yes, then you should consider citing. If, on the other hand, you have good reason to assume that somebody implementing your solution in a totally different programming language or calculating everything with pen and paper would arrive at the same results, then you should not cite.

Contributions of the second kind are what, amongst others, you can put in your acknowledgements, where in a thesis it’s usually up to you, who and how many people you mention.

Is it worth pointing out the difference between citation and acknowledgement?

@Floris: I sort of do now.

Correction of major and utmost importance: the 666th digit of pi is 5.

I totally agree with you, especially the phrase "It’s roughly comparable to the contribution of somebody fixing the microscope".

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text:
Bad answer to a bad peer-review
I submitted a paper together with other people to an important journal. A couple of days ago we received the answer from the editor and the paper was rejected (I was 3rd author) with very bad comments. One of the reviewers wrote that the paper was lacking innovation or originality. Another one sent us more than 20 comments. To be honest the comments weren't really appropriate because we did particles loaded with gold or FITC and one of the comments was "It seems that the FITC and gold are encapsulated inside the nanoparticles, not the other way around." He did not understand a lot but still, he also did a lot of interesting comments.
Anyway, the main author yesterday emailed the editor saying that the reviewers do
not have enough knowledge to correct this paper, that they are unqualified and that people like this should not correct this kind of work. This person sent the email to the editor without speaking to any other authors, therefore we discovered today what happened and some of us still don't know.
Do you think that the journal, following this email, can do something to the authors of the paper? Like, e.g., sue us? or ban us to publish there? or stuff like this?
What should we do now?

If they are really upset then they'll have a good laugh and let it go. They've gotten angry replies in the past. No biggie. No, you won't get sued or banned. Journals need authors as much as authors need journals.

Depending on the tone of the response, the editors may decide to accept your rebuttal, to ignore it, or tell you off for insulting the reviewers. It is never wise to directly challenge the aptness of the reviewers (the reviewers may think the same about the authors, and they have more power), but certainly ok to comment on their mistakes and point out so many of their mistakes that the editor will come to that conclusion themselves. It's definitely not ok for your co-author to send such a mail without consulting you. That's a real no-no. But no, they are unlikely to sue you unless defamed.

In order to sue, they would need to be able to demonstrate a loss of some kind. There's no loss here - except to your colleague's dignity

One issue is that if reviewers (even if actually incompetent) misunderstand key things about your article (e.g. the nanoparticle issue), then it's a sign that random readers may also misunderstand these things, and that is something that needs to be fixed until that idea is clearly transmitted also to a less-competent reader.

Sue you?? How??

What do editors do when authors send them angry emails questioning the competence of the reviewer? When I edited a journal, if the author provided technical arguments against the reviewer's comments, I would forward those to the reviewer(s) and see what they say. If they didn't, I would usually say something generic about our faith in our peer review process and apologize that we cannot accept the paper. Either way the dispute does not usually escalate beyond the three of us (author, editor, reviewer).
Filing a lawsuit would be unprecedented. Banning you from submitting is more conceivable, but still unlikely. After all, it's to their advantage that authors submit potentially-publishable papers there. If it happens my guess would be that the author wrote something that crosses into the realm of personal attacks: for example, "tell your reviewer to take a gun and shoot himself".
In any case it is not something to worry too much about - after all it's not you that sent the bad answer - unless the author did write personal attacks, in which case you could send the editor an email distancing yourself from the author's behavior.

Three answers down to find a good one :) +1

"Filing a lawsuit would be unprecedented." The journal where you were an editor, has never been sued by an author?

@user1271772 I interpreted the question as asking if the journal could sue the authors, in which case I've never heard of it happening; the journal has never been sued by the authors either.

Actually your interpretation is correct I'm quite sure. I would have imagined the authors are more likely to sue than the editors, because authors sometimes feel that the paper was not given a proper evaluation.

RE: "Banning you from submitting is more conceivable, but still unlikely." -- Yes total banning would seem very extreme, but the editor is likely to remember a hot-headed response in the future. That of course isn't a positive outcome.

@user1271772 Even for the case of authors suing the editors, I'm not aware of any law (in any country whose laws I remotely know) on grounds of which that could happen. Can you clarify?

Papers get rejected. It happens. Sometimes they get rejected for good reasons. Sometimes they get rejected for bad reasons. Sometimes they get rejected for a mix of reasons. And, yes, when there's a not great referee's report, appealing to the editor is an option, but it rarely works. The best course of action is generally to take the useful critical comments and use them to improve the paper. And make sure to have explicit detailed explanations added which address any of the misconceptions. Then, send it to another journal, probably a journal slightly less prestigious to the one one sent it to the first time.
But you definitely need to make some of the changes. Not only will some of them almost certainly been good changes, but you make get one or more of the referees again. It is really tiring to referee a paper for one journal, and then a few months later to referee the paper again for another journal and find that the authors have made none of the changes one recommended in one's previous report.

Let me say that I disagree with the statement done by my colleague. Paper can be rejected and you should just take the comments and use them to improve your manuscript for the journal or for future submission. What I am really worried about is if the authors can have any consequences even if the first author sent and signed the mail by himself.

@micuzziddo That aspect seems less of a big deal. Unless the letter was really rude, the editor is going to forget it five minutes after they read it. They also are strongly limited in how they could retaliate even if they wished to do so.

I'm not sure if the question was edited, but this does not seem to answer the question that was asked: "Do you think that the journal, following this email, can do something to the authors of the paper? Like, e.g., sue us? or ban us to publish there? or stuff like this? What should we do now?"

@6005 The answer is specifically on the "What should we do now."

Do you think that the journal, following this email, can do something to the authors of the paper?  Like e.g., sue us?

Sue you for having had a research colleague privately express the view that someone is unqualified for a piece of work they did?  No, of course not.

....or ban us to publish there?

Yes, they could do this.

...or stuff like this?

Those two things are completely different.  The journal editors could do any stuff they have authority/control over and no stuff they don't have authority/control over.

Banning is pretty unlikely for anything short of ethical lapses. Possible, yes. But you probably don't want to publish with such a place anyway.

I agree entirely.  But considering that OP is not even sure if he can be sued, it seems that a more basic answer of what is actually possible will be helpful here.

Let me say that I disagree with the statement done by my colleague. Paper can be rejected and you should just take the comments and use them to improve your manuscript for the journal or for future submission. What I am really worried about is if the authors can have any consequences even if the first author sent and signed the mail by himself.

@micuzziddo I do not think that you are going to be in trouble if only the first author's signature is there. It's unpleasant, but unless it's a really bad email, I'd let it go. Else, you could send an apology with the other authors for the form of the mail - but that will likely create a rift with your first author, unless you can convince him of it, too, so handle with care.

If a referee did not understand your paper, it indicates that it was not written clearly (this is the mindset you should take, especially if you want later people who read it to understand it)
Worst thing what can happen is that this criticism is forwarded to the referees. I know some researchers in higher position who are vengeful. These people decide who can attend conferences, survey grant applications and also are referees for multiple journals.

Of course the chance of this is not so high, probably people will just remember your name but not the incident so this could be a good thing.
My suggestion would be that the person who sent this email sends another one to retract the email and apologizes. Also the head of your group should send an apology that he didnt instruct the author well enough and this wont happen again.

To me there are two important criteria:

Did the main author send their angry email while giving the impression that they were speaking in your name too, or only in their own name? (e.g., do they say "I" or "We"? do they sign with their own name only, or also yours?)
How bad was their email? i.e., is it just some understandable or reasonable disagreement with the reviewers, or something worse like aggressive personal attacks?

If the email was especially bad, and/or gave the impression to be speaking also in your name, you could send a quick email to the editor to clarify that this email wasn't written or approved by you.
In terms of consequences: most likely nothing, and certainly not a lawsuit. In fact, if the journal takes any measures except against the specific person who sent them the email, I'd argue that this is misguided.

Editors have better things to do than sue over angry rebuttals.  After all, they can simply decide not to publish the paper and that’s punishment enough.
The editor sent the paper to referees, who also function typical readers with (presumably) an interest in the topic else the referees would have declined.  It is unlikely that all referees were not qualified.
Unless a rebuttal points to technical problems with the report, it usually is a bad idea to attack referee: what is more likely is that the text while correct might not be clear to a typical reader.
The concrete proposal would be for this person to write a short email to the editor apologizing for the outburst.  I would also recommend all authors prepare a point-by-point rebuttal and explain why some comments are not applicable.

If the Idiot Reviewers misunderstand your work, that is prima facie evidence that your work can be misunderstood.  Revise it.

Although I agree, I think the question is more what to do about the fact that the coauthor wrote an angry response.

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text:
How does the lockdown affect the application and admission processes in the Western Europe, Scandinavia, and the US?
I am about to submit my PhD thesis and thus my studentship will terminate. Along with my studentship, naturally, my scholarship and my stipend also will be gone.
I have some savings, but I doubt I can manage more than 3-4 months.
I need to apply to postdoc positions, and unless it is a low profile university, I cannot find any positions in the country I finish my doctoral studies, and even neighboring countries. It is kind of a unwritten policy in the Central Europe.
My viable options are western Europe, Scandinavia, and the US.
How are the application and admission processes in those places? Will new positions be available in a short time? If so, will foreign applicants be able to travel there?
Comments based on experiences are highly appreciated!

The process was unchanged for me (recently applied for a phyics postdoc in Spain). The job I applied to was posted just before the lockdowns began in Europe and so the interview was via Skype. I obviously couldn't visit the place but that didn't matter to me as I had visited previously. Arranging the contract has been slow but that is due to bureaucratic and logistical issues unrelated to the virus. So, overall, things seem normal (but this was my first time entering the job market so maybe someone with previous experience would think differently).

Also depends on what post they offer and how that matches to the skills you bring.

I work at a Finnish university. My department established around April a moratorium that new hires could only begin their contract starting August 1st. There are also recommendations to avoid receiving visitors (and I guess new hires, but I'm not sure since I haven't attempted to hire anyone since earlier in the year) until the Autumn. We also have the policy that you need to be in Finland by the start of your contract (i.e., you can't start remotely), meaning that travel restrictions from specific countries could prevent you from getting hired in practice. Things are at a stall during July because of the holidays, but as new outbreaks take place throughout Europe and the situation continues to be quite bad in some countries, I expect the university to update their official policies in early August, after admin people are back from the holidays. Generally, even though Finland had an easier time than most of Europe during the pandemic (so far), the university has been quite strict about enforcing remote work, and we're preferentially working remotely until mid August, when we will start gradually to go back to normal. But this can be revisited at any time.
This is for my particular university in Finland. I believe other Finnish universities have similar policies. Other Nordic countries have probably similar rules and practices, although I don't know about Sweden, where the Government has been notoriously bad about their handling of the pandemic, compared to the other Nordics.
In summary, the situation is quite volatile and things can change rapidly, although right now looks much better recruitment wise than a couple of months ago.

The main problem for you now is not COVID-19 but simply the summer holidays. If you are looking now, you won't find much. The number of job offers may increase again in September, October.

In my university, new positions are posted before the summer holiday, and admissions are done after the holiday so that the applicants can start by the new semester. Maybe it is different than the places I have mentioned.

In the universities I am familiar with people try to finish the hiring process before the summer holidays if they can, so they tend to avoid posting new positions a couple of months before the summer holidays and during the summer holidays. Also post-doc positions are less tied to semesters.


text:
Is the phrase "thanks, but no thanks" appropriate in an email sent to a supervisor?
I recently have had a discussion about my friend's tone in his email.
His supervisor asked him whether he wants to attend a summer school in May. He wanted to thank him for his invitation and also wanted to keep the mail short. As a result, that is what he came up with:

Hello Professor,
I have plans during that period. Thanks, but no thanks.
Regards,
  John

He is getting along well with his supervisor, but I believe that the phrasing is a bit disrespectful nevertheless. It might be the case that I am not a native speaker.
Am I exaggerating the situation and this is something can be overlooked?

Comments are not for extended discussion; this conversation has been moved to chat.

Note that your "It might be the case that I am not a native speaker" means just "I may not be a native speaker". I am sure that was not your intent. Also, your "Whether or when should someone use such phrases" is awkward. It should work if you remove one of the options, like so "Whether should someone use such phrases*, which is clearly wrong. You probably want "When and how" or more likely just "When". Be careful of the temptation to add more words to appear erudite. This question may be better suited to the English Language & Usage community.

@Borodin you're right. I have changed the situation.

Padawan, anyway let us know if you let your friend reading these answers and he decided to apologize...

@MassimoOrtolano He indeed reads this and convinced that I was right about the tone. The rest, I do not know but I guess he'll apologize soon.

It sounds extremely rude, I am afraid. I would assume mitigating circumstances for a non-native speaker, but the "no thanks" permits "thanks" to be interpreted as substantive, and thus has a highly dismissive connotation which should never be used with your superior, and neither with a friend you would like to keep.
The connotation that shines through (at least in the UK) is a sarcastic "Yeah right, you think you do me a favour? In future, please spare me your ideas."

+1. I get the same connotation as a US speaker, for what it's worth. "Thanks, but no thanks" is always rude/flippant, if you ask me. It's fine to say to a friend in a light-hearted or joking way, but that's about it. "Thank you, but [some explanation]" is a better way to phrase this if you want to keep it short.

"mitigating circumstances for a non-native speaker" - however, what OP is saying is that OP is non-native, and does not indicate at all that their friend is non-native. So it seems that the non-native speaker is showing more common sense than the (ostensibly) native speaker.

@silvascientist Of course. But for the answer to be more generally useful, I added this caveat.

@sgroves It is not "always" rude/flippant. Your comment would have been fine if you had said "is often considered rude/flippant." There is nothing rude nor flippant about the phrase itself, but it may be viewed as such by certain sensitive people. If you want to be careful, it is better to avoid it yes, but "always rude/flippant" is an exaggeration. It's just like telling someone they look fat: some people would be angry at me, but my wife would thank me and change clothes before going out. It depends on your tone and the listener's sensitivity.

-1: definitive assertions given without evidence, and ones that go against my experience (as someone from the UK), including "sounds extremely rude" and "highly dismissive". Moreover, the connotation may shine through for the answerer, but by no means is this "completely standard (in the UK)". The answerer's connotation didn't even cross my mind.

As a non-native speaker, I know of two connotations for this: among friends, it can be a "you know I don't want to even talk about this topic, please stop" but in general it is mostly a sarcastic "keep your tips for yourself or people who want them".

@SamT Added explanation, why it sounds dismissive (with which connotation most posters here seem to agree); thanks for pointing out the lack of evidence.

@Captain Emacs Good point regarding the "thanks" being seen as a substantive. I am German and in my mother language there is no danger of this misunderstanding happening, so I never read it this way in English either. Good to know!

@CaptainEmacs Still very assertive without evidence. Most of the people here appear to find it rude, but it is mainly a US community, and it's possible that this is a cross-Atlantic difference. I'm not particularly old (23), but I feel I've been around long enough that not being able to recall ever having hear this with negative connotations is enough to discount the "completely standard in the UK claim". In fact, I would use (and have used) the phrase when I want to show particular politeness, with no hint of objection from the person I'm talking to. [cont...]

Clearly you find that it is rude -- and I'm not at all saying that you're "wrong" to do so. However, I think this is just one of those things where it's different for different people. As such, your firm claims I feel are incorrect. That said, because some people may find it offensive, it is definitely not good to be used in the context suggested by the OP!

@SamT Actually, not being a native speaker, I used to interpret it neutrally/friendly when I first encountered it. However, the far overwhelming lot (not just some) of interpretations of the "no thanks" idiom I hitherto encountered were the negative one. I should think it is safe to assume that semantics ultimately emerges from actual use rather than literal meaning - the meaning of a term is a convention of the collective. Or do you believe that formulations always retain all their original interpretations? "Yeah, right." ;-)

In a way, it is about opinion. BUT, when it comes to something being perceived as rude or not, opinion is what the question is really about!

This isn't just a question of sensitivity, as some here are suggesting. Like others, I've only ever heard this used in a sarcastic context. Therefore, if someone used it -- particularly in an email, absent things like tone and facial expression -- I would naturally assume it was written sarcastically. That's not because I'm super sensitive (I may not even mind that they're being sarcastic), but because it's a common phrase with common usage. In other words, it's possible for the reader not to mind the sarcasm, but still assume it's there.

Given that "thanks, but no thanks" is often used as a mocking euphemism for "gee, that's a stupid idea, I will of course not do that" I would suggest not using it on your advisor.
What's wrong with just writing "thank you, but unfortunately I won't be able to make it for reasons A and B"?

Right: this language usually refers to either a stupid proposal and/or an attempted deceit.

Ditto. Your friend has mistaken an idiom coined for snide usage as a literal phrase that means only what it seems to, taken literally. In person it could be moderated by tone and phrasing, but in an e-mail it's likely to be taken wrong. However if the supervisor knows your friend well and they get on well together, they may recognize what's going on, and understand the intent.

It's not the use of a "slang" expression that's the issue.
Saying "thanks, but no thanks" implies that s/he was trying to trick you with the offer to which you're replying. The phrase is imbued with a bit of hostility and disdain.
So, don't use it. Also, the way your friend phrased your email sounds flippant. Turning down an offer from someone's advisor should be done with more of a justification. It wouldn't hurt to be polite and respectful, and write something like

Hello Professor Smith,
I want to thank you for the offer of XYZ; unfortunately, I've already made plans to [important activity that clearly should not be canceled to take the offer].
[Possible counter-suggestion regarding the offer, e.g. doing something after that period of unavailability.]
Regards,
  John

Still pretty short.
Notes:

The reason doesn't have to be super-specific, but the more vague it is, the more it's likely to sound like an excuse.
If your friend dislikes his/her supervisor, or doesn't appreciate him/her, or the offer - that's double the reason to be polite and respectful of him/her when rejecting.

You don’t need to necessarily give the detailed reason and you can be vague (“a family event” rather than “a wedding” for example). It’s just important that it be politely phrased.

I'm not sure "implies that s/he was trying to trick you" is the right way to describe the use of that phrase, though I agree with everything else in this answer. I would say I most commonly hear it used in response to an insincere offering (like a joke) or in rejecting an unappreciated offer.

@RoboKaren It depends a lot on the kind of relationship one has with their advisor. Trust is frequently built on the details.

There am be a great deal of personal variation, but as a faculty member and advisor, I do not have the right to ask for such personal details and students should not feel pressured to provide them in order to prove “trust.”

Advisors propose activities to students to give them opportunities: to learn, to build connections, and to become known in their field. All things that can be useful for the students' future careers (many of my current colleagues are actually people who I first met at a summer school).
Thus, I would consider your friend's email offensive (and, no, I'm not a particularly polite person in everyday life).

You don't actually explain why the student's email is offensive.

@DavidRicherby From the point of view of English usage, others have already explained why such an answer is impolite: my implicit point is that, moreover, that answer is offensive because it doesn't take into account the motivation of the proposal. That is, a professor doesn't propose activities just for the sake of it.

(Speaking for Germany, as the question is not localized) the offer to attend a summer school is nothing to be lightly turned down over here. So besides the issue with the rude idiom, I'd say that this is a point where John should give a good reason for refusing (hint for the scale: holidays = no good reason*, John's own wedding on that summer school Wednesday = good reason; * if John as employee of the university did ask for those holidays already a while ago, i.e. months in advance and got the OK for the holidays, the situation improves to "maybe OK" depending on further circumstances).

The point is to communicate that John appreciates the offer as important opportunity. So IMHO "Unfortunately [good reason]. Would it be possible to attend this summer school next year instead?" Or possibly "Would it be possible to attend [other summer school] instead? IMHO otherSummerSchool fits more closely with my project" would be a good way to show that John is not just evading education and clearly doesn'd lightly disregard the opportunity.

'Thanks, but no thanks.' is sarcastic and rude. Your friend should NOT use such wording, ever. If he has, he should personally visit the professor and apologize for having done so. If he is not a native English speaker, he might be able to blame it on that. If he is, he should have known better, and will have trouble explaining his use of such a phrase.

"Thanks, but no thanks" is a sarcastic insult, plain and simple. If I were the supervisor, it would end any feelings of good will I had toward the student. From then on, I would provide the student with the statutory support required by my contract, but no more, and devote my energy towards helping other students.
A sincere apology might put things right.

I think this is an exaggeration. I would never take such a drastic shift in my position towards a student based on one unpleasant interaction (unless perhaps it rose to the level of physical violence or death threats). But I agree that it comes off as quite insulting.

@NicHartley You are right that from one interaction only, one should not make a decision about a person, however, it would definitely put the one on the receiving end on higher alert in future interactions whether this pattern repeats and in which spirit it does so. Also, for someone known as foreign or usually polite, one would assume some mitigating circumstances.

@NicHartley I thought the most valuable sentence in the response is: "A sincere apology.." And a quick one it should be; this is the best response. I find that on realising a gaffe or upset of any sufficiently serious kind, an immediate and unconditional apology (no ifs, buts, or excuses) does wonders.

Your friend seems to have gotten the idea that "no thanks" is needed to indicate that the answer is "no", while "thanks" is needed to indicate gratitude for the offer. That is not the case. If the email were to contain nothing but the word "thanks", that would be inferred to be acceptance, but "thanks" in an email that otherwise indicates other plans would be understood to be only gratitude, and not acceptance. And "no thanks", as the words indicate, communicates both a negative answer and gratitude.
Thus, "thanks, but no thanks" is redundant. Unfortunately for your friend, it is a form of redundancy that has been used to indicate disdain. To be precise, I would say that it not so much is rude, but has been associated so much with rude intent that it should be avoided (although of course there is a point at which "is taken to be rude" becomes the same as "is rude").
You say that you are not a native speaker, but don't mention whether your friend is. If I were speaking with a non-native speaker, I would give them the benefit of the doubt and not expect them to be familiar with the entirety of English-speaking culture. Even with a native speaker, I would be willing to entertain the possibility that they chose their words poorly without considering the pop-culture context, especially if I had had previous dealings with them in which they were polite. Other people here have indicated that they would be less charitable, which I find unfortunate, so your friend will have to consider the possibility that the professor will share their attitude.

This answer is the most accurate answer so far. It is both technically correct, and it also points out the negative stereotype that many people have forced upon the phrase and addresses this. Many of the other answers exaggerate the situation with suggestions that the phrase "definitely is rude and you need to apologize" or "I would not give you the time of day after that beyond what was contractually necessary" which do help OP to see how some people blow this way out of proportion but also are inappropriate responses. This is the correct answer. +1

+1 for a good explanation - however, what's missing in the response is the reason why this is interpreted as rude; in my opinion it is the case because the "thanks" in "no thanks" can be interpreted as a substantive; in other words reading as: "thanks, but [actually] no thanks [for that]". I was stumped by that, too, when I first learnt that phrase.

This is the right answer. In the absence of other motivations for thinking a person is being deliberately discourteous, the sensible response is to assume they meant what they said. Injecting meaning that was most likely not intended is just silly.

If I was invited to attend something that I couldn't I would simply say, thanks for inviting me, but I'm sorry I'll have to decline, as I'm busy that day.

Just stating that you are "busy that day" is not incorrect but might still be not the best solution. It might come across as "I don't want and have better stuff to do". However, if you are on holiday or have another very important appointment, you should explicitly state this. This says "I would like to but cannot unfortunately".

What @J-Kun says is true for overly sensitive people. There are some people who read anything with an "I will interpret anything negatively if I can" attitude. At that point, where people are distorting your words (user87312 never said "I don't want to") that is their fault for poor reading skills, not your fault for poor communication skills. It still might be preferable to appease people like this as well, but that is a separate issue from saying something that many people will assume has rude intent.

This question might be better on https://english.stackexchange.com/, but I think you already have a few excellent answers. Let me add my own two cents' worth.
"Thanks, but no thanks" often comes across as sarcastic and even contemptuous to the native speaker's ear.
A far better phrasing would be:
"Hello Professor,
Summer school does sound very interesting. Unfortunately, I have already made plans for that period. I must therefore respectfully decline your thoughtful invitation. Thank you very much.
Regards,
John"
It may be a bit longer than your friend intended, but it's not unduly verbose.

I believe the phrase becomes significantly more polite by adding a simple comma, implying a different intonation:

Thanks, but no, thanks.

Still, I agree with the other answers that this is uncommon style. In this case, it's not necessary to repeat the decline (but no) or the thanks.

I'm afraid the comma doesn't fix it. There's just no way to fix "Thanks, but no thanks." There are plenty of other ways to say, "Thanks for the invitation, I really appreciate it! Unfortunately I have a previous commitment and won't be able to make it."

As a native English speaker, the phrase does not strike me as offensive. It means, "Thanks (for the great offer.) No thanks (because I'm busy.)"

Maybe you’ve never come across the idiom before, but that’s definitely not what it means.

Think more along the lines of "thanks for nothing", which is an accusatory and rude phrase - and the "no thanks" comes across just like it in this context.

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text:
Is it rude not to attend courses which have no attendance requirements?
I wonder how it is perceived if a student does not attend the course in which attendance is not taken.
I am a PhD student and I skipped most of class in two courses. Now, both of the instructors are mad at me. In one course the professor gave me an F on an oral exam because I could not explain one point in a chapter, after explaining the rest correctly. And the other one ignores me when I try to greet him, as opposed to 3-4 weeks ago. I feel that I have been very strictly judged, and not fairly graded by the first Professor. An F means zero points, and I am afraid the second Professor will grade his oral exam with some biases, based on the previous Professor's behavior
Is it natural for them to behave this way? What can I do to convince people that my intentions were not to offend? I feel that most of them believe me to have a "big head" who just moved in from another country. And think that I'm a know it all. This is completely wrong; I know it is a very, very bad habit to not attend lectures. But I feel I don't need to when I've studied and understood the concepts.
To clear out some points in the comments, let me explain my train of thought. But please note that the examples given below are just some stupid examples. They do not reflect real situations and my thoughts:
1) I think it is very impolite to deliberately refuse a greeting from a colleague, especially when that colleague is on the same floor. I understand that it's a teacher-student relationship, but wouldn't you agree that it is common courtesy to greet back after being greeted? I feel that this teacher has a vendetta of sorts.
2) I'd like to give an example. Suppose that the professor is speaking English, and it's clear that they have a bad accent. When students arrive, they'd like to be able to understand the professor. Sometimes, they get mad at the professor because they can't understand them. But ultimately it's the faculty committee that they should be getting mad at. The faculty committee is the one that hires the professor. I feel that being angry at the professor is pointless. Similarly, if the university doesn't require professors to take attendance, but they want students to attend they shouldn't be angry at the students. Instead they should take it up with University Policy
3) Finally, is attending class considered a matter of respect? I don't think so. At the end of the day, the professors are there for teaching the specific subject. Students, according to university rules and policy, are not obligated to attend these classes. I feel that the professors are not doing students a favor. On one hand it's their duty, and on the other hand people have free will. I feel it's worse to attend class and not even listen.
--
After viewing your detailed answers and comments, I am fully convinced that attending classes is a matter of respect to the professor. I understand now that it is easy to be misunderstood and misjudged by not showing up to class, without any excuses. I see now that it can be easily interpreted as an act of carelessness or self-importance.
Adapting to a new culture is harder than I thought.

Comments are not for extended discussion; this conversation has been moved to chat.

Is it UK or USA?

I think the question is not "Is it rude?" but "Do lecturers find it ok?" as the answer to the latter is not universal but varies a lot.
Here is what I think about students skipping classes: Personally, I also do not have any attendance requirements (actually, where I am it is currently forbidden to have such requirements) for my classes and there are students who skip some or most classes. Since I do not have such requirement, I am not mad at them, but I note that they miss opportunities to get into a dialogue about the contents which help them learning the material deeper. I do get mad when these students come to office hours asking for clarifications of stuff I treated in the lecture since this basically amounts to unnecessarily teaching the stuff double. When I note that students skip many classes I get thinking "Hmm, let's see how they manage to grasp all the material…". When it comes to exams and I note that the students missed some point which has been stressed in the lectures over and over, I feel like the students really missed a crucial point (even if it is just one) just by skipping the lectures and I do not give any benefit of doubt. It's like "it was obvious that I considered this to be a central point, and you did not get it - sorry for you." However, some bright students that skipped classes managed to impress me during an exam and scored great grades.
As for not greeting students: If you haven't shown up in classes that often, your face may probably not be that familiar to the lecturer… Here in Germany we often have hundreds of students every semester so it is impossible to know the all students who are enrolled but did not show up.
As for the question What can I do to turn it around?: Show that you learned a lot by being great at exams and show that you deeply grasped the material. Do not go to office hours with questions that have likely been answered during the lectures.

Thank you for answering the second part of the question in a brief and very clear way.

I believe, especially in intro undergrad classes, class size can go up to 400+ in the states. In upper-level and graduate-level classes, sizes can be as small as 5 or 6. I assume classes are tiny at PhD level, enough that you can tell when someone is missing.

One of the classes have 200+ people. Maybe tutor really counted on me attending.

I always attend lectures, even if I'm pretty familiar with the material to be discussed, for that purpose, concepts or subjects that are emphasized, along with interesting discussions that arise during the class, whether they pertain to the subject or from a whole another subject

Years ago in grad school I took a grad-level quantum mechanics course. I had a fabulously well-taught quantum course as an undergraduate. I knew the book's material cold. Still, I went to every single lecture and got a lot out of it. Why? The grad course was taught be Ed Salpeter, and what I learned was not the nuts and bolts of quantum, but how he thought about quantum mechanics. That alone made it all worthwhile. I could attack real problems correctly and easily, not just by following the book or syllabus. Soaking up the professor's experience can be very useful.

To begin with, start going to classes.  Your professors have assumed that you are an adult, mature enough to understand what is important in life.  Further, they likely believe their classes are important to your degree, or they wouldn't bother with them.  (Professors at that level have a great deal of influence over the curriculum.)
As others have said in the comments, not taking attendance does not necessarily mean attendance is not expected; it depends on the culture, the regulations of the institution, and the expectations of the individual professors.
Is it legit?  Consider that the first professor didn't "give" you an F.  He gave you an examination, which you failed.  You earned that F.  As for the other one, I'm not sure I understand "try to" say hello.  If you're passing in the hall and he ignores a "Hi," then it's safe to assume he's preoccupied, or perhaps irritated.  If, however, you're trying to engage him in smalltalk, you should assume he's busy.
To try to turn things around, call on each professor during office hours.  Apologize for being absent, and ask whether there is anything you can do, other than studying the text(s) and talking to classmates, to learn the material you missed.  Then show up for every class.

+1. The only thing I might question here is the part about asking the professor for suggestions on ways to learn the material you missed.  I always find that very annoying in these cases; if you wanted to learn it from me, you should have come to class.  The point being, it's up to you now to figure out how to learn what you missed.  For example, you could try asking classmates who did attend classes, or reading material or reviewing posted lecture slides.

@Jeff: I've edited my answer in light of your comment.

@cagirici:Because, in your question, you wrote, "One just gave me an F because I could not explain one point in a whole chapter in oral exam..."

@KonradRudolph:  Thanks!  I've edited my answer in light of your comment.

I think another good question would be: "Should a PhD student be obliged to fulfill the expectations of the professors whom they take courses from?"

@cagirici For institutions I know, for Ph.D. students both D and F are failing grades. The only real difference is just how much lipstick you put on the pig. That someone with decent attendance got a D for missing the same point indicates that the professor thought it was a majorly critical point -- perhaps something you'd have known if you attended class. (BTW, I do agree that the professor should be honest, and disingenuously marking you down "for the question" when it's really "for attendance" would be bad - but I don't see that here.)

@cagirici examination, noun, "a formal test of a person's knowledge or proficiency in a subject or skill." The fairness of the grading is irrelevant; if he was testing you on your knowledge of the subject, he gave you an examination.

@AnthonyGrist Are you sure? formal, adjective "done in accordance with convention or etiquette; suitable for or constituting an official or important occasion."

@Cagirici the phrase "oral examination" uses examination as a noun.  Your definition is for an adjective.  For example "examination room" uses it as an adjective.

my definition is of word "formal" not "examination"

@cagirici: You are quibbling about trivia when you have a real problem. If you do not address the real problem, your progress toward your degree is fraught with peril.

My main problem is not taking an F or professors dislike me. My main problem is not being able to convince professors that me not attending the classes is not something to take personally. Maybe the question was posed not in a good way.

This is a very strange answer, to say the least. The goal is to learn the material, not to "attend the classes." -1.

Based on your answer, I edited my post. I do not claim that he "gave" me F. I took an F.

And are you even sure there was no attendance taken?  My mother used to teach at a community college.  Due to the number of lost students and students changing class she never took attendance the first week.  Couple that with the fact that she was blind and a star athlete who somehow got in her course thought she could just show up on test days.

The short answer is Yes, at the PhD level, not attending courses is rude. At a guess I would say that these professors do not have a specific attendance policy because their experience is (a) at the graduate level, the students are motivated to be there and they don't need a formal policy to drive home the fact that (b) attending class is an important part of mastering the material and becoming part of a learning community.
You say that these professors know you and see you in the hall every day. I assume you know what you are talking about, and since this is a PhD program these are not large courses and your absence is noticed by everyone, including your fellow grad students, who probably resent you for not showing up. Let's assume that your read of the situation is correct, in terms of the professors knowingly and intentionally acting in certain ways towards you. Since you believe that "There is no explicit attendance requirement" means "I do not have to show up if I don't want to", Professor 1, without revising her syllabus, decided to show you that (a) you are missing things by not showing up, and (b) if you're going to fall back on the letter of the law, the letter of the law says I can ask you anything I covered in lecture on an oral exam. Professor 2 is letting you know that if you don't have time for him, he doesn't have time for you.
I will finish with your question of "What can I do to turn it around and convince people that my intention was not to offend them?" But first I want to address (a) your graduate program, and (b) the purposes of attending class other than learning the course material.
You have clarified in the comments that these two courses cover material which you are already quite adept in. Assuming you know what you are talking about, then you just may be in a program that is a poor match for you, because they are not working with you to structure the program to your interests and capabilities. If that is the case, you have to decide whether to try to get into a program that is a better match, or to get the most you can out of the program you are in. Getting the most out of it would mean repeating some material you already know, but trying to go deeper in your studies. This would require communicating with the professor about your preparation, asking whether you can demonstrate your competency, and then asking whether you can take the work in a more advanced direction. This does create a certain time demand on the part of the professor, so they may not be willing to do this, but you should still do your best to impress them with your competency and maturity. If you are not willing to leave the institution, you may just have to grind your way through a handful of uninteresting courses, which may not be fun, but will at least be easy. Try not to yawn in class.
Beyond that, attending class, especially at the PhD level, is also a way for your professors to get to know you personally, learn what your interests are, and possibly figure out if they would want to work with you. It is also a way for the PhD cohort to bond--an important part of having required courses early in a program and in a fixed sequence, before students move into more specific research interests. Even if you know the material, you could be helping the other PhD students learn it, both by your insightful contributions during class meetings (which hopefully are not just straight lecture) and by working with them on assignments outside of class. If you intend to go into academia, this is an opportunity for you to learn to be a teacher, possibly helping the other students learn material that they may find more challenging than you.
If you want to stay at this institution, want to start attending classes (this is important--you're not getting out of this with "I'm sorry I hurt your feelings but I'm still not coming to your class"), and you agree that these there are legitimate reasons to attend a class beyond just being an information-delivery system, then you need to sincerely apologize to the professors involved and let them know that you intend to change your behavior (i.e. come to all class meetings going forward). I would start out with a written apology and then request to schedule a time to meet to discuss the course. I would try to avoid making a claim that you already know the material, which obviously Professor 1 doesn't believe, and doesn't seem to be the issue with Professor 2. You might say something like you have always worked independently, and thought that the lack of attendance requirements meant that you could treat the course like an independent study. You of course now realize how disrespectful you were being towards the professors, and you apologize for acting like an undergrad. You reiterate your intention to attend all future class meetings, and ask if there is anything else they would like you to do to demonstrate your commitment to the course and to the PhD program.

Thank you for your response. I will indeed apologize. However, it is not that I don't have time for the professor or for the course. This is the point that was misunderstood. The professor might not have time for me, this, I cannot even question. He might even hate me just because of my hairstyle, and this I cannot argue with. But I just don't want to be judged based on a misunderstanding. I think of course do not think that I am "something" and underestimate other people. I am well aware that I am just a student.

@cagirici In a graduate programme, you are both a student and an apprentice colleague and not just a student. This is part of what makes it disrespectful not to attend. This is somewhat so, but much less so, at undergraduate level.

If a professor makes it clear that they do not care whether you attend class, then you ought to be fine skipping it some of the time.  (That is my usual policy in upper-level courses.)  However, missing almost all the classes is almost certainly a bad idea, for several reasons.  First of all, it's going to make it hard to learn the material.  You apparently did not master some subject matter that you were expected to in your first class.  Conversely, if you are a graduate student and can learn the class material essentially entirely on your own, it may not make much sense to enrolled in the class at all.  Second, it makes it difficult to build any kind of relationship with the professor.  The professor will not get to know you and cannot get the kind of positive impression of you that might be useful for, say, future letters of recommendation.  If the instructor is giving students individually tailored oral exams, they will want to have interacted with the student previously, to gauge what the student's level and interests are.  Third, it may give the impression that you are not serious about the material.  Even though I do not grade students who miss a lot of classes more harshly, I know from experience that such students very rarely do well.  The professor may not expect much from frequent absentees, and they may not feel as inclined to put in extra effort to help a student who does not seem willing to put in the time and effort themself.
If the class does not have a formal attendance requirement, but the instructor has not specifically indicated that attendance is optional, I would tread even more carefully.  All the reasons I described above still apply, but even more so.  In this kind of situation, an instructor is probably willing to be lenient if you have to miss a class now and then, but they may still be expecting you to be there to learn and participate most of the time.
In the future, I would suggest you attend classes more and get clarification from the instructors if you are unsure what they really expect.  For this semester, I would try talking to the professors and explaining that you misunderstood the expectations, but it's unlikely they are going to be swayed.

It is mandatory to take some courses, unfortunately most of them I have already completed during my master's studies.

Well, you gave your own answer: if it's mandatory, it's mandatory. If you disagree with the rules, pick a university where it isn't. While I sympathise to not want to repeat stuff, the fact that your exam didn't go as planned is an indicator that your last round of attending lectures may have not been as successful as might be expected from a PhD candidate. Of course, personal reasons on the side of the examiners may have been involved, but we know too little about that.

@cagirici: do the lecturers know that you've taken the courses before? Because mind trading is a tricky business. The rules might be the rules,  but I would suspect that you might get a different treatment if you did some explaining for why you didn't show up.

@Gerhard or better: get an exemption. However, I have to admit that this may turn out to be a bureaucratic impossibility :-)

@Captainemacs: agreed, that an exemption is the better option, but as you state, not always possible in rigid systems. But I know very few lecturers who would not find a common sense solution in such cases - like eg. not expecting to attend the lectures if they are not compulsory anyway, and only take the exam. But without knowing the situation, there is the risk the OP experienced that the lecturer will not be particularly happy if his lectures are not being appreciated.

@CaptainEmacs The exam that I have failed is not the course that I already took. Sorry for ambiguity. And I can say that you are correct about the rest.

@cagirici From my experience, this is the common students fall into. "I have covered that topic during my undergrad studies" is usually false conclusion, if you make it at the beginning of the semester. PhD classes may essentially cover the same topic as undergrad classes, but go in far greater depth.

Attendance record for classes can say many things about you.
Not attending:

it can say that you think you don't need to be taught the material
it can say that you don't think the professor has anything to add that a textbook doesn't have
it can say that you think you know it already
it can say that you think you will just understand it without being taught
it can say that you don't care about the material
etc.

Attending:

it can say that you value the professor's time
it can say that you acknowledge that the professor knows more than you
it can say that you at least tried to learn the material
etc.

Now consider this from the professors: you were given an oral exam in which you think you explained everything from a chapter except one point. Maybe the reason you were given that chapter to read was to understand that one point, or maybe you didn't explain it the rest of the chapter according to the professor's expectations. Either way, that likely would have been indicated in a class, and you may have found out if you attended. If you were attending classes and still missed something about the expectations, the professor may have cut you slack with the understanding of "the student was there, maybe I didn't explain myself well enough".
Also to note, you are not colleagues. You may be performing research, but you are still trying to get your PhD. The professor has a PhD, and is trying to impart that knowledge to you, to which you are saying "I don't need to hear what you have to say" by not attending (whether that is your intended statement or not).
In summary, you need to attend the classes. They are held for a reason, and the successful completion of them are the expectations of your PhD candidacy. If you fail those courses without attending any classes, you have no recourse to appeal any marks (particularly if you think the professor doesn't like you; your appeal will be thrown out as soon as the professor indicates you were not at any lectures).

Thank you for clear reasoning. These are legitimate and logical reasons. But unfortunately not true. I have been taught and therefore I do not think I know the course, I know the course. It is my very own research area and master's thesis topic. It is not that the professor has nothing to add that a textbook does't have, it is that someone else already taught me what is being introduced in a certain level.

@cagirici  -- you clearly believe you know the course, but your exam performance is suggesting otherwise.  How can you be sure that the prof offers nothing beyond the textbook if you're not there to experience it.

@ScottSeidman There are two different courses and I got F from the first one. I believe my performance did not deserve F. It is not subjective, my answers were approved. I am now worried if second course, which I have taken before and sure know it, will be not fairly graded in the oral part.

Hmmmm....having done all the PhD coursework in just two years and attended almost every class, I'd wonder why you'd waste money on courses in which you didn't like the professor or lecture?
Introducing oneself to the professor is simply good manners and should be done early, before dire need arises.
As a single example, I was taking a fast-moving summer course at Oklahoma State University in Electrical Engineering.  I asked the professor if I could miss ONE day in conjunction with the Fourth of July to harvest wheat.  Much to my surprise, he'd harvested his wheat and was only too happy to oblige.  He said that if I believed the theorem about line integrals around poles.  I asked what it was.  He explained it in just two or three minutes!  I was astounded and said I never would have thought of that! (But yes, I believed!)  He said he would probably spend all hour trying to recruit believers!
When I came back, I asked how class went and he said something like he had only about 2/3 believers!  (Which indicated that I missed nothing!)
So, show up!  Get to know your professor!  Ask the man who can help you!  Be sincere, on time & humble!  Best wishes, hope this helps!

What can I do to turn it around and convince people that my intention was not to offend them?

You need to stop making so many assumptions.
Though it is not entirely clear from your question, piecing together information from your comments, it seems that there are two things that have led you to believe that your attendance has caused you to be treated harshly.

You received an "F" grade in one exam when you felt you deserved a "D". That could potentially be a fairly subtle distinction. The best thing to do here is to talk to this professor, and ask about your grade. Adopt a humble approach: don't go with the intention of disputing the grade, but say that you were disappointed with this grade, and you would like to know what you could have done to improve it. Again, judging by your comments, you seem to assume that you are the perfect judge of whether or not your answers were valid. Try dropping that for a moment and get an expert opinion!
You are worried that, because your professor failed to acknowledge you in the corridor, that means they are vengeful and they will give you a bad grade. If I understand correctly, you've not even received your grade yet. You are getting way ahead of yourself here. Wait and see what your grade is before assuming that this professor is some kind of spiteful monster.

In the question, all reasons why I think like this are clearly explained. I neither claim to be the perfect judge or an expert on any topic. And I did not even imply that the professor was a monster or something. You are just exaggerating my words with your own interpretation and try to  make me look like a conspiracist or paranoid person. Your answer is based on "if a student thinks that the teacher is wrong, then student is wrong" which, unfortunately dos not answer any part of my question.

Perhaps it is a language issue, but "vengeful" is a very strong word. My point was that I don't believe it is justified by any of the facts. And I'm not trying to say that you are definitely wrong, but that you could be. There is a huge difference. From what I can tell you have not attempted to get the professor's side of the story with regards to the F grade. Once you have done that, and you have your grade from the other professor, is the time to draw conclusions as to whether or not the professors are being harsh or vengeful. Not before.


text:
Difference between private and public universities as a faculty member?
As a grad student I was, for the most part, shielded from issues like high-level bureaucracy, departmental duties and politics, and long-term career advancement.  Obviously these things become more important when you're looking for a faculty job.
Question: As a faculty member in the U.S., what are the most tangible differences between being at a public vs. private university?
I.e., how does it affect your day-to-day life, or alternatively, key events like promotion, student recruiting, etc.?  Obviously the question depends a great deal on the particular department and perhaps its ranking; I am interested mostly in departments "near the top" [ed: of some fairly arbitrary ranking systems...], but broad answers are also useful.
Thanks!

A few anecdotal observations. It must be said that these are trends, and exceptions to everything I say are plentiful.

As just-learning said, private universities tend to pay a little better. Also, they seem to have less faculty turnover (perhaps for this reason).
Public universities often have more BS committee work. For example, my university periodically mandates a lengthy process of "post-tenure review". Negative or positive reviews have no consequences, and therefore the process is a complete waste of time, but we have no choice.
At least among top-notch research universities, public schools are usually large, and many private schools are small. Large schools typically have advantages (big seminars, lots of courses that can be offered to students, etc.) and disadvantages (lots of grading, people can feel lost in the crowd, etc.)
A corollary to the above: public universities often influence their towns more, simply because there are more people working and studying at the university. For example UNC-Chapel Hill and Duke are excellent universities (public and private respectively) which are ten miles apart, and it is Chapel Hill that has the really outstanding K-12 school system.
Especially at public universities, there might be many clubs which are largely student organizations, but faculty members and others also participate in. Especially if you are not yet inclined to "settle down", this could be a huge positive.
The campuses tend to be different. Many private universities are surrounded by lush greenery, where at public universities it is more common that you can walk across the street and get something good to eat.
Sports culture is more prevalent at public universities (although it is also very big at many private universities). I am a bit of a curmudgeon, annoyed at the overwhelming football culture at my school. But those more laid back than me simply enjoy the games.
Student attitudes tend to be different. At wealthy private universities many of the students will be more optimistic, and more ambitious goals and dreams seem to be more common. The downside (from what I have heard) is that entitlement and grade-grubbing are also more common.
Public universities serve the public. My university enrolls a number of students from disadvantaged backgrounds, many of whom are the first in their families to attend college. I attended a graduation ceremony, and when many names were called there was a palpable and obvious joy on the part of large crowds in the audience supporting them. Witnessing this was a deeply moving experience.

These are all good points.  Regarding the sixth: it really just depends on the location of the university.  I agree that private universities, and especially private liberal arts colleges, are more likely to be located in very, very small towns (whereas the size of a public university places a lower bound on the size of the town that contains it).  But for instance there are places like Columbia, which surely get optimal marks for "you can walk across the street and get something good to eat".

In the US, the private universities apparently tend to pay more to their faculty:
http://www.aaup.org/file/2012-13Economic-Status-Report.pdf
http://www.huffingtonpost.com/2013/04/08/faculty-pay-survey_n_3038924.html
On the other hand, the private universities should, for obvious reasons, be less affected by the state budget cuts.


text:
As a novice scientific writer, how can I publish a scientific review?
I like to write and investigate in science; but it is not enough;
 Precisely I want to write a scientific review, as a beginner I don’t know how to publish it;
I don’t have a support, is it possible to publish a scientific review alone and for free?
 Otherwise, do you have any idea how can I find chemists co authors that may accept to work with me;
 Thank you very much in advance for your suggestions;

(1) Your second paragraph seems like a distinct question to me that you better ask separately (also, what should “international awards support for beginner scientific writers” be? I never heard of something like this). (2) As for your first question: You will likely get better answers if you say a little bit about your experience and qualifications (i.e., scientific degrees), in particular your experience with (reading) scientific literature. (3) Welcome to Academia SE.

If "international awards support for beginner scientific writers" means you want to actually get paid to write a paper, then you truly know nothing about science writing.

Thank you for your answer, Definitely not ,  what I meant : if a funding support in order to publish the scientific review exist. As I mentioned above, I don’t  know exactly how does it work but I know that I must pay the journal in order to publish a review and if  such a funding support exist;  for sure my aim is not to gain money from publishing, (the quality is important) , all what I want is to learn and enjoy learning no more no less.

“I know that I must pay the journal in order to publish a review” – No, you do not. There are such pay-to-publish journals, but there are also pay-to-view journals, where the reader pays the publishing costs.

Publishing a review on your own can be done.  However, it would be better if you found a senior researcher in your field that you can co-author the manuscript with.  Publishing a review alone may not do much for your professional career (it can even harm your career if it turns out your review is not good enough).  Co-authoring a review with an expert on the subject can be considered highly prestigious and by working with a senior person on this publication, you will learn much more than if you work on your own.