text:
Including conferences in the CV of an undergraduate student
Do you think it is important to include a list of attended conferences in your CV when you are an undergraduate student?
And what about the seminars you have attended which did not provide you with a certificate confirming you took them? Should they be mentioned too?

I include a list of undergrad attended conferences only if I presented at them. You can bring up other attended conferences in interviews or admission letters if you feel that it contributed to your knowledge/research.

Okay, but when an undergraduate, you really don't have so many chances to present some work at a conference. That's why I think including such a list, would show you true interest.

If you're in the US, consider looking into NCUR. Here's another list: http://www.cur.org/resources/students/presentation_opportunities/ I agree that there aren't as many chances to present, but it is important to try if you can. Including a list will show your interest but not your capabilities. If you attend conferences, the networks/contacts you make there are more important than a list on your CV.

There's also an international conference ( http://www.icurportal.com/ ) I think you can present via video conferencing if you can't travel.

I just looked into it! Really interesting. Still, not helping when not in U.S.. I didn't find something like that in Europe. Do you have any information about Europe? Thanks a lot!

Do you think it is important to include a list of attended conferences in your CV when you are an undergraduate student?

Sure, why not?  It's not likely to make a big difference in graduate school applications, but it can't hurt and might help.  This is not a particularly valuable form of information, but it's worth including when you don't have lots more to say (and undergraduates are generally in that position).

And what about the seminars you have attended which did not provide you with a certificate confirming you took them? Should they be mentioned too?

In the U.S., certificates confirming attendance are irrelevant. I couldn't recognize an official certificate if I saw one (there's no standard format or protection against forgery), so I consider them meaningless, and this is a common opinion here.  If you are sending your CV to a U.S. institution, then you don't need to worry about this at all.  In other countries the customs may differ, however.

In my country, there are different opinions about the certificate. Some say it is not allowed to include such conferences or seminars and other say: " Why not? Nobody's gonna tell you show me the certificate" . That's why I decided to ask the question over here. However, thanks!


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Is it ok to call the professor in this situation?
I had a telephone conversation with a proposed Ph.D. supervisor last Monday and he agreed that he will double-check my research proposal before I submit it. Then I emailed him the proposal. However, I haven't heard from him for a week, so I sent a reminder email to him this Monday. And yet still no feedback from him so far. I know that professors are busy and slow responders, but Christmas is coming and I do not want to miss the deadline. I wonder whether it is ok for me to call him at the same time as last time if I do not get his response before next Monday? Or are there any other solutions in this situation?

Why don't you call or email his assistant first? He could be traveling. Or, maybe he doesn't check/use email (yes, that happens, even in Computer Science).

@cabad Unfortunately, he has no assistant.

Personally, I both find phone calls these days intrusive and unpleasant, and ignore those from numbers I don't recognize for sure. So I would consider this unpleasantly pushy...but that is only how I feel of course. For safety, I'd rather sent a brief follow up mail with a crisp, friendly, good title short enough to get the gist of your mail w/o even opening it.

If he does not care about your PhD proposal and about your emails, maybe he is not the right advisor for you...

First, ask yourself whether you are sending the right email.
One of my professor mentors had a very useful heuristic for ensuring effective communication with busy people.  For any busy person, email typically gets triaged into three bins:

Email that can be safely ignored.
Email that can be responded to with trivial effort, thereby clearing it from their "todo list."
Email that requires non-trivial effort to respond, and must be put off for later... and later may be a long time, because now it's competing with their other "large" duties.

If you want a response from a busy person, write a short email that includes precisely one question, and make sure that question is easy to respond to.  For example, in your case, if you send email saying:

Here is my research proposal, as discussed.  Can you please send me feedback?

then that might get no response until the professor has the feedback ready, and preparing your feedback may get pushed off and pushed off again.  The professor might also misremember the deadline and have a lesser sense of urgency.
If instead you write:

Here is my research proposal, as discussed.  Please recall that I must submit before the deadline of XXX, and I would like time to revise if necessary.  When can I expect your feedback?

In this you've posed an easy question, which should get a response, and also gotten them to commit to a specific date.  If you don't get a response in a day or two from an "easy" email like this, then you need to wonder whether this person is actually somebody you want to work with.
What, however, if you send the right email, get them to commit to a date, and then they fail to either respond or tell you they need more time?  At that point, I would recommend against either emailing or calling on the phone.  Instead, go find the professor in person.  I have found that with busy people who fail on their commitments, that finding them in person is the best way to get yourself back in their queue.  Again, however, you should ask yourself whether you really want your whole Ph.D. to be this way, because it is likely to be a pattern...

If you are danger of missing a deadline, yes call her/him. @jakebeal's answer is great for email, but sometimes people just don't check their email.
If you are worried about seeming too "pushy" or aggressive, just be really polite and give a sense that you are trying to get things done and moving, rather than blaming her/him for the delay.

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Is it appropriate to submit a previously presented workshop paper to a peer-reviewed journal?
I have a paper that was presented at an NRC workshop and was not peer reviewed.  Moreover, although this work is accessible at an NRC website, it is clear from reading the literature that search engines do not discover the paper and no one is aware of its existence.
Is it ethical to submit this paper to a peer-reviewed journal for publication?

Different journals have different standards for what counts as prior publication.  For example, most computer science journals happily accept "extended journal versions" of existing papers that are intended to supersede the prior publication, as long as there is at least 30% new content and the relationship to the prior paper made explicit.  Some high-ranked biology journals, on the other hand, are so obsessed with "novelty" that they will consider a submission improper even if only an extended abstract has previously appeared.  Check the policy of the journal(s) that you are considering: either it will be listed clearly online, or the editorial staff should be able to give you a quick answer about their policies.

A lot of journals give their politics for conference paper in their websites. It is mostly like following:

Journal of Machine Learning Research
We will consider research that has been published at workshops or conferences. In these cases, we expect the JMLR submission to go into greater depth and extend the published results in a substantive way.

Some of them give numerical new content like %30 new material.
Find suitable journal which accepts such submissions. Clearly cite this is an improved version of your workshop paper. Improve your paper as suitable and submit.
As long as reviewers and editors are aware that your submission is an extension of workshop/conference paper, this should not be issue.

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Question on "Awaiting Production Checklist" Status for Manuscript
After my paper was accepted, the status in the ScholarOne manuscript center changed from accepted to "accept" with the additional "awaiting production checklist".
Now it has been about 3-4 weeks with this status after the acceptance. I would like to ask from you: does this status sounds like a normal status after acceptance?  Personally, I would think and expect the status now be, for example, "checklist complete"? I have received so far only the official acceptance mail.
I also would like to know how long the delay may be after acceptance to the first on-line view (the journal does not indicate the different dates of acceptance, on-line etc.)?

You need to find out the journal's policies on "Online First" vs. paper issue publication.  The reason is because the date that a paper is accepted may be very different than the date when it is formally published, if the journal is still tightly tied to paper issues and has a long publication queue.
If the journal does online publication in advance of its paper issues, then you should be expecting production to begin shortly and a citable preprint of your paper to become available very quickly (though the final official publication date might be many months in the future).
If, on the other hand, the journal schedules its publication based on print only, and does not publish early online, then it might stay in this status for a long time, as the publication staff may not have any reason to work on the article until it is approaching the final publication date.

Yes, the paper has early online publication in advance of paper issues. So, the paper should be in the queu for publication. I was afraid of the status that gives an impression that it is "awaiting" something. If it is not moving in a few weeks, I will ask from the assistant. Thank you very much jakebeal.


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Referencing figures or tables in discussion section?
I got a reviewer's comment on my manuscript that suggests that the most common convention is that tables and figures are not referenced from the Discussion section of a paper. This is something that sounds new to me and I wonder if it's true in some fields (such as biology)?

Every field has a large number of different types of publishing venues with different requirements and expectations for the structure of manuscripts.  If the reviewer is making a legitimate complaint, it is likely to have to do with the particular journal that you are submitting to.  Some do have very particular requirements about structure and what exactly goes where, so perhaps that is what the comment is about.
Absent particular structural constraints, however, I think that it's fine to reference figures or tables from a discussion section, as one is discussing them (in fact, it would be strange not to do so).

I agreed with this answer until I got to "it would be strange not to do so". That generally depends how much one "explains" the figures in the results section. I'd argue that both styles are quite common (referencing vs. not referencing figures in the discussion), but +1 for the overall answer.


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Should I put a "technician" pseudo-internship on my resume for biology grad school?
I completed a pseudo-internship-like experience offered by one of my undergraduate professors this semester. The job title was "biology technician," but my jobs were more geared towards learning than actual work.
Tasks I learned were: cleaning glassware in the biology department, organizing microscopes slides, cleaning microscopes, calibrating digital pipettes, and basic autoclave operations.
There were many other tasks, but I fail to remember them now, but would these skills be a boon to a grad school application, and if so, how would I incorporate them into a 1 page resume? I even filmed a video on autoclave use for instructional purpose.

How much else do you have to put in the resume?

@PatriciaShanahan    Not much, my grades are not stellar, 3.0ish GPA from a State liberal arts school. 1 or 2 research projects in the work. And a potential volunteer position at the local hospital getting water and pillows. I still have 1 year of school left though.

Yes, why not? For a grad school application, you might as well list anything that shows your interest   and involvement in your field. List it as whatever your job title was, and if possible add a line or two describing your activities.
But if possible you will want to inform them about it in more depth. If the application includes a cover letter, statement of purpose, or similar essay, use it to describe what you did in this internship and what you learned. If the application requires recommendation letters, consider asking the professor who supervised your internship to write one.


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Can I use map, fold, filter in publications?
I have to write down algorithms in my thesis, and these are getting way shorter if I use "map," "fold," and "filter" heavily.
This generally results in a "map, fold, filter"-chain with a depth of 3.
Structure:
fold( map( ..., filter(...))...)

Is it okay to assume that these functions are known, and what is the parameter convention?

I'm voting to close this question as off-topic because the second part of the question is asking about introducing a LaTeX package which seems to be on-topic for TeX.SE website.

@EnthusiasticStudent better to edit it to remove the second part of the question, I think (and have done).

@jakebeal At this early stage, I think it is up to the users to decide to whether edit their questions and rescue their questions from getting closed or leave them as it is. I personally do not agree with you to major edit the content of the questions/answers of other users at the first day the content is posted. At least, we should wait for some time to let the users to decide about their questions (and get familiar with the website's close/reopen feature). After some time of inactivity (about one or two weeks) we may major edit the questions, reopen them or rise close/delete votes on them.

Are you using a functional language? In that case: you must! They are part of the basic concepts in functional programming and will make code more familiar and easier to follow (a fold/filter/map has some properties that always hold, while a generic recursive definition can do everything.) It may be different for imperative languages where the programmers think in different terms (although map and filter ought to be simple enough to understand. fold would probably be the confusing bit).

@Bakuriu The related software is actually C++, but the presented algorithm/method is explained in pseudocode. It contains many list operations, so these functions are in my opinion a good fit. But related to the given answers/comments it would be good to cite a source where these functions are generally defined, just to be sure.
My audience are computer scientists (shouldn't be a problem) and chip designers (not so sure). Btw: I am happy with the changes to the question.

If you are writing to a computer science audience who would be expected to have a some knowledge of functional programming, then yes, these sorts of basic elements are quite reasonable to assume knowledge of.
If you are writing to an audience without such background knowledge, then you will need to explain what they are (and give a reference for more information) before you use them.

+1, should be fine for a CS audience. For a different audience, I suggest not using them, even if you explain them, because functional programming can be confusing for the uninitiated.

@Marc Arguably, it can be confusing for people who know what it is. :P


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What are the pros and cons of being a volunteer editor for ACM XRDS?
I am a senior undergraduate student, and I received a mail from ACM about the openings for ACM XRDS student volunteer editors. What do these editors do? And what are the pros and cons for how would it affect my career in research?

What did ACM (whoever they are) say when you replied to their email, asking what volunteering would entail?

@EnergyNumbers: Regardless of what ACM says, I think it's reasonable to ask this question here, to try to get an independent view of how the job works in reality.  I assume ACM is the Association for Computing Machinery and in principle it should have been spelled out, but anyone who could answer the question would know this.  And "how would it affect my career in research" isn't likely to be answered objectively by the ACM organizers.

I might suggest revising the title to take out the word "feel like" which sounds like you are asking for emotional responses, rather than practical experiences.

Cons: it will take your time away from research

While I don't know ACM XRDS in particular, in general the pros and cons of service of this type as a student are:
Pros:

You will get to know the journal publication process well, which will help you with publishing your own work.
You will get to know your field more broadly, and likely pick up interesting networking connections.
You will get to affect (slightly) the scientific dialogue.
You will get a nice bullet-point on your CV.

Cons:

It might be a lot of work, and thus might detract from your efforts on classes, research, other projects, or having a life outside of research.
You might discover that you hate the work, and be faced with a decision of sticking it out or quitting.

The likelihood of the cons applying depends very strongly on the particular journal, so I would recommend emailing a couple of the current editors to ask how much work it is and how much they are enjoying it.

If this is a honorary position, just go for it. You can quit any time.


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Two concurrent different versions of a paper to journal and conference; do I need to paraphrase?
I know that, especially in computer science, it's legal to publish an extended version of a conference proceedings in a journal if the 'new' content is above 30%. However,
Is it ethical (and legal), to send the extended version to a journal if the conference acceptance still not announced yet provided that I disclose the situation. Will the journal accept it?

"I know that, especially in computer science, it's legal to publish an extended version of a conference proceedings in a journal if the 'new' content is above 30%". Only if the journal allows that and usually for extended versions of papers already ACCEPTED at specific conferences and special issues dedicated at the conference. In your case, none of these conditions applies.

Please ask one question per question;  I have answered your first question, about simultaneous submission.  The second question, on paraphrasing vs. using the same text, is a duplicate of an existing question http://academia.stackexchange.com/q/12085/22733  I have accordingly removed that portion of your question.

As Alexandros says, first you need to make certain that the journal you are submitting to allows content reuse by the typical guidelines, as not all journals do, even in CS.
Assuming that is the case, the typical custom is to wait until your shorter paper is accepted to a conference, though it doesn't matter if acceptance has been announced to anybody besides you and the conference program chairs.  There is nothing hard and fast about this custom, however, since your manuscript will be separately reviewed by the journal to its own standards.  Confirm with the editor that it's OK before submitting and clearly disclose the situation in the cover letter so the reviewers will know as well.
If you do this, however, you are taking a risk, because your submission to the conference may not be accepted.  If your paper is rejected then you probably cannot submit to another conference.  This is because the new submission would now be a subset of a paper under review, not an extension.  You might thus end up with a piece of work that stays in limbo for much longer than usual (CS journals often don't have much sense of urgency, because of the existence of conferences).  You need to decide whether you are comfortable with taking that risk.


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Research Questions / Hypotheses for an Engineering (CS) Thesis
I am writing a PhD proposal on a solution to an AI problem that hasn't been solved before (although there's related research). I am having trouble determining what kind of research questions / hypotheses are appropriate for this topic. I can't propose my solution is better, faster, more efficient than some previous technique (as is common in CS theses) as there is nothing to compare it to, it's a novel problem. I am not testing a hypothesis as to how something works (such as a theory of evolution, or quantum mechanics), nor developing some set of equations to describe some phenomenon. Rather I am using some standard machine learning algorithms to solve the problem. What form then should my hypotheses take? That I solve the problem to within some degree of accuracy?

Formal hypotheses are over-rated, but still often necessary for scientific communication, especially for a pedagogical exercise like a thesis proposal.  The key question here is this: how will you know if you have succeeded in your intended work?
If the problem hasn't been solved before, then your core hypothesis is that it can be solved effectively with your proposed approach.  From that spills out a whole bunch of secondary questions:

Is the problem well-defined enough that "solved" is meaningful? This is often especially problematic in AI (e.g., "human-like behavior in a chat-bot", "good book recommendations")
Relatedly, how can you measure whether you have actually solved the problem?
What is the difference between a trivial/toy solution and an effective solution?  Again, a big problem in AI, where it's often possible to make systems that technically solve the problem but practically do not (e.g., for real applications they require unavailable curated data, or a thousand years of training time).
What sort of "partial solution" milestones are there along the way that will help you tell whether you are on the right track?
What would an optimal solution be?  Can it even be identified?
What will you learn if your chosen approach doesn't seem to be working?  Will it be possible to definitively tell that it cannot be a solution?
How will you know when you have done enough?

If you can provide good answers to all of these questions (or even just most of them), then you will have a very solid thesis proposal, built around the hypothesis of "Approach X can solve Problem Y."


text:
Disclosing hidden disability to employer
I'm doing a project-based postdoc in an European university.
I have serious ongoing eye conditions that significantly affect my reading speed and as a result it took me 5 years to complete my PhD in a country where a standard Ph/D/ is only for 3 years.
I have been selected for this postdoc position, I think, mostly because of my particular fieldwork and user engagement experience, which is essential for this post. So I still got hired despite my very weak publication record. And because the interview was via Skype, the PI did not discover my hidden disability, nor did I disclose it.
However, as I've been working in the position for several months now, it becomes apparent that I'm falling behind other colleagues of the team. Despite working extremely hard, I couldn't finish the work designated by the PI on time and I think I'll need a thorough explanation for that.
The question is, will disclosing a hidden disability ruin my employment? This is a 3 year position and the initial contract is only for 1 year. Given this is an externally funded, project-based postdoc, I'm really worried that my contract will not get renewed at the end of the first year.
And also how do I explain this to the PI and the university? For example, the choice of terms, hidden disability vs. chronic illness vs. long term health condition? Do different terms imply different levels of legal protection for employment?

I presume that you are performing at the same rate that you were during your PhD. If your PI did not ask why your PhD took five years to complete, or why your publication record is sparse, then you could argue that that is his/her failure.

Do you legally have a disability? I.e. you have documentation that under the Law you have X% disability due to your condition? Because that's all that matters for the contract. From your question it's not 100% clear that this is the case.

In most European countries, it is usually against the law to fire people because of disabilities. So long as you're capable of performing your assigned work with reasonable accommodations, you should not be afraid of being terminated. However, you will probably need to have documentation of your disorder to provide as evidence to support your claim.

thanks! I have all hospital letters date back to when my condition was first diagnosed. My concern is, I only have a one-year contract. so they could just not renew it by the end of year without involving the dismissal procedure? it's not a three-year contract with one-year probation

@confusedpostdoc, you have the same risk from not telling them, and them deciding you are not a good working because you are slow.

This is to complement aeismail's answer:
It might not suit the specific details of your condition but if you do end up disclosing your disability, you could also suggest to your employer various types of reading aids that could help you be more efficient at your job. There are devices that can alleviate some types of reading handicaps:

Video screen magnifier (I am not making a suggestion, I am only showing this as a reference; also it says it only works with Windows XP) Especially great with an old CRT monitor with accessible contrast and brightness settings
A similar system, but using a video projector instead
USB magnifier
Digital copies of all hand-outs, to read via a text-to-speech program
Optical character recognition software

Many employers are more than happy to cooperate with the employee in order to accommodate disabilities (in part because they can save money in the long run if it does help the employee), and in some locations they are even legally required to do so. Some governments even issue tax cuts and compensations to the employers.

Most European countries (even the UK) have advisory boards or charities about such issues. All countries have lawyers that are competent to various degrees in the matter.
I can imagine you are looking for some reassurance or reinforcement, but if I were you, I would consider taking advice either from a lawyer, a board or charity as a matter of urgency, rather than opinions from the Internet.
Keep in mind common sense may differ across land and time, but it will most certainly differ from the law of the land.
Good luck.


text:
Associate Deans' power
If a student complains to the associate dean about an adjunct faculty member, does the dean have the power to intervene?  In this case, the student is complaining because the faculty member won't accept late work, although the syllabus states that this is so.   Can the associate dean override the syllabus and force the faculty member to accept the late work?

The power and responsibilities of deans etc. vary very strongly from country to country (and sometimes even within a country there might be different regulations). Please clarify this point.

Which question do you want answered? The Dean's power or the Associate Dean's power or late homework acceptance?

As was already pointed out, the answer to your question varies a lot. My impression is that at my institution, if a student complained to the associate dean in a situation like the one you described, the associate dean would simply refer the matter to the department chair. In a large department like mine, the chair would refer the matter to an associate chair. So the student might as well complain to the associate chair in the first place.

Your question is unclear.  Does the syllabus say that late homework will not be accepted?  Does it say that late homework will be accepted (until when? for what acceptable reasons?  with a penalty?)  You also have not described why the homework was not turned in on time.
As a general rule, as long as policies, procedures, and other rules are being followed consistently and fairly, higher-ups tend not to intervene.  It's unlikely that a dean would intervene to overturn the decision of a faculty member to not accept late homework when the syllabus specifies that late homework will not be accepted.
It's possible that if there are unusual extenuating circumstances (e.g. the student was hospitalized after a car wreck and missed the deadline), and the faculty member is unreasonably insisting on applying the rule without considering those circumstances, then the dean might intervene.
On the other hand, if the syllabus said that late homework would be accepted (perhaps with some defined penalty) and the faculty member refused to follow the policy in the syllabus, then a dean might well intervene.


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API to get citations from DOI
Is there any API service to provide just the number of citations by DOI of an article?

I'm not aware of any. I don't know why you want such a tool, so I'll just leave that here: https://academia.stackexchange.com/q/37021/19627

An increasing number of publishers are making their citations open. When this happens, you can get them from the Crossref REST API.
This query lists all of the DOIs for which you can get the references, currently 20,455,807
http://api.crossref.org/works?filter=reference-visibility:open,has-references:true
Here's an example lookup. Look in the "reference" field:
http://api.crossref.org/works/10.1179/1942787514y.0000000039
You can also look at the Initiative for Open Citations and OpenCitations.net.
(I work for Crossref)

If you are a publisher member of CrossRef, you could use their Cited By service, and enumerate the results from that. If you had access to that, though, I expect you wouldn't be asking your question here.
You could try their REST API, although I don't know what information you can retrieve via that route.
The Scopus API (Elsevier) looks promising, and there seems to be a free version.
If you have access to Web of Knowledge/Web of Science, they also have an API.
SciFinder also has an API.
There are numerous unofficial scrapers for Google Scholar. Example 1. Example 2.

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text:
How CVs in discipline with numerous co-authors are examined?
In some disciplines such as theoretical physics, it is common to have tens (or even) hundreds of co-authors, probably because of the essential role of many people to run highly advanced facility.
How is the list of publications in these disciplines judged? For a faculty appointment, how does the search committee realize the scientific contribution of the applicant?

Theoretical physics? Did you mean experimental physics? Usually the mean density of authors/paper in theoretical fields are low.


text:
Is it fine to ask for a deadline extension from an academic publisher
I have signed a book contract with a reputable academic publisher a while back. I have finished half of the work and so far it's right on schedule. Now I'm about to give birth and after a discussion with my doctor, it will be a c-section. My doctor said that I would need a much longer time to recuperate because of it, but he cannot tell how long exactly. The agreed deadline in the contract is still in six months, but now I know that I will not deliver on-time. This is my first time publishing a monograph of my own. Is it fine to ask for a six-month deadline, or is it too long? I prefer to be safe. Is there a big risk that the contract will be cancelled? I suppose a medical certificate would also be necessary? What is the best way to ask for the extension? Thank you for your tips.

It's absolutely fine to ask for an extension, especially for medical reasons which everyone can relate to. Most probably they'll just extend the deadline and forget about the book project for another six months. In fact, for most book projects, the deadline is just a very flexible date, and the publisher will be happy as long as you deliver the book eventually.

Is there a big risk that the contract will be cancelled?

No. They want the book, after all.

I suppose a medical certificate would also be necessary?

They're highly unlikely to ask for a medical certificate because they want the book.

What is the best way to ask for the extension?

Write to the editor assigned to your book (i.e. the person who sent you the contract) and tell them you need more time because [reasons]. That's all.

I agree that it is very likely to work out fine, but for a text book, it might require rescheduling for a year later. So, six months wouldn't be too long. They will certainly want to work with you. Good luck with health and motherhood.

@Buffy what do you mean by "rescheduling for a year later"?

Textbook publishers like to coordinate release to the academic year for two reasons. One is the copyright date and the other is just sales boosting considerations.

The problem for your publisher is the "publishing cycle," which requires advanced planning on their end for the complicated sequence of steps to create and market the book, including knowing which books will get placed in their catalog next year.
However, please know that in publishing, like in life, things don't usually go exactly as planned. There are all kinds of hiccups and delays, and extending deadlines is common. I don't think you should hesitate to ask for an extension in your case. I doubt that the publisher will ask for a medical note as it's easy to understand your situation. Do, however, ask for a deadline that you're reasonably sure you can meet. As Allure points out, this is a mutually beneficial relationship and so the publisher is likely to want to accommodate you.

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text:
Is it OK to call an editor by her first name when she addresses me by first name?
I sent an edited volume proposal to a series editor, and she replied, starting her email with: "Dear [my first name] (if I may?)". She also signed with her first name.
I'm fine with first-name basis, so I would certainly say that she may.
Now my question is, should I address her by first name too?
My dilemma:

If I do, I'm afraid that I might sound disrespectful, since:

She's a very senior professor (there is a "power imbalance" between us)
She doesn't invite me to do so (but maybe this is tacit, since she signed by first name?)

If I don't and keep addressing her Prof. [Last name], I'm afraid that I might sound aloof.

What is the etiquette in academia? I've worked with volume editors before, but they're about my age and position, so we reverted to first-name easily.
My instinct is to stick with "Prof [Last name]" until I get an obvious invitation (e.g. "please feel free to call me [first name]").
Thanks for your insight.
P.S. She's based in the UK, if that means anything.

Reverse the question: why would someone sign a message with a name by which they refuse to be called?

It should be fine (and likely correct) to use her first name. AFAIK signing with one's first name is typically a signal that you can (even preferably) address them by their first name, and the fact she specifically asked to address you by your first name in my opinion strengthens this. If you stick with Prof., she may feel uncomfortable addressing you by your first name, or may even consider it a subtle rebuff toward her request to address you informally.
Anecdotally, I also found this fairly difficult when I first started out in the UK - I stuck with using Dr., Professor, etc. regardless of familiarity early on, until one of my supervisors directly asked me to address them by their first name.


text:
If I publish my PhD thesis chapters, can my thesis be later still published as a monograph
My supervisor told me that it is not required to publish my papers before submitting my thesis.
We are required (in German universities), however, to published our monograph thesis later as a book.
One of my chapters is already published as a book chapter in Routledge (it's too good an opportunity to miss). The published chapter is not entirely the same as my thesis chapter, as the Routledge editor edited it too (asking me to add this and that, which I did).
Now, another chapter of my thesis can be published in a conference proceeding too, if I so wish.
I understand that this is common practice for a cumulative thesis, but can it also be done with a monograph thesis?

Do you still have copyright to your paper(s) or did you yield it to the publisher?

I'm not sure about thesis by monograph, but for a thesis by publication, each chapter can be published separately, and there may be noticeable differences between the thesis and journal article publications due to different editors being involved, and the fact they may be published a few years apart.

Which aspect are you concerned with?  (Also, note that in many cases for "published as a book", it is sufficient to have your thesis in an online repository of the university library.)

This depends both on the rules of your university and the publisher's that you're working.  Most publishers are willing to allow you to republish papers as chapters of theses, and many universities are willing to accept compilations of published papers as theses, but there are exceptions in both directions.

This depends on what you or your uni mean by "publication". Many German universities don't require publication with a publisher but accept an online or microfiche publication that can be accessed by other libraries via interlibrary loan. Most German universities accept publication with a vanity press that will also publish stuff that has already been published elsewhere, as long as there are no copyright issues. –

From what I can think of there are two potential issues.
First is the copyright issue. In my previous university, for example, when each of the chapters could be either a conference or a journal paper, the university still could publish it online, but it was a grey area. But if you wish to publish your whole thesis to a new publisher as a monograph but excerpts of it, in the form of chapters, are already published with another publisher, then I see a conflict, if you have signed the copyright form. So you need to read on what you have signed, particularly if you are dealing with two different publishers.
The second problem, which could arise even if you are publishing with the same publisher will arise in the form of self-plagiarism. The plagiarism detecting software will obviously flag already published chapters as "copied" and your thesis might not be able to cross the threshold to be accepted for publication. Again, this might require you to convince the editor.
This completely depends on the copyright documents of the publishers which usually vary. So it is necessary to go through that.
Personally, as an aside, I sometimes feel dismayed at the current state of academia when researchers are compelled to look for avenues to regurgitate their work like this. Marketing has taken more prominence over doing original research.

You need to ask the relevant people and sources for the information you need.

Ask your advisor what he will accept for a PhD thesis. I suppose having the chapters accepted in peer-reviewed journals will be welcomed as it proves a high quality standard.
Read the copyright agreements of the journals. Usually you transfer the copyright to the journal, but most often they grant you the right to use the paper in your thesis. But you only know it for sure when you read the agreement that you accept(ed) when publishing it there.

In most places, PhD theses whose chapters are simply reproductions of work published elsewhere is acceptable. At the very least that's the case when you just publish the thesis yourself -- the situation might be different if you publish with a company that will likely insist on transferring your copyright to them.
Regardless of this, as in most of the other questions on this forum, the right answer is almost always "Talk to your adviser".

+10 for the last paragraph [though I can only give +1 :)]

Even if a publisher requires you to transfer copyright to them, they may have a special allowance for PhD theses. For example, Elsevier allows papers that are not open access to be reused in a PhD thesis.


text:
Is using the same topic title as a book title plagiarizing?
There is a well known book "Scientific topic X. Philosophical reflections." It contains a collection of articles on the topic. I am writing a paper myself. To what extent is it allowed to use the same title?
I am not stealing or borrowing the title because it is particularly original, it just concisely summarizes the goal and content of my paper (without redundancy). I also came up with about 10 alternatives, but I like this one still more.
I suppose it is ok, after all - there can be only so many permutations of words for a particular topic/approach, e.g. "Introduction to philosophy of science, Basic course in Calculus, etc."
What are the academic standards on this issue?

Would Cultivation of Potatoes: Philosophical Reflections be the tuber equivalent to your proposed title? Because that's not plagiarism.

yes, the title has a similar structure (also 3 words for the topic at stake). However, the approach of my paper is different from those of the articles in the book. I was just a bit skeptical, since the book title is well-known.

I suggest you think of a more useful title.

Why not take this as an opportunity to practice a little originality?

I'm with @Dave Clarke. Moreover, I'm skeptical that "Philosophical Reflections" cannot be improved, particularly for a scientific topic.

Thanks for the (critical) remarks. As pointed out above, I don't have a lack of alternatives, I just have a personal (subjective) preference for the original one. My main question was whether I should be aware of some publishing policies (I don't feel that I am doing something wrong or "stealing")

Why not:  Philosophical Reflections on Potato Cultivation. Even with the same five words, there are multiple combinations.  Potatoes: A Philosophical Reflection on Cultivation

@RoboKaren - You mean permutations don't count as plagiarism? It IS the same five words.

There are no official policies on things not being allowed to have the same name.
It doesn't seem to be a legal problem: How many books are called Algebra? and how many songs are called I love you? How many companies have been called Smith and sons?)
It is not a technical problem since title is not the most relevant citation information
Is it an ethical problem? I don't think so.
Still, if the other book is well known, it can lead to confusion and people can think that you are a bit bizzare to reuse the title. I wouldn't do it.

thanks for the answer (unfortunately I cannot upvote, since I don't have enough credits)

I published a book with a title that had never been used.  I research every title that I want before using it.  Then, 5 months later, a writer on the New York Times Best Seller List came out with his book using that same title.
If that writer did his research, he knew that the same title was used just 5 months earlier and should have used another title for his book.
Of course, being a Best Seller, his book always comes up when someone searches for that title.  If someone searches for my book, they get his.
I don't particularly appreciate it, but as mentioned, it is legal unless copywrites apply.
Just felt like getting it off my chest.  My book is better, by the way!


text:
How do I re-plot my results against existing results?
I need to compare my results with other result, so I need to re-plot the other author's results against my results.
For example I want use this fig as a way of comparing results
so is there any way to do that or any software can do that?

Write a short email to the authors, asking for the data for this plot. I don't say that it will work, but it's certainly worth trying.

There are two ways to about this. The first is to contact the authors of the paper containing th graphs and ask if they can supply the data. Otherwise you can search for digitizing software on the web. I have one (open source) that comes to mind Engauge Digitizer but that is not the only one by far.

I use  Engauge Digitizer but its not going very well ?

Two very useful alternatives are G3Data Graph Analyzer and GetData Graph Digitizer. Both of these are very simple to use, simply set up your axis and select the points. If I remember correctly, GetData even has an algorithm that recognizes the marker shape and grabs them all.

Here is an example of the microlayer thickness data: https://www.dropbox.com/s/qwu6zzljw33lq6f/data.csv


text:
Do U.S. PhD students who engage in research during summer or intersession breaks get vacation time?
When a PhD program in the United States like this states that students are expected to engage in full-time research during the summer months and the January intersession in addition to their regular coursework, should one expect that vacation time is out of the discussion, unless it is unofficially granted by the advisor?

Your work schedule (as a Research Assistant at least) is all unofficial (no specific days and hours), so vacation time is too.

If your advisor is providing your pay, then you should negotiate vacation with your advisor.  About 2 weeks per year is considered standard in US employment.
If your advisor is not providing you with pay, you should still discuss it with your advisor to make sure they think you are making progress and are committed to your research.  However, your advisor should realize they are not in a position to dictate terms.
Do not be surprised if nobody cares.  But don't abuse it.
I recommend planning your vacations at the same time as everyone else's.  The benefits are that other people will not notice you are gone, and it can be hard to get work done anyway when the people you work with are gone so less is missed.  Typically these times are late December and August.

Thanks for the helpful answer. I imagine that a week off in winter in addition to a week off in summer are not such a big deal and a continuous full-time schedule may lead to exhaustion.

My university is officially closed (skeleton crew only) from Christmas Eve through New Year's Day, and lot's of graduate students take this time off (and more). OTOH, there are plenty of profs that work their students to the bone and demand work over Christmas break, every other holiday when the university is closed, and every weekend, too.
If personal time is important to you, you should discuss expectations for time spent working or in the lab with a potential advisor before your sign on to work with them. My PhD supervisor expected people to put in appearances most weekdays in the lab and to be productive, but I know others that have Friday meetings that generate Monday deadlines.


text:
What is the relative importance of the parts of my application?
I'm thinking of applying to American universities for a Ph.D in Maths and I'm currently studying in the UK.
I was wondering how important each of the pieces of the application are, which I believe are: my personal statement, the references I get, the GRE scores and my academic transcript.
Thanks very much!

Depends on the school, and sometimes on the specific program you're applying to. Even those which use a shared application form may evaluate it differently. There is no single answer.

It is a very closely run issue, and as stated above can vary by school, but in general, the order goes:

Letters of Recommendation
Personal Statement
Transcript
GRE scores

If for some reason you don't get into the program of your choice you may consider applying to a U.S. Master's degree program that will get you up to speed, and make your application much more persuasive. Many schools offer 1 year masters in a variety of subjects, which are valuable in themselves, and are easier to get into for international students.
Letters of recommendation tell the committee a lot about you as a person, which is very important, since they are stuck with you for 5+ years. People coming from outside the U.S. are better off getting letters from scholars who have attended university in the U.S. because it is frequently difficult for U.S. scholars to weight the relative merits of courses, research and so forth from outside the country and someone intimately familiar with the U.S. system can help them parse that by making comparisons to things current in the U.S. Coming from the U.K. (or Australia, New Zealand, Canada, Germany and a few others) the systems are similar enough that the assistance is minor, but perhaps worth it all else being equal. Above all else make sure that your letter writers can speak in depth about you as a scholar and don't go for fame over substance.
The personal statement serves essentially the same purpose, but it shows the committee what you want to research while at the institution. The title "personal statement" is misleading, however, because you should treat it as a research statement. The biggest challenge students everywhere, but especially from overseas where different academic traditions may prevail, is completing a dissertation as a major research effort. Schools need to know that you have at least some idea what creating original scholarship means, and why you think going to their school is valuable to you as a scholar. They don't care about the time your dog died, and it inspired you to be a better person.
Courses show that you have the basic understanding of the topic, although unlike British or Continental programs, almost all U.S. PhD.'s include significant coursework, which will get you to where you need to be to write your dissertation. Grades don't necessarily compare across systems, and the committee knows that, but as long as you have done well and are prepared for the program.
GRE in almost every case is just a way to winnow out the thoroughly unqualified. FYI, most maths intensive disciplines (Math, Economics, many natural sciences) at top schools will not even consider you unless you have a perfect quant score (currently 170, formerly 800). Most schools don't hide their cutoffs, and if they do an e-mail to the department secretary will usually find it out for you, so don't waste your money applying to places you will never get in because you don't clear this obvious bar.
Finally, I highly recommend the book Succeeding as an International Student in the United States and Canada by Charles Lipson.


text:
Using a source and being unable to cite it
I am writing my thesis, and during my work, my advisor supplied me with some confidential documents that he still has from his previous work. Part of my work is based on these documents and I am unable to cite them because they are confidential. My advisor says that I can use them without citation because they are not available to public, but I am afraid using them without citation might be considered plagiarism and may come to hunt me me in the future.
What to do in this case ?

What is the rule that prevents you from citing confidential documents? Are they so confidential the one can't even acknowledge their existence?

Related: How to reference confidential data in reference list

"My advisor says that I can use them without citation because they are not available to public," This is strange for reasons you said. The advisor should be able to answer questions you have and discuss this in a reasonable way. If he gets defensive or weird about it, just insisting he is right, I'd go to an ombudsman. Plus, what Corvus said.

By "his previous work", do you mean results developed by the advisor himself, while he was hired to do research which was (or could have been) applied to something confidential? I don't claim to know what is the correct approach to this situation, but if, for example, the advisor was a physicist working in Los Alamos during the war, and he found a nice result about logarithms, which he never published, but it was collected as part of his (confidential) documents. How would using his result harmful or unethical?

What to do in this case is EXTREMELY dependent on the exact nature of the documents involved, and particularly on who declared them confidential and why.  You need to talk about this in detail with your advisor and understand the situation extremely carefully, because otherwise citation may be the least of your concerns.
Let me outline a few of the scenarios that you might be facing here:

Your advisor may have supplied you with classified information, making you complicit in a serious crime and subject to high fines and a possible long prison term.
The information might controlled under other legal regulations, such as privacy legislation, insider trading, international arms control.  These are far-reaching laws that can interact with lots of bits of science you might not think relate.  Once again, potential criminal prosecution unless the information is carefully managed / abstracted / de-identified in a way acceptable to the agencies that enforce these regulations.
The information might be related to patents, trade secrets, or other IP not yet fully disclosed, in which case you might end up on the receiving end of a civil lawsuit unless appropriate permissions are obtained.
The information might be related to something that another group is planning to publish on first, and it has been disclosed to your advisor with the understanding that they get to publish first and not be scooped.  In this case, you need to coordinate publications schedules.

Many other situations might apply as well.  In some of these situations, some form of citation or acknowledgement is appropriate.  In others, the information must be carefully "fuzzed" and citation is inappropriate or even illegal.  The details cannot be guessed without a thorough understanding of the exact nature of the information and how you are using it.
Bottom line: go have a long heart-to-heart with your advisor and work out exactly what is the nature of the confidential information and what is the appropriate way in which traces of it should be handled in your thesis.

You cannot use ideas, data, or wording without indicating their source.  If they are based on a document you are not allowed to cite, then you have a major problem.  (Note that you can cite documents that are not available to the public.  That's certainly problematic, because other people can't verify or use the source, but it's different from not citing anything.)
Theoretically, you could attribute ideas or quotes to an anonymous source if the source approves but asks not to be named.  That would be exceedingly unconventional, and I don't think I've ever seen it done in an academic paper, but it would at least be intellectually honest and avoid giving the impression that the ideas were yours.  The same is true in principle for data, although it's not clear why readers would trust data from an anonymous source.
What worries me about your question is that you say your advisor still has confidential documents from his previous work.  Maybe I'm reading too much into your description, but it sounds like the reason your advisor will not let you cite them is that he is not allowed to share them with you (and he may not even be allowed to possess or use them himself).  If that's the case, then the whole project sounds unethical.  It might be justified in some rare circumstances, for example involving whistleblowers or similar leaks, but outside of these cases, you cannot use confidential documents without explicit permission.
In any case, there is certainly no principle that says you can use documents without citation if they are not available to the public.  Either you have misunderstood your advisor or he is wrong on this point.

"Anonymous. Personal communication." certainly sounds bogus as a reference. It will definitely pull attention and draw readers to investigate what this source is. If there is any way outsiders can find out / make an educated guess as to what the information and source is, I would say that the safe assumption is that they will make it, thus blowing at least part of the confidentiality.

Yes, that's one reason you shouldn't cite an anonymous source without the source's consent.  Anonymous sources are definitely weird and problematic, and they would make sense only when absolutely necessary (when you have to acknowledge that an idea is not yours, but the source does not want to be identified).


text:
If I have dropped out of a Masters can I then go on to do a PhD?
I attended a masters program in IT and completed everything except for my capstone. Its been almost 7 years since I started and 5 years since I moved out of college.
I now want to apply for a Ph.D.
In these 5yrs I have had one really good research paper published, one patent filled, and worked for two fortune 500 companies. I am presently working as a manager in the same discipline as my masters in a top 5 tech company.
What are my chances to get into Ph.D program?
Also can I use coursework from the masters for a Ph.D?

Did you drop out because of time constraints or because you failed to pass some exam/thesis?

I think the answer to your question very much depends on the institute which would accept you into their PhD program and also the school you attended for the masters program.

@Raphael, because of time constraints, i was decent on my grades.

@scaahu i am looking at umich, GATech, VA Tech, IUPUI for my phd and my masters school is RIT

You might misunderstand my comment. I was not asking those info. I was saying the answer to your question depends on those schools and their policies. It also depends on what PhD program you will be admitted.

ok now i get it. but do u think dropout status on my masters would generally hamper my chances? (i know its yes) what can i do to counter that negative mark on my profile apart from more research papers and do u think patents in the same filed help? do you think my current position in the same field helps?

I believe industry working experience will help you a little, but not much. Research paper definitely helps. Patents should help some, too.

I did this. Worked out fine.

I assume you are applying for a Computer Science PhD. The following answer is based on my application process (Stanford, Berkeley, CMU, George Mason) in interdisciplinary departments that included CS.  I had two interviews with Universities where I was not subsequently accepted, so I learned something about the decision criteria and process.
That you have Masters-level course work is a positive. That you didn't finish your Masters is probably neutral-to-slightly-negative.  Your published paper is a positive, but your patent will be irrelevant unless it has relevance to research.  Your industry experience is probably also irrelevant to being accepted into a PhD program in CS.
All of these are less important that other aspects of your application: 1) GRE scores (esp. Math), 2) your research goals and 3) recommendations (by one or more academics or researchers).
What I learned is that Math GRE score is a "hurtle" -- you have to have a score above some threshold level to be considered.  They won't tell you what the threshold is, but you should assume that it is the average for their accepted PhD students.
Most important of all are your research goals (and your preparation to achieve those goals) and whether they are aligned with a particular professor in the department. Most PhD students are funded through Graduate Research Assistantships or Graduate Teaching Assistantships.  In CS, it's mostly GRAs.  Mostly, professors admit PhD students that they believe will be good "worker bees" to support them in their research projects.  You may be the most wonderful, inspired, gifted, hard-working applicant in the World, but if your interests don't align with at least one professor who has research funding, then you won't get admitted.
Related to this is recommendations. Admission committees respond especially positively to recommendations from people who are important and relevant to the specific area of research.  Glowing recommendations of your many personal and professional qualities will mean less than specific recommendations that substantiate your aspirations to do research in your proposed area from someone who is important and well-regarded in that field.
Finally, each University has it's own rules about whether they offer credit graduate-level course work.  Mostly it's related to how long ago you got it and where you got it.  Given that it's just 5-7 years ago, you should be fine.  You can position this as: "My previous graduate course work will accelerate me through the PhD program, and allow me to focus time on courses that relate to my research focus."


text:
How should I email a group member from an international group in my area that I previously worked with?
I am PhD student in biomedical signal processing area. Before starting my PhD in January 2015, I was researcher in a research group in which I had the opportunity to know one of the best researchers in my area of interest who is also a member of the best group in the world.
After starting my PhD I decided to continue in the same area but with a different group. Now I want to get in contact with the researcher, I mentioned above, and ask for collaboration.
What should be the content of my email regarding the researcher's relations with my previous group? Should I explain the about the reason's of changing group or not?

Young students are expected to move around for any number of reasons, so I don't think there is any particular need to explain your reasons for changing groups unless the other person asks.  Instead, I would recommend getting back in touch with a simple greeting and a focus on the new collaboration that you are aiming to establish.  An example of an email along these lines might be:

Hello, Dr. X:
You may remember me from our previous work when I was studying under Prof. Mysterio.  I am now pursuing my Ph.D. under Prof. Moriarty, working on the same subject of penguin wrangling.  As before, your work on penguin tracking devices would be very useful; would you be interested in continuing our collaboration?

Adjust as appropriate for your particulars.


text:
How to reference multiple authors of a chapter from a book [APA]?
I need help deciding how to cite a specific chapter of a group for my thesis.
My problem is basically with the different types of authors the chapters of this book has.
The authors titles are: Coordinating Lead author, Lead Authors, Contributing Authors and Review editors.
So, which ones do I include?

Could you give an example? Also what citation style are you using (APA, MLA)?

Thank you for your reply. I am currently using the APA citation style.

The following is the chapter i need to cite.
Chapter 17
Cultural and Amenity Services
Coordinating Lead Authors: Rudolf de Groot, P.S. Ramakrishnan
Lead Authors: Agnes van de Berg, Thaya Kulenthran, Scott Muller, David Pitt, Dirk Wascher, Gamini
Wijesuriya
Contributing Authors: Bas Amelung, Nesa Eliezer, Aspara Ram Gopal, Mechtild Ro¨ ssler
Review Editors: Xu Jianchu, Hebe Vessuri

I really wish i could post it with the proper paragraphs. My problem is that there are 4 different author titles. i dont know which to choose or if there is a priority.
every chapter has different authors as well.

From the APA blog this is what you need to site in APA

Author, A. A. (Year). Title of chapter. In B. B. Editor (Ed.), Title
  of book [E-reader version, if applicable] (pp. xxx–xxx). Retrieved
  from http://xxxxx

You will see in the purdue OWL that you should only list seven authors. So your chapter citation should look like this. I'm assuming this is the chapter you are referring to at this link.

De Groot, R, Ramakrishnan, P.S, Van De Berg, A,  Kulenthran,, T, Muller, S, Pitt, D, ... Rossler, M. (2005).
  Chapter 17 Cultural and Amenity Services (Xu Jianchu and Hebe
  Vessuri Ed.). In  Rashid Hassan, Robert Scholes, and Neville Ash (Ed.), Ecosystems and Human Well-being: Current State and Trends (Vol. 1, The Millennium Ecosystem Assessment, pp. 455-476). Washington: Island Press.

For in text citations use the following link

Six or More Authors: Use the first author's name followed by et al. in the signal phrase or in parentheses.
Harris et al. (2001) argued...
(Harris et al., 2001)

thank you very much for your help in this. I had no idea about the seven authors part.

@YiannisPaneras no problem. If the answer helped you, you can upvote it and accept. That's the usual way for thanking on this site.


text:
What should I put in the Introduction as opposed to the Literature Review?
My question is rather short one, how much information should I include when writing the introduction, and how much should be left out for the literature review
Note: the reason for this question, is because my advisor told me that my introduction is to light and he raised several question that eventually will be covered in literature review. When I pointed that out, he said that the introduction should inform the reader about the theme being addressed by the thesis/paper so that the reader will have an overview of the paper from reading the introduction.

note: my introduction contains the following:

1.1 Background
1.2 Problem Formulation
1.3 Purposes of study and hypotheses being tested
1.4 Data Sampling
1.5 Structure of the paper

You may want to have a look at this question for some general guidance on Introductions http://academia.stackexchange.com/questions/14695/what-should-i-put-in-the-introduction-chapter-of-my-thesis

(In economics at least.)
Introduction (5 pages)
• start with some broader motivation or backgrund
– maybe a sentence or a paragraph at most
• quickly explain your problem/puzzle
– show not tell
– don't say your work is pathbreaking or the problem is interesting (arrogant)
• clearly, concisely explain what is novel
– crystal clear
• report key results
– no hiding the punchline!
• discuss implication
– what does it mean for public policy? for theory? etc
• Layout:
– a clear roadmap
– Section 1 does this. Section 2 does this. Section 3 etc...so they can find what they want. (This is the easiest paragraph to write)

Of course, this varies a lot by discipline, type of manuscript, journal and so on. But speaking about a prototypical  psychology single study paper, a common structure is: (1) introduction, (2) method, (3) results, and (4) discussion. The introduction is commonly composed of (1) an opening; (2) a literature review; and (3) a description of the current study.
By this breakdown, what I call the opening is what you call the introduction. The opening is commonly between 1 and 5 paragraphs. I previously wrote a post on how to write an introduction in psychology where to quote myself, "the opening section typically moves from showing why the research is important, to situating the research in context, and then to setting an outline of what is to follow."
In general a good strategy is to find some similar articles to that which you are writing and carefully deconstruct these. How are aims presented? How is the research motivated? How is the importance justified? How is the gap in the literature framed? Where is this content presented?

It seems to vary among disciplines.  I suggest you choose two or three papers that have been published in the journal you're targeting -- papers that attempt to do something analogous to what you're doing -- and copy those papers intensely.  Of course, I don't mean plagiarize them.  I don't even necessarily mean that you would copy any particular words.  Instead, I mean that you would copy these papers in terms of how much info to give and where to give it, what kinds of issues you should cover and what kinds of issues you should avoid.  Doing research is different than writing it up.  In some sense, these papers become your mentors to show you the tone and style of the journal.  You've read a metric ton of these papers in the past, so it probably feels like you already know how they go, but when you follow a mentor paper closely there are things that will become apparent that you never noticed before.
In addition, I recommend something I've done over the last few years that has helped me.  I keep a clip-file called "Nicely said!" in which I keep examples of how authors deftly handled tricky issues in their write-up.  I use these examples as "mini-mentors" to guide me when I must handle a tricky issue.  Here again, I might not use any of the actual words they did, but having an excellent example in front of me helps a lot.  I'm not trying to reinvent the wheel.


text:
Citing a Hollywood movie in a scientific paper
I realise this is a bit of a silly question, but I'm writing up a conference paper on a model that's named after a Hollywood movie. What is the appropriate way to cite the movie in the paper? Should it have its own entry in the references (and if so, in what format?), or should I simply say something like "...after the 1986 movie of the same name"?

I don't think it's a silly question at all.

I'm not sure that you have to cite the movie, maybe leave it up to the reader to make the connection.

But Footloose was released in 1984.

no need to be vague. what model/movie?

@vzn it's a cellular automaton with the curious property that gliders cannot be destroyed except by colliding with other gliders. The gliders meet until only one immortal glider remains - so we call it "Highlander".

I've done this at least twice.

@JeffE: Bruce Kitchens' 1979 Master's Thesis at the University of North Carolina (Chapel Hill) has the title Tori! Tori! Tori!, which is a word play on the 1970 movie Tora! Tora! Tora!. His thesis has even been cited in this published paper. For what it's worth, I know this because the two of us took two or three classes together in the late 1970s, and I remember how pleased he was with using this title.

I'm coming from a humanities background so there may be some differences in actual citation styles but I think the following would be used by most styles.

Name of movie
Director
Distributor
Year of release
Medium consulted (DVD, VHS etc)
Sometimes the main performers(depending on citation format)

In text styles of course depend on whatever citation style you are using.
I know for example MLA is (Director, Movie Name) and APA is (Director, Year).
For your example of Highlander in the APA style it would be (Mulcahy, 1986) for a inline citation and your reference entry (assumed DVD) would be  - Mulcahy, R. (Director). (1986). Highlander [Motion picture on DVD]. Thorn EMI.
This Link has a pdf showing examples in MLA, APA and Chicago style.

Thanks, that's great. The conference uses an APA-type style, so I'll use that. (I'll leave it a couple of days before accepting, just in case there are other answers.)

Great, I was going to ask what style but I though I'd give the link for a few to make the answer useful to others that may have same question.

+1 Since humanities papers cite movies and other works of fiction all the time, academic conventions already exist and should be adhered to unless otherwise stated by the publication venue

You should probably add "Edition" if applicable; was it cinema, TC, director's or extended cut?

If in your citation style link is desired, I would add one from http://www.imdb.com/.

In my research area (databases/distributed systems) projects often have a name taken from something out of pop (or not-so-pop) culture. It seems that if any reference for the allusion is given, it comes in a simple footnote. Your suggestion of "after the 1986 movie of the same name" would likely be perfectly adequate.
On the other hand, if some aspect of the movie actually influenced your work and you discuss it a bit, a full-on citation might be more appropriate.

If it is just the name, I would not cite it. (Unless you really want to or the title may be otherwise strange, ambiguous or misleading (never assume that everyone gets any cultural reference, no matter how popular among your friends).)
I always though that it is up to reader's wit to catch the reference. The same as for project, grant or technique names being contrived acronyms. For example, for FROG (i.e. Frequency-Resolved Optical Gating) I would be surprised by someone citing an article on amphibians.
And from my personal experience: I published an article with title Qubism: self-similar visualization of many-body wavefunctions, but there is no citation of Cubism.

I dunno. I've seen a few mixups in FROG and RABBIT papers.


text:
Are itemized lists discouraged in scientific papers?
From my experience in biology (by experience I mean reading other papers), it seems that there is an unspoken rule that itemized lists do not belong in the body text of a paper.
I have almost never seen a paper have a bullet point list or a numbered list which is formatted as a separate entity in the body text (although I have seen them in eg. the sidebar, or figures which essentially are a numbered list). The closest I've seen is an "in-line" numbered list:

Our paper raises three points: (1) yada yada, (2) blah blah and (3) bip bap boop. Point (2) is particularly important, because yakkity yakkity...

Are bullet point or numbered lists, formatted similar to how StackOverflow formats them for example, discouraged in scientific publication? If so is there a reason why?

I have used itemized lists, especially in the methods section, in several published papers (field:biomechanics).

Do articles in your field have strict length constraints? This would explain why bullet lists are underused --- they take up space.

As a first guess, I'd say its due to length restrictions, perhaps a holdover from when journals were primarily printed on dead trees

@Jigg Actually I would very much like to take a look if you could provide a link to the paper.

I agree that itemized list are not very common in the biology literature. However, I do not think it is a requirement of the publisher (I check in PLoS Biology, Cell and Plant Physiology), but more a choice of the authors. I personally tend to include itemized list when it is necessary and I never had any comment from the publishers.
One possible reason to choose inline list over an itemized one is that is take less space. Since some journal have a pay-per-page policy, it might be an incentive. The same goes for grant application in which the number of pages is usually limited.
An other reason, but I am speculating here, is that itemized list might be seen as an ugly (the term is not mine, but from a reviewer of one of my paper) or cheap writing style. I personally disagree with this view, since the importance is the message, not the writing style, but I think it is out there anyway.

+1 for the space requirement. In CS, as Suresh says, bullet/numbered lists are common and I find them more readable. Hence I tend to use them unless I need the space to meet a page-limit.

The message is key but if it is lost due to poor writing style, writing style becomes important as well. So you cannot set one against the other

@PeterJansson I agree, you nice a good balance between both. But I maintain that message comes first and proper style should be used to deliver it as best as possible. And I think everyone would agree that scientific writing is not high level literature...

It is extremely common in my areas of computer science (TCS and machine learning) to see a paper itemize a list of contributions as a bulleted or numbered list. I use it regularly as a technique to highlight and emphasize contributions and key ideas in a way that stands out.
So while any such answer is area specific, I'd say that in the areas of CS that I'm familiar with it is definitely not discouraged.

We see them probably less than we should simply because they take up oh-so precious space (damn page limits). There are often inline lists that would have benefitted from itemisation.

There are no rules for or against lists, and as has been indicated by other answers, their use may vary between disciplines. That said, there are some points you need to consider. Lists can be useful if used correctly and detrimental if used too often. Lists disrupt the reading or flow of the text. One should thus consider if a list is useful or really necessary before making one. Does it help the reader to understand the text? Lists have a tendency to express issues in brief statements. This can be good but can also mean the text loses important logical steps. Having too many lists may actually make things confusing, because you lose track of them all.
So, use lists as a tool in your writing toolbox but be aware of overusing them in a text.


text:
What copyright issues could arise if I write a book based on one of my articles?
If I publish a 187 pages article extracted from a 244 (yet unpublished) page book, do I have the future right to publish this book without consent from the article copyright holder?
What if the book would become much longer than the 244 pages mentioned above?

Almost certainly not.

A 187 page article‽

@BenjaminMakoHill: There are journals which publish 200 pages and even longer articles

@porton: There are predatory journals that publish anything that comes with a check for USD$500. :) What field or journal are you thinking of?

You always need consent from the copyright holder. If you have published in an libre open access journal (e.g., CC BY licensed), you probably have it. Very often, copyright agreements people sign with journals (at least in the social sciences) allow authors to republish article content in books and dissertations. If this is what your agreements say, you already have that consent. Sometimes, you will need to ask for consent but, in my field at least, it is usually given.
Generally speaking, book publisher are also OK publishing books that contain work previously published in articles. That said, I think your example of trying to turn a 187 page article into a 244 page book is unlikely to fly.
For one, acquisition editors at scholarly publishers are fundamentally interested in selling books. One thing they think about is whether or not there is a market for the book. If a book proposal describes work that is already published in journals, editors will want to see what the book adds on top of the existing published work. It's going to be hard to show that in the example above where 77% of the book is available verbatim elsewhere.
Book editors (like judges in copyright cases) are not robots. Intention and acting in good faith matters. If it looks like you are trying to game the system to score extra publications or extra book income without much extra work, people will notice and do what they can to stop you. Since, editors have a lot of power, that will often be quite a lot.

If you have published in an open access journal, you already have it - not necessarily. Some OA journals (especially predatory ones) do require copyright transfer, and they may retain some rights (like exclusive publication).

Good point. I've edited the sentence to make it clear that I was referring to libre open access and made the statement more tentative.


text:
How to get back to my previous workplace after a prematurely severed postdoc (USA)?
I was hired at a postdoc at a national lab. However, the postdoc was a total failure and mainly for reasons that were out of my control. First, there was a coding / computer science part that was occupying most of the postdoc, but all the challenges foreseen in this part of the project were actually due to a super trivial error in a library. Fixing that ate up 75% of my project. Second, the code shouls have been validated against an experiment but the experiment was late by like one year and a half. So I was there doing nothing and my PI seemed unable or not keen enough to redirect the activity. Unfortunately, in a lab like that and in a group like that, I had no control on funding to do that myself.
Some people from many collaborating groups, including the one paying providing the money, were start asking questions / complaining about the situation. Therefore I decided to quit as soon as I found something else (6 months into a 2 year postdoc). That was my dream job, but the project was overtly failing and it was feeling that I would have been fired soon anyway if I didn't quit.
My feeling turned out to be probably correct, as the main PI, the one who wrote the project proposal, left the place soon after. Three are the possible reasons:

the higher-level management didn't forgive my PI for my departure: I was strongly wanted by my group and my academic track is already much better than my PI's (it was a stupid error on my side to accept an offer from someone with such a poor resume, but I was pretty unexperienced back then).
the management ackowledged the failure of the project and fired him (he wasn't the main person to blame, but he was still the one who proposed the project and who was putting his name and face on it)
he decided to resigned and change field: this is the official version he wrote on his linkedin profile, but it is highly unlikely that it the true version. When I resigned we sat down and give them feedback as to which profile my replacement should have had, and other long-term, project-related stuff.

I tend to absolutely exclude a fourth reason: my departure disrupted the project to the point that it failed and either he resigned because of this or he was fired. My duty (checking errors in databases and code-checking) was so trivial that a replacement could have easily be found, or some other grad student or postdoc could have taken over. Also, most of the what I am tellung you about (especially the super late experiments) took place before covid. So the pandemics is not a credible reason.
This is the story. However, that lab is still my dream workplace and I want to get back. Normally, it would be impossible since a postdoc resigning so prematurely would take all the blame. However, my PI also prematurely left, which (1) is a big indicator that something was wrong in the project and (2) that this became blatantly clear to the management.
Given this, I wonder how I could do that. All the closests colleagues are not accepting my friendship on linkedin, which might indicate that they have resentment towards me. However, the higher level management (who know me), are accepting my requests.
The best strategy would probably change group. Other groups in the lab know me and they sure know how I left. The question is: should I find someone in the old group justifying the decision to leave to a potential new team? Should I find out in some way what really happened (i.e., why the main PI left) and bring that forward as a good justification as to why I left? How to approach in general the managers to make them know that I would be more than happy to be back on a more sound project?

So how much did you talk to the group management well before you left?

I gave them advice on how to redistribute the few work I had to do or on the profile of my replacement and about the issues of the projects (which were the same critiques they were already receiving by senior employees and partly from the sponsoring team). I never targeted or told something bad about anyone specific. They also asked me if I was available for future technical support if they needed, which I accepted in written. (Apparently) we parted cordially.

By the way, it was clear to everyone that I out talks were a mere formality. They wanted to develop a code that they found out they had already and compare it to an experiment that was never done. We all knew that the axe was pending on PI and that funding (another BIG problem even before I left) would have stopped. I did my duty and resigned in as good as possible faith.

It was not your 'duty' to resign. Meeting with your group manager earlier on and discussing the issues with the project was a duty, and likely would have gotten you a different assignment.

Did you even read that the SPONSOR - not only myself - was complaining about these issues? That was 4-5 months before I resigned. Nothing changed and PI lost his job. My postdoc was funded within that project, which is why I couldn’t get new assignments even if I was proposing new ones since the first month into the postdoc. We barely had the money for that project, changing assignment was completely out of question. They even told me to do what I proposed in my free time.

Fair enough - not everyone keeps in touch with their manager (not PI), as I well know. Finding other work for a good postdoc is usually fairly easy though, at least in my experience. As for 'duty', you used it in a comment above: " I did my duty and resigned in as good as possible faith".

‘’ Finding other work for a good postdoc is usually fairly easy though, at least in my experience.’’ It depends. Where I am now I have almost total control on all topics. In a (weapon) group of a (weapon) lab, changing topic was totally out of my reach. For both funding and ‘red tape’ reasons.

That’s why losing my PI/manager would have been a tomb stone even if I didn’t resign. And he lost his job because he was fired. I know for sure that he had long term plans there  (for personal reasons of my PI, which I am not going to discuss). I have always taken the lead of my research, both in my PhD as well as now (I believe that’s my main strength), but in that situation I was on a sinking ship.

Was the PI actually your line manager? Don't confuse those two roles, they are usually quite separate at a US national lab. And you continue to presume that your PI was fired, which takes a lot of doing at a US national lab.

"I did my duty AND resigned in as good as possible faith". And means that I did mi duty (doing my job, proposing new directions) AND when everything failed I left.

He was my PI and scientific advisor. I can’t know for sure if he was fired but I know is that he was hired as he was considered and one of the few experts on the project and he left. In the meanwhile I was doing nothing even if I raised the issue, proposed new directions in the first 3-4 weeks and even if I didn’t raised the issue it would have still been clear (from our multi-weekly meetings) that I was being paid to stare at a screen. Still nothing changed. I left and in my new place I took over all the projects in my area, totally rewrote them and produced 3 papers. How can I be blamed?

[continues] and even if I had a share of the blame, how does this answer the question? I.e. how should reapproach the lab on some new project, also considering that many colleagues didn’t blame me for leaving (quite the opposite) and the PI also left the project and the lab (either for his or management’s decision)?

Even more: I read from your profile that you're in ABQ, which is a fairly good hint as to where you work. Have you never heard of stories like mine? There are many reports like this among postdoc and interns, even if I still acknowledge that most people generally have superb careers there. Which is why getting back is almost an obsession to me (together with my love for the mission). If I sniffed even the smallest chance to adjust my postdoc I’d still be there. For external reasons or maybe inexperience I couldn’t. Still it is the only occasion where I couldn’t manage to produce good science.

I did half of my PhD work on my initiative, in addition to my official assignment, I decide everything which is of scientific nature where I am now (the manager only takes care of funding and set the general field of projects). I can’t say I lack initiative. I have a quite an important network so I couldn’t even say that I am weak on a communication standpoint. In that group and in that project it just didn’t work out neither for me nor my PI.

It may be the case that the bridges are burned and there's nothing you can do. You should make peace with this as a possible outcome. While this may be a dream job, there are other dream jobs you can find. You may also want to consider that you may have an idealized version of what working at this place could be like, but some of the structural issues that led to the failure of your first postdoc could still be present and manifest themselves (perhaps in a different way) if you return. You may find that it's better for your mental well-being if you move on.
However, working under the assumption that you are going to re-apply, here are my thoughts.

Do not say
anything negative about your former PI, be it in your written materials, during an interview, or just chatting with people informally. First, focusing on negative aspects of a former employer while applying for a job is almost always a red flag against you, because the people with the power to hire you are going to picture you saying the same things about them. Second, as you've said, you have absolutely no idea what happened with this PI. If it was an ugly situation, you do not want to get caught in the middle of it. Stay professional, and if asked comment only on your role in the group. As far as you know, you have nothing to do with why your PI left (and why should you, it's not really your business). That is the truth, and saves you having to get involved in what is likely a very delicate situation.
It is not worth your time to speculate as to why the PI left. Ultimately it is irrelevant; that is their story.
In your written materials (cover letter, CV, research statement, etc), I would not go into too much detail about your history with this place, and focus instead on the future: what do you like about the culture, what research do you think you can accomplish at the lab, why is your background a good fit.
You should prepare an answer for the question "why are you interested in working here again?" This could easily come up in an interview. You have a fine line to tread here, since as stated above you don't want this answer to focus on things you did not like about your former PI. I think you have to acknowledge that you left, but you want to be clear that the reason you left is specific to your working relationship with the PI. (You want to implicitly tell them that you aren't going to end up leaving for the same reasons). But, again, you don't want to focus on the negative. So you should quickly move on in your answer to the reasons you would be excited by the new position. Here is an example of what you could say: "In my previous position here, working in X's group was not a good fit because our interests were not aligned, and I decided to pursue other opportunities. However, I loved the overall culture of this lab and would be very excited to work on Y project, which overlaps with my interests A, B, C."
The "anecdotal" pieces of evidence you present, like LinkedIn requests, are not very convincing one way or the other as to what people think of you, and you shouldn't overthink it. It could be that people in the lab aren't checking LinkedIn very frequently. It could be that the senior people just routinely click accept on requests and don't think about it. More to the point, whether or not people like you is not really relevant. What matters is if they think you will be a good fit for a job opening they have.
You could try to reach out to former colleagues there to see if there are jobs. I would not be pushy about this. Just a short email like "Hi X, Do you know of any job openings at the lab? I am interested in re-applying." Or, "Hi X, I just wanted to let you know I am interesting in applying for Y position, is there anything you can tell me about it?" You may find someone points you to a posting, or you may find someone tells you about some kind of position they want to fill that hasn't been posted yet. You might also hear nothing. It's not a bad idea to try to use your network. But don't expect anything and don't be too pushy, because it could come across badly.
At the end of the day, nothing is stopping you from simply applying to another job at that lab and seeing what happens. If they think you will be a good fit for that position, they will see your application and you will move on to the next round. If not, they won't hire you. That's ok. There are so many factors that go into a hiring position, including their needs (which are totally out of your control), so you can't even conclude from a rejection that they wouldn't like to have you back in an ideal world. These things happen, and you can find another good job.

I agree with most you said. Some comments: "It may be the case that the bridges are burned and there's nothing you can do. You should make peace with this as a possible outcome." The bridges are certainly burned with my previous team, but the lab has more than 10.000 employees, tenths of divisions and hudreds of groups. So I don't think I burned bridges with ALL the institution. [I continue in the following comments since I cannot split paragraphs].

"You may also want to consider that you may have an idealized version of what working at this place could be like, but some of the structural issues that led to the failure of your first postdoc could still be present and manifest themselves (perhaps in a different way) if you return." I know this as a fact, as I have heard many storied like mine. However, now I know which divisions are more susceptible to this kind structural issues.

"Do not say anything negative about your former PI". Rather than badmouthing my PI (as I have said, he put the face, but the real blame was on others), I was more referring to say what went wrong in the project, if asked about it. Just the fact that my PI lost the job soon after I left already says a lot. I don't need to add anything specific about him.

"While this may be a dream job, there are other dream jobs you can find." There are just three labs in the US that deal with that kind of job, this is the big issue. There are other labs in other countries but it is virtually impossible to get in without being a citizen of those countries.

You could try to reach out to former colleagues there to see if there are jobs. I would not be pushy about this. Just a short email like "Hi X, Do you know of any job openings at the lab? I am interested in re-applying." -- That's probably the best way to go. Some encouraging aspects: (1) I was previously warned about this (structural) risk before starting, (2) many employees where solidal with me when I left, (3) I quit a project that was already heavily criticized by many (including the sponsoring group) for being stalled and unclear in its goals.

To sum up, it is a dream place if you are lucky find the right mentor, but is kind of a coin flip. I have heard of many brilliant experiences, but also of many people leaving after terrible experiences such as mine.

@casper That all makes sense. It's a shame you've had such a difficult experience. I'd still stand by everything I wrote. One thing I didn't think of is that you'll probably be asked on the application form if you've worked there before. Because of that, you might want to have a sentence or two in your cover letter to explain why you are applying again. Just keep any explanations short and don't let them overshadow your credentials and excitement about the job, and don't say bad things about your former PI. I wish you luck with everything.