text:
Should one list incomplete degrees on a CV?
When applying for jobs after my PhD, should my CV include an incomplete degree I read towards years ago? It's a field completely unrelated to what I'm doing now. However, before my final year when I started getting sups and failures by the dozen (my reason for quitting) things actually went swimmingly. I worked with a renowned professor as an undergrad research assistant for a spell and even published a paper (on my own) during that phase of my academic journey. I didn't get a certificate out of it, but I nevertheless feel I honed some valuabe skills then (and of course I have a transcript listing the passes and failures).
I have since moved onto a completely unrelated humanities field. Should I mention the incomplete degree on my CV? If I ignore it, prospective employers might wonder what I did for three years of my life, surely? Should I list my science publication on my CV when it is irrelevant to what I'm doing now? Does quitting and switching tracks make me look flighty?

Don't omit it. Changing your mind at some point during your education or your career is nothing to be ashamed of. Just make sure to put it in a way that does not imply that you actually got the degree.
Not listing it would be an error in three ways at least:

experience even in unrelated fields is always valuable;
if you omit that stint, there will be a hole on your CV, and you will have to explain it (so you'd better mention it upfront);
you got a publication from it, so it was actually a successful experience, even if you didn't complete your degree

In fact, my advice would be to always list what you've done on your CV, even if it is not an academic activity. Even if you spent two years traveling and selling onion rings on Australian beach grill house, put it in your CV. The pros outweigh the cons (and if that experience leads a potential recruiter to turn you away, ask yourself: would you have wanted to work with someöne who has such as narrow view of life?)

+1 Explaining career gaps is often more difficult than explaining career shifts.

Changing fields in and of itself does not make you look flighty—many faculty members have changed research fields and even academic departments during the course of their careers, and it doesn't make them look flighty!
What would be a problem is not having a valid reason for making the career switch. Struggling with a major in a science field is not a big deal; however, the fact that you managed to publish a scientific paper in that area actually represents a significant degree of accomplishment (particularly if you were an undergraduate at the time).
Moreover, ignoring the degree on your CV could come back to haunt you if it is discovered later on, as "fudging" the CV is often grounds for termination for a position, even years afterwards. So I would not try to "hide" this. Instead, I would make sure that I have a logical and convincing explanation for that period of your life: why did you choose to start in that field at that time, what led you to leave it, and what lessons did you take from the experience.


text:
Questions about contacting a professor for getting PhD
I have contacted a professor about the availability of a PhD position.
And I got the following responses:

I would be interested to explore the opportunities for you to come and complete a PhD in the Precision Livestock Management group that I lead. I have attached a formal application form for you to complete. One of the issues that we will need to address is funding. I do not have any current direct funding, however, it is possible that depending on the project area I could seek some indirect support from the University to waive the overseas fees. We would still need to find funds to cover your living expenses. Do you have any opportunities for funding to support your PhD?
I would also be interested to hear what areas of research you would more specifically like to focus on that might relate to precision livestock management?

My Response:

Thanks for your message and consideration.
Actually, as you may know finding the financial support is not simple, usually. Honestly, I am not so optimistic to find one. However, I will keep eyes to find any financial support.
Herewith are the topics that I would prefer to do the research on them:
      .
      .
      .
Besides, in the case you have any suggestion about a topic please let me know.
To complete the application form I have to attach the research proposal. Thus, I would be grateful if I could have your confirmation for the topic.

Then, I sent him a required information and got the following answer:

I will give some thought to possible project areas. In your initial application you will need to say that you are applying for a full fee-paying place. We can then explore options for securing funds for a project.

Actually, it is my first serious contact with a professor.
Does his response include any sign that I may get the position?
How serious is the position?
Should I count on this position?
He asked me to fill in the application form. Am I supposed to send the application form to him or the admission office?
He told me, he will give some thought to possible project areas. One of the required documents for application form is the research proposal. Should I wait for his thoughts and write a research proposal based on that? Should I follow up his thoughts?
Within which timeframe should this procedure usually be completed?

Do you have any opportunities for funding to support your PhD? — The correct answer is "Yes. You will pay me."

Usually, "I do not have any current direct funding" should be read as "I do not have any current direct funding FOR YOU".

What country is this professor in? In some countries, being paid to get a PhD is more often the exception than the rule.

This doesn't look very good. The guy is happy to take you on, but requires that you pay full tuition fees for your studies and is only willing to “explore options for securing funds” after you do so. This would be expected at undergrad level, but for a PhD it means either he is not very interested in you, or he doesn't have funding but is not willing to decline a potential student. In any case, it doesn't look good.

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text:
What does YEAR: NNff means in research papers? eg 1965: 47ff
I am reading a book called Foundations of Statistical Natural Language Processing, in which there is a section called further reading. It states the following:

Chomsky (1965: 47ff, 1980: 234ff, 1986)

I am not able to find any paper of Chomsky written in 1965! Any help?

"I am not able to find any paper of chomsky written in 1965": see the bibliography at the end of the book. It does not refer to a paper but a book.

"ff" stands for "and following" so in your case it is page 45 and following pages that are indicated. It should be used when no stop page can be given. The abbreviation comes from the latin for page foilum plur. folia. Originally one would write page 45f to indicate just the following page, i.e. "45-46". The two f's indicate more than one page so "45 and on".

what does 1965 stands for ?

That is the publication year of the work being cited

@krammer as jukka said, I searched the bibliography of the book and there is a book written by chomsky named "Aspects of the theory of syntax"  written in the year 1965

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text:
Does ACM have a style guide for authors?
I am writing a paper for an ACM transactions publication precisely using the acmsmall format. However, I am yet to find a comprehensive Do's and Don'ts for writers with regards to style. For example, I've seen some papers say, "in Equation (5) ..." while others abbreviate it to "in Eqn. (5) ...". I have also seen some papers merely refer to equations by their numbers i.e. "in (5) ..." as is done in the IEEE. I've even seen these used interchangeably.
The first case is correct though, as it was used in a sample paper provided, however, are Eqn. (5) and (5) acceptable equivalents?
There seems to be consistency in referring to figures and tables though: figures are always referenced thus "in Figure 5 ..." and never abbreviated, for example as "Fig.".
At the moment, I'm just picking styles from already published papers which I'm not sure is the best way.
So where does one find clarification on these issues? Which is right in the above cases mentioned?

My personal impression (which could be wildly inaccurate) is that few disciplines are as anal-retentive as the psychologists, who have published an entire book about how exactly to publish (the APA Publication Manual) that specifies everything down to where to place the periods and colons in the references. In any other field, I suggest that you don't worry overmuch. Concentrate on content. (In psychology, concentrate on calling people "participants", never "patients".)

I'm not sure what you mean by "writing a paper for the ACM". You probably mean that you're writing a paper for a specific conference or journal run by the ACM. In that case, said conference or journal will have its own style guidelines/style files.

You should take a look at the format that the ACM template gives to you, but there is no straight answer for an specific format. Try to focus more on the content (like they have advise you on one comment) that in the format. Actually I have seen in some ACM published papers that they put things like (considering your example):

In Equation 5... or
In Eq. 5 ... or
(put the variant you think here)

Consider that is one of your least worries, if you had some problem with the format the reviewers will point to that, but if the content is good is what really counts.
Good luck!


text:
A PhD student without an adviser
I joined "X" university (US) for my PhD to work with a specific adviser (Y). For 3 years, I prepared my background to work in Y's area (through education and research exp.). But now Y says that, "I am not sure if we can work together. I am not saying no but I can not say yes too."
During my admission process, Y told me that we can work together. And I made my decision based on this promise. Since everything worked out well, I did not feel the need to approach other faculty members from the department. But as a result, now, I am without an adviser. And Currently, my department is trying to patch me up in areas that are completely new to me.
This situation has forced me to start thinking about my options and I came across following queries,
a) should I graduate with a 2nd masters degree?
b) since I want to gain my PhD, do I need to explain my 2nd masters in my statement of purpose?
c) is 2nd masters going to raise red flags while being considered for the PhD admission in new university?
Any advice on (a), (b) & (c) will be really helpful. Thanks in advance.

Why can't Y work together with you? Has Y got too many students / too little funding / incompatible research focus?

I am not sure about the reasons. Y has 4 students and 2 of them are partially advised. During admission process Y told me that we can work together. But situation changed after I joined.

Definitely the first step is to get Y to elaborate on the reasons then we can provide better advice. Don't panic...yet!

Haven't you talked in 3 years with your advisor? It seems strange that this comes out of the blue. The problem I sense is that maybe he is not satisfied with your performance. Have you published anything? Have you something almost ready for publishing? Because 3 years for literature review, sound a bit too much.

I am not saying no but I can not say yes too — He is too saying no!  He's just unwilling to admit that, even to himself.  Wimp.

I am mystified: were things fine for the first three years ? or did you not have any contact with your advisor ? How could the situation have changed "after you joined" if it's been three years since you joined ? I do agree with @JeffE that the advisor is saying NO as clearly as they appear to be able to.

@Alexandros: Just to clarify, I did my masters in Z university and I published 2 papers during my masters that are exactly in line with Y's work (but with different adviser). And I was in touch with Y for last 1 year regarding the PhD position. (I joined PhD after my masters). So my question is if Y had not intention of working with me then why did they accept me?. When I applied I had admits from 3 universities. I chose X because of an adviser.

Maybe you can transfer to a PhD program in another university that has advisor similar to "Y", but is willing to work with you.

You joined "X" university and then "X" is not used again in the remainder of your post. I hate it when people do that ...

if Y had not intention of working with me then why did they accept me?

There are many ways to unpack this:

maybe Y did want to work with you, and then things didn't work out: funding, or mutual incompatibility, or interest changes. Stuff happens
Y could recommend you for admission as a competent student without feeling there was an implied guarantee that you'd work together. Maybe there are others in the department with similar interests.

As has been said on this forum many times, an advisor-advisee relationship is more two-way than one might think. There has to be a mutual fit otherwise even two perfectly reasonable people with mutual interests might not click.


text:
How to add a citation to a sentence that has parentheses at the end?
How can I add a author-date citation to a sentence that ends with parentheses? That can occur when using parenthetical remarks or when an abbreviation is introduced:

However, methane has a higher Global Warming Potential (GWP)(IPCC 2013).
Most environmental impacts were due to methane emissions (which has higher GWP factors)(IPCC 2013).

Having two parentheses next to one another sure looks awkward. Is there a "workaround" or should I work harder and restructure the sentences.
Update: I am writing my thesis and the university does not recommend any citation style.

This depends on the writing and citation style you are using. In APA you should use a semicolon to separate the citation from the acronym:

However, methane has a higher Global Warming Potential (GWP; IPCC, 2013).
Most environmental impacts were due to methane emissions (which has higher GWP factors; IPCC, 2013).

Source: http://blog.apastyle.org/apastyle/2013/05/punctuation-junction-parentheses-and-brackets.html

Thanks! Personally, I don't like how that implies a relation between the two elements in the parentheses. This may be quite misleading in some situations.

+1 for citing a style guide but... Eew that looks bad, for a guy not used to APA I definitely wouldn't read that as intended.

I understand your point. In those cases it may be best to recast the sentence like some of the other answers recommend.

I would make sure that, if you go with the two parentheses option, you put a space in between:

However, methane has a higher Global Warming Potential (GWP) (IPCC 2013).
Most environmental impacts were due to methane emissions (which has higher GWP factors) (IPCC 2013).

But if it visually bothers you, you can just set off with commas:

However, methane has a higher Global Warming Potential, or GWP (IPCC 2013).
Most environmental impacts were due to methane emissions which have higher GWP factors (IPCC 2013).

You could also rewrite the sentence if you want to make it a bit clearer you're not citing what is effectively your parenthetical:

The Global Warming Potential (GWP) of methane, however, is much higher (IPCC 2013)
Methane emissions, which have higher GWP factors, caused most [of the] environmental impacts (IPCC 2013).

So you would say that introducing an abbreviation for the first time in a manuscript is also acceptable like this?

It will depend on your style guide. I'm not in the sciences so perhaps someone from there could clarify if it's acceptable for them (it would generally be in the humanities)

If you are citing word-for-word, you can (and should) use quotation marks, like

"However, methane has a higher Global Warming Potential (GWP)" (IPCC 2)

Otherwise you can rephrase the sentence to remove the parentheses from the end of the sentence

Might look awkward but you're on the money.  No need to restructure.  After all, it's not because of you those sentences end in parentheses.


text:
Copying a proof almost verbatim
I am writing a math paper which has an electronic supplementary document. In the supplement, I want to put a proof of a lemma. This proof is copied and pasted from my previous paper and I have changed some symbols (eg. H becomes X) to put it in context.  Is this allowed? I have written on it:

Proof (proof modified from Proof of Theorem 1 in [paper]).
Blah blah...

Is this plagiarism or not? It is only in the supplementary document (which is published online) and I have cited.

Nope, at least as long as you give the reference and do not overstate your modifications to it. Avoiding repetition at all cost doesn't really help science.

I agree this is not plagiarism if you make it clear that is an essentially verbatim extract from your previous paper.
However, it also seems unnecessary, especially if your previous paper is readily available online.  (And if it's not, why not?  Consider posting it to arXiv or your personal web page.)  In such a case, I would probably rather just refer the reader to the previous paper ("see Lemma 4.3 of [8]").  If you feel it's necessary, you can say something like "changing all occurrences of H to X", but I'd expect that a mathematical audience will just do that automatically without needing to think about it.

Thanks. The previous paper is online.. I didn't want to refer the reader to it because I already have done that a lot, and the lemma is quite important to the paper so I wanted to show a proof they can easily access.


text:
How can one differentiate between Dr. (PhD) and Dr. (MD or DO)?
Reading the question posted here left me with a more general question:
Given the professional title and name: Dr. (First Name)(Last Name), is there some way to differentiate between the holder of a philosophical doctorate and a medical doctor? Wouldn't it be more appropriate for a PhD holder to have the title (First Name)(Last Name), PhD?

You can't immediately tell from the title, but then titles are not typically used by an individual to broadcast their occupation - we don't have variants of "Mr" for plumbers, bank managers, or rock stars - despite their very different occupations. Rather, the title is to be used by others when addressing that individual, in order to signify a degree of respect, typically for a particular level of training, qualification and responsibility, or else for a particularly respected position in society. Even the term "mister" is a meaningful sign of respect that historically would not have been as widely applied as it is today - the ratchet of etiquette has gradually eliminated everything below it.
The actual title "Doctor" means "teacher" (from Latin "doceo", "I teach"). This title is more often more relevant to PhDs than MDs, so you probably have your suggested solution backwards. That said, the solution is really neither necessary nor appropriate. Much like "Master" (from Latin "magister", in this case "teacher"), "Doctor" signifies that an individual has not only gained enough competency to practice in a particular field, but has developed enough expertise to instruct others. An individual who is sufficiently qualified to practice but not teach would historically have been known as a "journeyman", roughly equivalent to "professional".
In short "doctor" refers not to a field of expertise, but rather to a level of expertise.
Incidentally, most UK surgeons drop their title of "Dr" and revert to "Mr" after joining the Royal College of Surgeons. I've heard through a friend of at least one surgeon who reacted quite angrily at being addressed as a mere "Dr", which in such circles, due to a collision between traditional titles and modern medical training, could be unkindly translated as "trainee".

I think the Mr should be spelled out after joining the Royal College of Surgeons ie. Mr.Smith -> Dr.Smith -> Mister Smith

@user288447, do you have reference? I can't find anything on that.

Unfortunately not, it may just have been convention in one hospital that I was in several years ago.

You can't. That's why there are numerous jokes in English-speaking culture about whether someone addressed as "doctor" is a "real" doctor or not. Medical doctors are supposed to be the "real" ones in the jokes.

Regarding the jokes, I recently heard introducing a speaker (MD) in a conference "and then he became a real doctor when he did his PhD in...".

Also: 'not that kind of doctor'

Well, you could technically look at his degree on the wall :P

According to http://www.peoplefinders.com/search/searchpreview.aspx?searchtype=people-name&fn=doctor&ln=smith&mn=&city=&state=, there are 2 people named "Doctor Smith" in the US.  Do they have PhDs or MDs? I don't know.  Their first name is Doctor.

@Emory: Following the example of Major Major, they should enroll in a university and see if a computer error will summarily grant them a doctorate.

Ironically, it is neither MD's, nor PhD's that are the true, original "Doctors", but rather DD's.  Though try convincing anyone of that today ...

@RBarryYoung: What is a DD?

DD is Doctor of Divinity.

Umm, I'd say the MDs aren't the real doctors... (ducks before being flamed!)

To the people who reviewed my suggested edit: I wanted to add it as a comment, but at the time I did not have sufficient reputation. I also don't see how it deviates from the initial answer. the intent was to build on the "You can't." part of the answer.....................original edit/post: " That's why whenever someone is presented/introduced, especially in writing, it is as "Dr. Joe Smith, MD" or "Dr. Joe Smith, PhD". They are differentiated by putting the type of degree at the end of their name."

@TrishLing, you added nearly as much content to my answer as there was originally. That's generally not done around here.

@Bill Bart, of course, your answer is very short, as was my comment/answer ( they are approx. the same length really, 2 sentences each). What did you expect? I did not mean to offend or anything, but as I mentioned earlier, I did not have the ability to comment at the time, but I wanted to add to to your answer....what should I have done? Can you really say it was a bad edit/comment? I don't necessarily say it was wrong to reject the edit, but I do think your reason for rejecting it was erroneous, as it did not deviate from the original answer- in fact it added to it.

@TrishLing, by adding the paragraph to my answer, most readers will think that I wrote it. You should have added your paragraph as a separate answer. It's not that your words were wrong, they just weren't mine.

In the United States, in spoken address, both are called "doctor."
For personal correspondence, both are addressed as "Dr." as with an invitation addressed to "Dr. and Mrs. Smith." (Or maybe "Dr. and Mr. Smith." If they both hold doctorates, it is "Drs. Smith."  For a couple with different family names, use "Dr. Smith and Mr. Brown.")
For professional correspondence, both are addressed by name and degree, as "James Smith, M.D." or "Bob Brown, Ph.D."
Since the distinction is only relevant in professional interactions, there really isn't any ambiguity.
If you are speaking to a medical doctor professionally, you will know it by the setting, and you still say "doctor."  If you ask for medical advice at a cocktail party because someone was introduced as "doctor" you deserve anything you get!  I've been known to say, "I'm a college teacher type doctor, not a take-off-your-clothes doctor."  That usually sends the message and often gets a laugh.

I am not a medical doctor, but I often work in hospital settings interacting with both patients and medical doctors so the setting is not always informative.

I know a microbiologist and a physicist who work in a hospital.  Their degrees appear on their ID badges, as do those of medical doctors.

This was edited by "Anonymous" to introduce irrelevant commentary about women taking husbands' names.  The commentary on the edit also incorrectly stated that more women than men earn doctorates.  In the United States, at least, that is incorrect.  From the 2014 SED: "Overall, women earned 46% of all doctorates in 2014."

I have seen the difference in the written form of their name;
One is Name Family, PhD. and other one is Name Family MD.
The same applies to the people holding Engineering doctorates such as Name Family, EngD. or holding doctorate in business such as DBA. Also, in different countries there are usually different doctorate titles (link) awarded.
But all of these people are called doctors.

I've seen it for dentists too.  Name Family D.D.S

@jonescb just look at the link provided in the answer, you can see more than twenty doctorate titles for different countries and different majors...

A medical practitioner usually holds a MBBS or MD degree or similar and - at a reasonable level of proficiency - membership of a professional body such as the AMA ( American Medical Association) or the RCP ( Royal College of Physicians) or whatever applies in their part of the world.
A holder of an academic doctorate ( PhD, DrPh, EngD etc) has researched a topic or problem within their specific subject in sufficient depth to have generated fresh insights or made a breakthrough or contributed significant new knowledge to the existing corpus.
Both have earned the right to be addressed as 'Dr'.
However, it would appear to me that one or two posters have been watching a few too many episodes of 'The Big Bang Theory' as I think the need to differentiate between the two very rarely applies except in a medical emergency.

In hospital settings where patients may be interacting with both medical doctors and academics, there is a need to differentiate.

The usual practical solution is "ask them."

In Germany, it is common to denote the subject area the doctor was obtained in, such as Dr. med. for medical doctors, Dr.-Ing. for engineers, or Dr.-rer-nat. (rerum naturalium) for sciences like chemistry.

Doctor means you have a doctorate. Simple as that, a medic can have a doctorate in medicine and thus be a doctor, but if you do not have the degree then you are not a doctor, you can be a surgeon or a licensee of medicine but you are just referred to as doctor out of colloquial use of the title based on historical rots and customs.

You can tell from the context, but without the context, you can't. If the context is obviously far removed from anything clinical, such as "Dr. xyz has written a book on archaeology of early Los Angeles", then it's obviously the PhD sense. If it's a clinical setting, including emergencies and simply asking for health advice, basically when someone's health is at stake, then it's obviously the MD sense.
Things can get more ambiguous in biomedical research, because I personally know some MDs (without PhD) doing research instead of practicing medicine, including some molecular biology professors. When a research paper that uses clinical samples says something like, "Samples were obtained after resection from Dr. xyz", then it really can be either MD or PhD or both. Some people in our field have both.
Anyway, I don't make too big a deal out of it because we in California are typically on first name basis outside the clinical setting (this includes medical doctors). When we PhDs and candidates (at least in CA) say "doctor", we also usually mean medical doctors, like in, "Our postdoc health insurance is so bad that I'm terrified of seeing a doctor", where "doctor" obviously doesn't refer to ourselves. Some states, including California, have laws forbidding anyone who is not a medical doctor to advertise themselves as Dr. something in order not to confuse patients.

There is no difference in spoken address ('Doctor'), but one is a Ph.D. and the other is an M.D.

The confusing aspect is that doctor connotes medical treatment to most people, not a doctoral degree. Anyone smart enough to have a PhD knows the difference. I would not want a PhD doing my surgery, nor an MD teaching me philosophy.

It's not an easy question to answer. Ph.D's who are professors are just called "professor," and research assistants with a Ph.D are called "doctor" by secretaries and students. Titles are never mentioned in academic papers.
It's different with doctors: Patients and nurses call them "doctor;" if they are also professors, which they often are, the are called "professor" since professors have a higher status than mere M.D.s, and when they write papers in medical journals they put M.D. after their names. When practitioners without an M.D. refer to themselves as "doctor" they are just called "frauds."
Things are much more interesting in Germany. I was treated there by a woman doctor in a University Hospital who was also a professor of medicine. Her title was Frau Dr. Med, Dr. Professor Mueller. Some Professors have three degrees, meaning that are called Herr (or Frau) Dr. Dr. Dr. Professor.

I have never heard medical school Professors introduce themselves to patients as Professor. In the UK holders of a Bachelors in Medical Science (BMedSci) call themselves doctor and it is not fraud.

Titles are never mentioned in academic papers — ...in some disciplines.  In others, they are mentioned quite prominently.

In French (maybe other latin countries too), but I don't know about English, you can make a small difference by adding ès : Albert Einstein, Docteur ès Physique.
Then twice in a row you have specified that he was a scientific doctor (not a medical one) and his field of research.

Hi Rucikir, welcome to Academia.SE. Your answer does not really answer the question. Basically you are explaining how to say Albert Einstein, PhD in French, which is not what the OP is asking.

Well, I just didn't know if it could be used in English, apparently not, so it was irrelevant. Thanks for pointing it out. Sorry.
But I'm not the only one to have done that, other answer about the German way.

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text:
How do I complain to chair if my advisor regularly writes to scam journals to get tenure?
My advisor and his PHD Students are writing regularly to journals published by a publisher, which is on Beall’s list of Predatory Journals. I emailed Beall and he told me that the journals were advertising as non-profit but usually publish if you pay them.
I am in US. So recently the PHD Student and advisor published to this predatory journal’s conference taking place half way down the world and obviously it got accepted. So my advisor approved the student’s trip to that country (almost 1500 $, so it had to be approved by chair), but the chair rejected it saying it’s not worth the expense.
Now I want to directly email my chair and point out to him about my advisor’s publishing record. I am angry that instead of publishing to genuine journals, my advisor (who I believe is incompetent but has good political clout in the university) is publishing to these scam journals and wasting university money to achieve her tenure requirements.
Since I am still working in lab, I need advice on how to approach my chair so that I can keep myself safe from possible wrath of my advisor and at same time negate the contributions of these journals for his tenure.
Edit 1: The conference listed Google Scholar as one of its sponsors, so I emailed Google and they told me they never sponsored this journal and will order removal of their name from the sponsors list. So yeah, these are all first rate scam journals and I have all these emails, if I ever need to communicate with the chair. I have done my investigation; I just need to get my results across.

just to clarify: you are also a Ph.D student of this advisor ?

@Suresh nah , i am an MS student doing thesis.

oh well this changes everything. I'm not sure what the protocol is here. My guess is that your relationship with your advisor maybe a bit less important than the relationship between a PhD student and his advisor. My advice below still stands for PhD students, but I'm not so sure about MS students.

writes to scam journals to get tenure — Um.  If there's even a small chance of that strategy actually working, you should move to a different department.  And tell the old department why on your way out.

I agree with @JeffE. If you have any concert about this practice, than you should have more concern about the overall competence of your supervisor and the department if they allow it. Just shooting your supervisor leg will not make you a good publication record of CV or produce any research result.

Get new advisor unless you already have way too much time/energy invested in this one. Respecting one's advisor is pretty dang important. I'd avoid getting caught up in the politics--by the sound of it your advisor will be better at that than you are (and if not, is it really worth it). Steer clear, be kind, put yourself in a better situation. Esp since you are just a masters student don't get all caught up in this BS.

Your relationship with your advisor is extremely important for you getting a PhD. I would only contact the chair if you are absolutely certain that you would be able to find a new advisor if things went bad between you and your current advisor. When her tenure comes up for review, someone on the panel will know that these are scam journals. The fact that the chair has already denied one of her expenses means there is likely a red flag in her file (metaphorically). Now if she forces you to publish in one of these journals, you should absolutely complain, but don't complain about what she is doing with other students unless you think it is worth losing your advisor completely and creating enemies in the department. You can talk to the student who actually was going to go to the conference suggest he complains, but ultimately I think that is his responsibility. So again, refer to the first point; make sure you have an escape plan so to speak, and make sure that you are OK with potentially not earning your PhD because you stood up for yourself.

I did let the PHD student know that he was publishing to an scam journal (in case he didnt know).He said he doesnt care as long as he gets to put an "journal published " entry on his resume. Apparently , he and my advisor are on same wavelength. I am not. So you are asking me to graduate and then go ahead and out him?

That is unfortunate, but trust me, when he is applying for jobs, at least in academia, everyone will know he published in scam journals, even if they aren't familiar with the Beall's list of Predatory Journals. The first test is "have I heard of this journal" if the answer is no, the publication will likely receive almost no weight. Stick with your own morals and let these two people fail on their own accord in the near future. It's too bad, he is either going into industry or that is a very short sighted move on his part.

my advisor worked in industry for significant no. of years before becoming prof, and this guy is most likely headed there because of connections .So yeah , these journals wont have any affect on his career in near future , which is kind of sad. "Pretend Research" along with connections seem to be the mantra, according to my advisor.

Also if you think you can find a new advisor that may not be a bad idea. Don't bad mouth your current advisor when doing so, but if you get along well and have similar research interests with someone else, go for it. Your advisor having a bad name might affect your future. If you really believe strongly in this, switching advisors might be a better move than complaining to the chair. Note at some Universities it's very difficult to switch advisors, at others it's fairly easy assuming there is another professor who wants you.

honestly i have lot of malice towards my advisor(read my past posts) and i was just building up a case all these months to show his true colors to others. And this may be my opportunity.I was thinking of sending an anonymous email to chair but i dont know if that is the best way to go.

Yeah, not the best way to go, although I understand your general annoyance. I'd say, if you don't want to switch advisors, collaborate with other professors on your committee. Build strong relationships with them. This way you can get the mentorship you need from people you respect without offending your current advisor.

It sounds like the chair may already be aware of the situation, if they are not approving travel to said conference.
Typically those in the field, especially those who've been around a few years, and especially those in positions of authority in universities, will know which journals/conferences are high quality and which are not. These are generally backed up by various metrics (e.g. impact factor), which try to quantitatively assess the quality/impact/popularity/etc.
Academics are often measured on such metrics, rather than simply number of papers published. A single article in Nature, for example, would give significantly greater benefit to one's publication score than a dozen in the International Conference for Scamming and Profit. I would hope your university uses such metrics in some way or another, and from what I've seen, more and more universities are doing this, with a variety of standard/external and customised/internal performance metrics.
If you really feel you must make a point of it, I'd suggest simply having a discussion about the List of Predatory Publishers, rather than a specific discussion about your advisor.
You may find the chair is well aware of the list, but has their hands tied by university policy. Or they may be enlightened by the list and be able to have the tenure policy changed to exclude or reduce the benefits of such publications.
Just remember it's not your job (and is someone else's job) to assess the advisor's academic performance, and you want to be careful how you come across if you try (a) tell them how to do their job, (b) make academic assessments of tenured staff as a student, (c) heavily criticise your advisor, which will likely be ignored if there's any suggestion of an existing grievance between the two of you.
For all you know, your advisor and the chair may be close friends, or at least closer colleagues to each other than "some unqualified upstart of a masters student!" (hypothetically their words, not mine :P)

but isn't spending univ. research funds on publishing to scam journals just to get tenure, an waste of public university research funds?Also as a student of univ ,if a faculty is trying to misuse the system to their advantage by following questionable practices , how is pointing that out inappropriate?

I didn't say it was inappropriate, I just said it may not be effective for you to do the finger pointing, for a variety of reasons.

Another tack you could try is getting data on the entire university's publications, and how many of them are going to predatory publications. It may be quite common, and something to be brought to the attention of the council/board/whatever rather than dealt with at an individual level.

i did verify that .Seems my advisor is the only person to publish to that press. I have also found that the press originates from same asian country as my advisor . So there's that.

You definitely don't want to bring that up (nationality)

@MHH but isnt it kind of an uncanny coincidence? How come my adivsor is the only prof. in univ who is publishing to these journals and they coincidentally seem to originate from same country.  Kind of strange.

no not strange, cultural norms may be different amongst different countries, but if that is the case, you need to let her bring that up in her defense. That is something that doesn't need pointing out.

@MHH How come a prof. who did PHD and MS in US and worked in industry is US for almost half a decade is still not used to cultural norms of US?Cultural norm seems to be a poor defense here

Not saying it's a good defense, just saying it's a really bad idea to bring this up. I really don't see any benefit, and there is a lot of potential for it to make you look not so great.

Do not bring it up explicitly, wetlab is right. You obviously are not subtle, so I don't trust you to do it without offending someone. :) (jk I don't really know if you are not subtle that was my attempt at a joke :)) You need to be careful of separating what you think is true, on one hand, from what is important to say to people, and who to say it to. No matter the answer to the first, the answer to the second and third are rarely 'everything' and 'everybody.' Caution beats valor, especially for the lowly masters student. :)


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Can I host my published software at Dropbox?
I am about to publish a software in Bioinformatics Journal. May I keep the files for online availability at Dropbox as public link.
If that's not a good idea what are the options?

Github is far more suitable to host code.

On arXiv, as "supplemental material".

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

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

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

If you did not already do so, you can see whether the journal allows you to publish software as a supplemental material or similar for your publication. Even if they do not state so on their site, they may still do it on request.
In addition, I would suggest that you publish your software on Github, Sourceforge or some other repository designed for publishing software. This way, you can easily update the software, others can contribute to your software and so on. If you do this, I recommend to add a link to the repository in your paper (or the source code attached to your paper), so people can obtain the latest version.
I am no expert on Dropbox, but it does not seem as long-lasting to me as most dedicated software repositories and probably has no special features for hosting software.

I would strongly advise not to use Sourceforge. Their ethics (or rather, lack of) leave a lot to be desired.


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Independent research and license usage
I want to  continue working on the research I used to work on when I was in school.
The thing is that I am not a student anymore, and I also do not work for the company that works on the research project I used to work on. It used to work on the research project by myself while I was in school (a little help from professors), meaning I can probably work/project on it by myself.
My question is that since I am not in school anymore, do I need to concern the license issue as commercial? All I want to do is do my personal/individual research project and submit a work to academic purpose, such as journal or conference. I see some software or programming library I am using say "Acedemy" or "Commercial", and since this is for the academic purpose, I am not so sure which one I need to follow.

In the absence of any specific information, this can only be a solicitation of opinion.

@EnergyNumbers yet, the answers currently given are not opinionative… I think it's a valid (and common) question, even though there is no single definitive answer

You need to read the exact terms of the licenses, and see what they call “academic” or “commercial”. There is no general definition, these types of licenses depend entirely on the software publisher.

In adddition to @F'x's point:
As your situation is different from both the usual academic and the usual commercial situations, maybe you could email the developer/author/maintainer of the library.
Whatever the license says, software licenses are almost always non-exclusive*. That means whoever holds the copyright to the software can grant you another license that covers your use of the library. This can be as easy as an email saying "go ahead and use it under the terms of the academic license" and would give both sides legal certainty.
* Or at least, software with exclusive license usually doesn't make its way legally into the public. Although one could think of an exclusive license granted to the public...


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Presenting a paper at a conference/seminar that is currently under review by a journal
Do you think it is against the academic code of conduct to present a paper at a conference or a departmental seminar that has already been submitted to a journal for publication?

In mathematics I do not know of any such academic code and I see this and do this myself routinely.

What is your purpose? Do you want that it be published as a conference paper if it wasn't accepted in the journal? Otherwise, note that you might pay double for your paper in both journal and conference.

There are two aspects to your question:

“Duplicating” a publication by having both a conference paper and a journal paper about it.
This has been discussed here before, and a short summary is that this usually not a problem: apart from Computer Science, where conference papers have a rather different status that in other fields, “publishing a paper does not normally prevent you from presenting your work at a conference”.
Presenting as-yet-unpublished results in a conference/seminar.
There's nothing wrong about that at all, and I think more people will actually enjoy you discussing recent results rather than old stuff. Customs, here again, depend on your field: I've seen more people discuss unpublished results in physics, and fewer in chemistry… but even in fields where it is less common, it is not forbidden.
One thing to note: if the paper is not yet published, it is probably polite to inform your co-authors (or ask for their permission, depending on your relationship) that you are going to present it at a conference. At least, that's what I do (and expect my co-authors to do).

Informing/asking permission from co-authors is IMHO not only polite but necessary: if both paper and presentation cover the same material, the author lists should be the same as well.

@cbeleites yes, if the presentation content is the same as the paper… but if the presentation is reviewing many things, including the paper, the author list might be different.

I didn't find what's the problem with Computer Science, wish you give a direct link to the post which discuss it.

In addition to F'x's answer:
it may be good to tell the audience that the corresponding paper was submitted/accepted and give the corresponding reference, so they can look up the paper once it is out.

In addition to F'x's answer:
I not only don't see this as a problem, but I think it is a great thing to do! By presenting a submitted (or not yet submitted) paper at a conference, you get instant feedback by a self-selected sample of people who were interested enough in your research to attend you talk - basically, the mother of all peer review. Of course, it won't be as in-depth as the reviews you get from the journal submission, but it can still be extremely helpful. And you can (and should) use the feedback from the conference to improve your submitted paper in the review process.

I do not know of any journals that do double-blind review. Having said that, here's a related scenario where there might be a problem.

You have submitted a paper to a conference that requires
  anonymized submissions, and you give a presentation at a public
  seminar on the material while the paper is under review.

Here, while there isn't an issue of misconduct, there's a sense of actively breaching the double blind guidelines. Again, there are caveats here: some venues are more relaxed about this than others.

I don't think it's a breach of confidentiality… otherwise, it would mean you're gagged from talking about your unpublished work, which is quite extreme.

How do you know the anonymous author is the same person who just happened to present the same result? It's likely the case. But is it really a breach of confidentiality?

The issue is one of intent. I've had this discussion before on this forum, while no one believes me :), in the communities I publish in such an act would be considered an intent to breach the double blind process. and yes, @F'x it implies that you can't talk about unpublished work, which is extreme and I don't like it !

While I think it is rarely an issue in the practical sense, I would still heed caution. Unless you are publishing your paper for open access, you are most of the time signing a publishing agreement with the journal and in so doing transferring copyright to them. While most journals have a liberal agreement when it comes to preprints, some do not. Hence, it is a good idea to check with your journal before you decide to publish something. Wikipedia has a helpful list of publishers and their preprint policies here.


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Financial Support
If I do have a sponsorship for continuing my masters degree, will that increase my chances of getting accepted, or is money irrelevant in admissions decisions? I am considering computer science or computational engineering graduate studies in the United States.

Admissions in the US are not necessarily need-blind at either the undergraduate or graduate levels, even if the university claims it is!
Especially at the graduate level, it is more or less accepted that ability to "self-fund" one's education, through fellowships and scholarships, or other arrangements, can be considered as a factor in admissions processes.

So if I am financially sponsored I have a better chance of getting an acceptance, right?!


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How to find out which math departments have a research group in mathematical logic?
I'm thinking to apply to PhD programs in math. I want to study mathematical logic. So I need programs that have mathematicians who do research in this area. I've searched the internet, the results were not satisfactory. The only list I've found find is this one
But this list contains only 9 schools (which are very difficult to get into!). I was wondering if anybody can guide me to some longer lists of schools and PhD programs that have expert(s) in mathematical logic?

I recommend browsing issues of the Journal of Symbolic Logic and looking up where authors are from.

Hopefully, some logician will come along and make some suggestions;  this is something where ultimately, talking to someone is the best plan.  That said, there's a reason that the US News list is so much shorter for logic than for core disciplines.  There really are just a lot fewer programs in it.

Jean Larson's list of set theorists (with school information): http://www.math.ufl.edu/~jal/set_theory.html Peter Cholak's list of computably theorists: http://www3.nd.edu/~cholak/computability/computability.html

Look for potential advisors, not PhD programs.

Berkeley has a Ph.D. in logic: http://logic.berkeley.edu/

I guess some logician is me. I don't know of any list of schools that have programs in logic, and it would be hard to keep such a list anywhere close to comprehensive---very few schools have more than one or two people in mathematical logic, so the list would change frequently based on whose hired/moved/retired recently.
Steffen Lempp keeps a list of logicians which, while not comprehensive, is pretty large, so the institutions those people are at is a good place to start.  Another idea is looking at whose spoke at recent logic conferences (for instance, the program for this year's ASL annual meeting, or the European equivalent, the Logic Colloquium).
Always, of course, if you know any faculty who are familiar with your interests (not necessarily logicians themselves), they may be able to point you towards some schools.
Also, note that there's no school with anything like a "generic" logic program---anywhere you go, your specialization within the field will be limited by whose present there. You likely have some narrower idea than generic logic that you're most interested in, so looking for people working in that area (or who've done work you think is interesting) is a good way to find schools. (You shouldn't obsess about this, though; you don't have to work in exactly the same area as your advisor anyway, and your interests are likely to shift at least a little over time.)

Although, Berkeley appears to have a strong logic subgroup of the math department.

Berkeley also has an actual separate logic track within its graduate program, with different qualifying exams etc.  I don't know of anywhere else with a comparable set up (though it seems CMU has something similar).  Obviously if you can get into Berkeley or CMU (and you want to study logic), you should go.  The OP pointed out that one might rightly want a backup plan.


text:
How often should my papers be rejected?
When submitting papers to scientific journals, it makes sense to aim slightly above the paper's level - after all, if you submit too high, you get rejected and can resubmit, while if you submit too low you end up just publishing there. Or so it seems to me.
An extreme strategy (which is equally impractical and evil) would be to make a list of all journals ranked from best to worst, and keep submitting to the highest ranking one that you haven't tried yet, until one of them accepts. With a strategy like that, the chance that the paper gets accepted in any particular submission is close to zero. At the other end of the spectrum, if almost all of your submissions are accepted then it's very likely that you're selling yourself short.
Now, it's impossible to know with any level of precision what's the probability of acceptance of a given paper at any particular journal. But it is possible to observe a general trend, and try to adjust your confidence up or down. Hence, the question:
If one is reasonable in their choice of journals, how frequently should their papers be rejected?
In other words, at what point should I start making a conscious effort to submit to better journals? At which point should I start submitting to worse journals?
For instance, my current strategy is to try and figure out how good a paper is, and first submit to a journal that's about the best that could possibly accept it, and then go down from that by a small but noticable margin. In a small sample size, about half the time the paper was submitted on the first attempt, and about half the time on the second, and so far I haven't had to submit anything three times. Hence, my papers get rejected around 33% of the time. Is this a reasonable frequency, or should I be more modest (or possibly more aggressive) in my choice of journals?
My field is pure mathematics, but I'm also interested in perspectives from other fields.

I don't think there's a right or wrong answer here.  Your personal "target" rate would depend on how you balance the competing priorities of "publish in the best journal" versus "get it accepted fast".  Different people will weight these differently depending on their personal preferences, career situation, the quality of the specific paper, etc, and both your extreme strategies could be valid in appropriate situations.

This also seems to apply to conferences, not just journals (in those fields where conferences are the main method of publication).

If you keep submitting your work to journals that are way too high for the potential impact or quality of your work, the editors of those journals may start to remember your name and have a special eye on you next time you submit, even though next time it might be appropriate to submit to such a journal. Take home message: don't start at Nature and Science every time you want to submit something.

The other factor is the type of work that you do.  In my area, there is the theoretical and practical community; the former likes proofs and the latter like to see experimental results.  They might not appreciate each other's work.  So getting published in the flagship journal of one will be difficult if it doesn't fit.  In other words, to improve your chances,  'walk like a duck, swim like a duck, and quack like a duck,'.

I think you're looking at this the wrong way: It's not a question about getting accepted or not, but of getting reasonable (constructive) feedback on your work. I posit that as long as you are getting such feedback on your first submission that leads to a noticeably better second revision (that gets accepted, possibly after another round of minor polishing), you're targeting the right level. On the other hand, feedback that boils down to "didn't bother to read, but doesn't look interesting enough" or "looks good, should be published as is" is a sign you submitted too high or low, respectively.

In other words, at what point should I start making a conscious effort to submit to better journals? — This is the wrong question.  The right question is: At what point should I start making a conscious effort to do better research?

@NateEldredge: You are very right, a lot depends on the personal situation. I thing that a general guideline exists none the less. There are also external circumstances: time used up by the journal, etc. For instance, the strategy "submit everywhere until accepted" seems unfair, even if it made sense from the personal perspective.

@JeffE: I'm sure you mean it in a constructive way, but it could sound a little dismissive. It goes without saying that everyone in the academia is trying to do the best research they can (or so it seems to me). But unless I throw away every result I get which is not at the level of Annals of Mathematics, I still need to figure out how high to send them. And I think there is value in publishing papers in a journal of the appropriate level. Arguably, that's the key reason for the continued existence of journals now that we have arXiv.

You could use the
principle of maximum entropy.
Thus, the first submission should be accepted about 50% of the time. When the first is rejected, next the second submission should be accepted about 50% of the time and so on.
This way you "make every time count": you maximize the amount of information (in the sense of information theory) that you receive from each decision.

Note that anyone can still submit to Nature or Annals of Mathematics with this method... just not too often.

This looks interesting. Can you make an example of the "submission strategy" that this would generate?

@FedericoPoloni Say, if I notice that out of those of my papers that get rejected twice, pretty much all are accepted on 3rd submission, then I'd think "Maybe I should try to submit to a journal more at the level of my 2nd submission rather than stoop to the usual level of my 3rd submissions".

Or are you thinking of something mathematically precise, with convergence guarantees @FedericoPoloni ? :)

I was just curious to see if you had a specific "mathematical" process in mind. But I am not sure if a meaningful analysis is possible -- one would need first to decide where to put the balance between better venues vs. faster acceptance time and not bothering editors --- otherwise the best strategy is clearly "always submit to the best journal in your field, then when rejected to the 2nd best, etc.".


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Is it appropriate for a PhD student to write reference for a PhD applicant?
I am a PhD student, and was recently approached by a (very bright) student in an exercise class I teach, requesting a reference letter for his PhD application. This makes me wonder: Is it OK for a PhD student to write a reference for a PhD applicant?
There are obvious reasons why I might be able to say something informative: I saw a lot of his solutions to assigned problems, and I saw him work through an extended period of time (as opposed to say, a lecturer, who only sees his grades, and possibly final exam). However, I am concerned that I am not senior enough for my opinion to be taken seriously. Is it a legitimate concern? Would the student be better of asking someone more senior?

Did the student check whether the school he is applying to allows PhD students to act as reference? Even if the school allows it, the recommendation would have more weight with you providing the text and substance of the recommendation and the professor of the course providing the signature based on his trust in your observation and judgement.

Very similar (but from applicant side): http://academia.stackexchange.com/q/32829/2692

Apart from the other points raised, it is very possible that the undergrad has no idea how recommendation letters work, and you should prompt the student to think about possible (good-) letters from faculty, in case the students has not thought in such terms. They might be more comfortable talking to you... not realizing the realities of the letter-writing game.

I think this is in part a cultural question. For example, in the US, I think letters from current graduate students are not given nearly as much weight as from more "senior" professionals. However, in German schools, it is quite common for senior doctoral students to write letters of recommendation for undergraduates, particularly in disciplines such as engineering, where the group sizes tend to be quite large, and in many cases the professor in charge of the group may never meet the undergraduate in question.

In the United States, there is nothing against it, but it is better to get the letter from a professor if possible.  Usually, especially with a junior graduate student, the graduate student's supervisor will be involved in the work as well, in which case the recomender really should be the professor.
That said, there are situations where the graduate student is the right person to recommend, because there has not been a professor significantly involved.  If the only options are:

a letter from a graduate student explaining in detail how they have worked with this student and praising the excellent research that the student has done, versus
a letter from a professor saying "this undergraduate exists and other people have told me good things"

then the letter from the graduate student is the right way to go.  As a graduate student, I ended up writing some letters like this for undergraduates who worked for me.  While it's impossible for me to know how their admissions committee rated my letter or what other letters they had, the people that I recommended did end up in Ph.D. programs, so it at least must not have been a problem to have me recommend.


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Should citations be as detailed as possible?
While writing my thesis (computer science), I was wondering how detailed citations have to be.
Let's assume I want to cite an article of a conference and have full information on author, editor, title, year, booktitle, subtitle, eventtitle, volume, location, DOI, ISBN, arXiv ID, ... you get the point.
Do I actually provide every piece of information in the citation or are some left out? Does any style guide (like IEEE, APA, MLA) address this topic?
Similar questions [1] cover only URLs, but my question is more general.
[1] Should I include a DOI/website URL for a publication in dissertation bibliography?

For my thesis, I plan on using the style guide from one of the popular journals in my field. I am a meteorologist, so will probably use the American Meteorological Society style guide (I used this in my undergrad dissertation). I may use the American Geophysical Union style guide instead (I am writing a paper for one of their journals at the moment).

Be aware that some supervisors have fixed opinions on how they want citations to look like. Thus forming an opinion on this without having asked your supervisor may be a waste of time.

@Wrzlprmft I've spoken to my supervisor and he does not care at all.

Follow the stylesheet your university has for theses. If no such stylesheet exists, follow what seems to be the norm in your field.

Generally the citation styles for your field, and thus for your thesis, will dictate this. The Purdue Online Writing Lab (OWL) website is a nice and popular resource to refer to what the most possible information would be desired for APA, MLA, Chicago, and Turabian - but you ultimately should refer to the exact, up-to-date published version of the style guide itself.
As an example, for APA when citing a Journal or Conference paper/article, you would at most provide (formatting stripped):

Author, A. A., Author, B. B., & Author, C. C. (Year). Title of
  article. Title of Periodical, volume number(issue number), pages.
  http://dx.doi.org/xx.xxx/yyyyy

If something doesn't have a DOI, the style guides say how to cite each type of resource. A book might be cited by ISBN, and if there is no DOI you might cite the arXiv in place of the DOI website - but you are never citing all of these things!
Cite only that which the style guide says you should, in keeping with the common tradition of papers in your field - no more, and no less.
When using reference management tools they often help do this for you, but they do not absolve the author of responsibility for ensuring that the citation matches the appropriate style of their field and that the data and style is followed accurately.
When You Don't Know Your Style
If you are unsure of what style applies to your field, a search for "{field name} style" can be helpful, but the Purdue OWL site linked above also provides further guidance on their Complete Discipline Listing. If you are unsure an adviser or your department office can provide further verification, and checking in with the department (whether that be the department office, chair, or secretary) is often a helpful technique.
Special Case: IEEE
I would note that the IEEE is somewhat of a special case (and is very common in computer, engineering, and various technology fields) in that there is a IEEE Citation Reference and IEEE Editorial Style Manual. However, they both specify that when the guides don't provide a specific answer to your question that you should consult the Chicago style guides. Thus the IEEE style may be considered a specialized version of Chicago style.
So in the case of this style you should first consult the IEEE guides, and if and only if they do not provide sufficient guidance you can consult the far more comprehensive Chicago guides.
Summation
So in conclusion: if you have 100 fields of information available, you don't include them all in the citation - just the ones that your field's style says you should. Any good style guide (all the ones I've had to read) gives rules of precedence and fall-back plans when certain information is unobtainable, with the information requested varying by the source being cited itself.

Thanks for the purdue link. So my field is computer science, which citation style would you recommend (ieee)? As said before, my supervisor does not care at all.

@ResterHall since you are using biblatex just put everything into your bib file and then let the bibliography style deal with the formatting.

@StrongBad the question was which bibliography style to use (e.g. style=ieee)

@ResterHall According to the the Utah State University, your field is likely to primarily use IEEE. https://cs.usu.edu/htm/thesis-style-guides-for-computer-science They also link to the IEEE style: http://www.ieee.org/documents/ieeecitationref.pdf and the author toolkit: http://www.ieee.org/documents/info_authors_kit.pdf So that seems to be your best bet, as far as I can tell (I personally have to learn IEEE style some time this year myself, having only written in MLA and APA before this).

@BrianDHall Thanks! I will read those links. I would upvote your post, but need 15 reputations ;)

@ResterHall I meant you can use style=ieee today and style=apa tomorrow until you find one you (or your advisor or journal) like since biblatex makes it trivial to change.

@StrongBad ok, that's true. But I wanted to know which piece of information should be provided in the citation of which is left out. And - assuming I understood the answers correctly - this is different for each citation style. To find out which information is relevant, I have to read the particular guide and thanks to BrianDHall I now know which one: ieee

@ResterHall I have expanded and revised my answer to provide further guidance on uncertain styles, finding your style, and the special case of IEEE style. Glad I was able to help, and hopefully this will make citing a bit easier! It's my least favorite part of the process, yet so important to do fully and completely.

@BrianDHall Thanks to your links, I found the style guide for the IEEE Computer Society which is perfect for me

The goal of the citation text (as opposed to citing in general) is to make it as easy as possible for your readers to find the works you cite. It cannot hurt to include as much information as you have. You are using a bibliography/citation management system like Zotero or BibTeX, right? So, once you've put this into your database, the formatting and typing out of all the relevant information should be automated. If there are constraints or unwanted information, the formatting package should eliminate them from the text it produces making your document compliant with the standards of your publishing venue.

Yes, I'm using BibLaTeX as a management system. I have not noticed that information are automatically deleted, I will try that out, thanks! Well the downside of using detailed citations is a long bibliography - especially on an article which is limited to a certain number of pages. Hence, I thought a style guide regarding this topic would exist (e.g. author is important, isbn is not)

The style for each venue will depend on that venue, so you need to include whatever they want. If that makes your bibliography long, that's the breaks.

I disagree, most citation styles explicitly limit the information in the citation. For example in APA style if you read a print version of something without a doi, but with a url, you do not list anything even though having the url would potentially make finding the article much easier.

@StrongBad what if the book (e.g. inproceedings) containing the article has a doi, but is not freely available, but the article was also published on e.g. arXiv / institute website

@StrongBad, right, but BibTeX is usually smart enough to only print the things that APA or IEEE or whoever wants even if there's more information in the BibTeX database entry. Am I wrong about that?

@BillBarth correct, I am all for including lots of info in the bib file. I was disagreeing with the first sentence, and to an extent the second sentence, of your answer.

@StrongBad, I think my stated purpose for citation text is correct. I suppose the second sentence is wrong as written if it stands alone, but the final sentence sort of makes is clear that you should comply with what your venue wants.

There are style guides for IEEE, APA, and MLS (also known as MLA), although IEEE style is slightly different from the others in that it is based on the Chicago style guide. Many publishers provide information in their online citation downloads that are not required for the citation. In these cases you do not include the extra information. This seems a bit strange given that this extra information could be helpful, put most journals stick rigidly to their style guidelines and do not want extra information.
I think the most obvious example of excluding useful information is related to issue numbers and APA sytle:

Per APA Style, when formatting periodical references (which include journals, magazines, and newsletters), include the issue number (immediately following the volume number in parentheses) when the periodical is paginated by issue (i.e., begins each issue with page 1). Otherwise, include only the volume number

It is often easier to find an article on a publisher's website if you have the issue number, even if the journal is paginated continuously. That said, journals that stick to APA style will remove issue numbers if you include them.


text:
How to acknowledge a deceased advisor’s contributions to a paper?
One of my advisors suddenly passed away while I was in graduate school.  We had some discussions and ideas about future publications, but he passed away before any of the work was completed.  When the work was finally completed and published, I and my co-authors were therefore presented with an ethical dilemma about how best to acknowledge his contributions to the ideas behind the paper.  Should we list him as a co-author?  Put him in the acknowledgements?  Listing him as an author would give credit for the original idea, however, we would have no way of knowing if he actually approved of—and would want his name attached to—our methods and writing.
In the end my co-authors and I decided to list him as a co-author with a footnote stating that he passed away before publication.
I’m interested to hear from others who have been in similar situations and/or suggestions on what constitutes “co-authorship” when one of one’s collaborators passes away before the publication or work is complete.

Actually, while ethics are an issue, I imagine that this is something which your university has a policy on.

I can't find any policy about posthumous co-authorship at my university (and we have LOTS of ethics policies).

My master's thesis adviser passed away suddenly after I had obtained my master's degree and after we had written a paper about it, but before the paper had been accepted for publication.  I included him as co-author as we had previously planned, but I added the word "(deceased)" after his name.

Two words: Paul Erdos :)

@Suresh: Good point, but I suspect any "rules" for situations like this will vary across disciplines.  For example, the thresholds for "co-authorship" are likely very different in theoretical disciplines like mathematics than they are in the experimental sciences.

Caroline Series, a mathematician, published a celebrated paper co-authored with Rufus Bowen, which died before the completion of the article; it is available here, you can have a look at the end of the introduction to see a way to proceed.

I was one of four authors of a paper that was undergoing revisions (suggested by referees) when one of the co-authors died. We kept his name on the list of authors, and we added a brief statement at the start of the paper, saying that he had died, and dedicating the paper to his memory.  I don't remember whether this required any consultation with the editors, but my best guess is that it did not.

Did the deceased researcher consent to any copyright transfer associated with publication?

@PatriciaShanahan In my case, the researcher died before contributing any text, so that was not an issue for me because he technically did not have any claim of copyright on the work.  The publisher either did not notice or did not care that his name was absent from the copyright transfer.  I could foresee that being an issue with some publishers, however.

I had a similar situation. In this case, we did exactly what you did: we indicated that the participant (not a team leader, but a team member in this case) was a co-author, but that he was deceased. I think this is the only fair way to recognize substantial contributions.
Of course, the difficult comes if there is a challenge to the work of the deceased. In our case, however, we had a very substantial paper trail which was audited and reviewed, so the individual work could have been sorted out and dealt with appropriately.
So, I think the best defense is generally to keep good working notes and use version control.

aeismail's answer is definitely good advice, but I'll add two more bits:

Check the journal policy and author guidelines. There may be something in there that can guide your choice, like the Journal of the American Chemical Society has:

Deceased persons who meet the criteria for inclusion as coauthors should be so included, with an Author Information note indicating the date of death.

Check with the editor, if in doubt. They have the final say in the matter, and these things are probably best run by them if no official policy is established.

In terms of papers with deceased authors, I think the record holder is probably this one:

Can you spot it? One author died in 1919, and one had her PhD in 1911: while no date of death is provided for her, I don't think she's still around. (Also, it was probably quite an achievement for a woman to get a PhD at the time.)
As we say: old chemists don't die, they just reach equilibrium!

Any idea what Werner's contribution was? Not knowing if scanavy-Grigorieff is alive or dead suggests to me she did not make a contribution.

The compound whose chemical structure is reported in the paper was synthesized by Werner and Scanavy-Grigorieff, but it had not been identified at the time. The MIT team identified and solved the structure of that compound, from Werner's collection (Werner was a famous guy, so his collection was kept as historical artifact)

I have not been able to find much information about Marie Scanavy-Grigorieff online besides the year of birth, which is 1881 according to her thesis bio and university records.


text:
Should I contact accomplished researchers listed as editors of shady journal?
I recently got an unsolicited email advertising a questionable-looking mathematics journal.  Upon investigation, it looks pretty shady: page charges, manuscripts to be submitted in Microsoft Word (legitimate math journals always use LaTeX), overbroad scope, and a promise for peer review within two months (unreasonably short for mathematics).
In its three years of operation, one particular author has been published in it three times, including an “elementary” proof of Fermat’s Last Theorem, and another paper that appears to be a proof of a statement for which an explicit numerical counterexample is known.  (Interestingly, it appears the same author has also published a proof of the Goldbach conjecture in a journal with a nearly identical name from another publisher indexed in MathSciNet, and has also apparently settled the Twin Primes and Collatz conjectures!)
(Since the preceding paragraph may not make any sense to non-mathematicians, let me say: this is roughly the equivalent of a physics journal publishing a paper that claims to have achieved time travel with household materials.  I should note that the journal has a subscription fee (which I have no intention of paying), so I can't actually read the articles in question; but their abstracts are pretty damning.)
However, the journal’s editorial board includes some names from reputable institutions; people with many publications in high-quality journals.  (There are many other names from institutions I know nothing about.)  Giving them the benefit of the doubt, it’s entirely possible that they are not paying attention to what the journal is doing, or they agreed to be editors without checking on the journal, or even that they have been listed without their knowledge (this has been known to happen).
Is it appropriate to try to inform these editors what’s happening in their names?  If so, how can I do it tactfully?
On the one hand, if someone was using my name on a shady journal, I’d want to know.  On the other hand, I don’t want to offend or embarrass them by just sending an email saying: “this journal you edit is crap”.  It’s even possible that they somehow approve of the journal (e.g. they have a philosophy that the world generally needs more journals and fewer barriers to publication), in which case, I fear no good can come of me criticizing it to them.

Thanks for your response. I have the journal now.  I would myself make a distinction between criticizing a journal and dropping names of editors of the journal: it is our job as practitioners of X to evaluate and monitor journals in subject X.  Criticizing a person seems much more, well, ad hominem.  Moreover, because the workings of the editorial board of a journal are totally opaque to an outsider, one cannot with any expectation of accuracy and justice criticize any one editor.  As you say, one may well wonder whether everyone who is listed on the editorial board is really "on board".

Maybe they know full well what they’re doing. Maybe they are also involved in real journals, which receive a lot of unpublishable junk. In order to appease these junk submitters, and thus cut down on repeat submissions of junk, they provide them with a junk journal to publish their junk in. Thus, the submitters think they get published, while real academics only read the serious journals. Everyone’s happy.

@Timwi: except for anyone whose library budget is partly wasted on junk journals because of restrictive bundling deals (not relevant in this case, but does happen).

Maybe the reputable authors were trapped? They agreed to join many years ago when the journal was new and then never left the editorial board, e.g. because the journal wouldn't remove them from the list or because they forgot that they are on the board?

This is the first post I read in this forum where it is not taken for granted that the whole world knows about the famous Mathematics conjectures and prizes, but explains what they mean to non-mathematcians! Well done! I would give +7 if I could.

I wouldn't worry too much about tact.  There's enough information in your question to identify the journal, and it looks impressively bad, even by the dismal standards of junk journals.  It's so terrible that I'd consider it unethical to be actively involved as an editor, and humiliating to be passively involved.  Bringing this to the editors' attention would be doing them a favor: if their names are being used without their knowledge, then they'll find out, if they haven't been paying close enough attention, then they'll get a valuable wake-up call, and if they are already well aware of how terrible the journal is, then at least they'll learn that someone has noticed their involvement and disapproves.  Of course it would be quite an awkward e-mail.  Perhaps the easiest solution is an anonymous e-mail: it won't make things less painful for the editors, but at least it won't affect your relationship with them.

I'm impressed that you could identify the journal from my information.  Unless you got the same email I did?

Goldbach proofs indexed in MathSciNet aren't so common, and the first one I found was by an author who fit all the other facts in your question.

The problem with this advice is that shady journals do not usually allow their "editors," who are involuntarily made members of the fake editorial board, to resign.

You are under no obligation to tell the editors, but if you chose to email them, it would not be out of place. The key is to not insult them or the journal. Something along the lines of "I see you are the editor of X. I research topic Y. Do you think my research is in scope at the journal? It seems like some of the articles take a less rigorous approach than others. Can you tell me about the peer review process and any publication fees?"
The email handles a number of cases. If they didn't know they are an editor, they now do. If they thought the journal was thoroughly peer reviewing stuff, they now know it is not. If they did it to be able to say they are an editor, they now realise that they have been caught. If they did it because they support this type of publishing model, it will give them a chance to express their views and since they are willing to sign on as an editor, they probably are happy to express their views.

I think this is a nice idea.  One comment: there are many STEM fields in which "this paper takes a less rigorous approach" is something measured to say about a paper which may have other merits.  In math, I think that almost anyone would read that phrasing as "some of your papers are totally bogus [why did you publish them?!?]".  I personally find that past a certain point, overly polite or oblique language comes across as condescending (but I guess many other people must feel that the type of language I prefer is overly direct and confrontational).

Not being insulting is very important. But I'm not convinced by the approach of pretending that you want to submit a paper. If they're a genuine editor, you're wasting their time. If they're not, they now think you're the sort of researcher who wants to publish in junk journals. I suppose they're likely to send you a reply saying, "Holy carp, I have nothing to do with those guys! I've told them to stop using my name." and you can reply to that saying that you suspected this all along and didn't really want to submit a paper.

@DavidRicherby I did not suggest to pretend that you are going to submit a paper there in the immediate future, but rather focus on determining if the journal should be on your "list" of journals that you consider publishing in.

This answer is passive-aggressive and not completely honest.  Better to do nothing.

I put this somewhat to the test.
I stumbled upon a journal with very similar characteristics in another field.
The main difference is that it has operated for over three decades.
I tried to contact all editors, except the top two, who were obviously “in on it”.

I could find current contact informations for eight editors and assumed them to be somewhat active, though many of those were older than seventy.
I could not find contact information for five editors, but I could reasonably guess their current or last institution. I presumed those to be very likely dead or at least retired.
I found three editors to be certainly dead, one since more than a decade.
I failed to identify or find any information about two editors.

I started with e-mails to two editors from Group 1, whom I considered least likely to condone the journal’s actions. One month later, I contacted the rest from Group 1 and the last institutions for Groups 2 and 3. Another month later (now), I evaluated this. I should note that none of the editors were even remotely in my own topical vicinity, so there was very little risk of this backfiring at me.
The basic e-mail I sent was (with some modifications when contacting the former institution and similar):

A dubious journal lists you as editor
Dear Prof. [name]
It might interest you that a allegedly scientific journal called [name]¹ lists you as an editor. Given the state of the journal², I presume that this is without your consent or that the journal has gone south since. Please note that this is not your typical pay-to-publish predator.
Best Regards,
[my name]
¹ [link to journal]
² [links to exemplary, recent, and clearly unscientific articles]

My result was:

The first two editors I contacted responded:

One was grateful for being informed and quickly managed to get their name removed from the journal’s list of editors.

One told me that they edited some special issue for the journal decades ago and never did anything since. They shared my concerns and acknowledge that many papers are “silly”, but rather see the journal as “taking chances”. Their name is still on the list of editors.

One former institution replied that they were looking into it. The respective editor is still on the list.

Nobody else responded and no other name was removed from the list of editors.

I don’t know whether I had a good hand picking the first two editors or whether the journal took some measures after I contacted them and before I contacted the second batch. I also have to assume that many of my e-mails to Group 1 went to inboxes that are no longer used.

You could phrase your concern in the form of a technical question:

Dear Prof. So-and-so,
  I noticed that you are on the editorial board of the Journal of Shady
  Results, which recently published the proof of a statement for which
  Other-Person provided a numerical counter-example [1].  Is the journal
  claiming [1]'s counter-example was incorrect?

If you prefer a more indirect route, write your concerns to Beall to help expedite the journal's blacklisting.  Once on the list, you can send an incredulous e-mail to the well-known person asking if he is actually involved with this journal.

This seems to be a lot of game playing.  What is the rationale for not being direct?  We are all adults.

When egos are involved ... one can't be too careful.

Beall currently only considers open access publishers.

The Beall part of the answer is now outdated.

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


text:
Is it safer to carry on undergraduate research areas to gradschool or start from scratch in an unknown area?
This question is in spirit a very general one. When a person (say in CS) is choosing among multiple options for gradschool, which one would experience and prudence point towards? Along with research interests and all that, things to factor in would be the extra strain involved, to be honest.
Case in point:

Choice A: PhD advisor in the field of computer vision and machine learning. My undergrad experience was mostly in image processing, with one instance of training a rather vanilla backprop neural network. So this would be pretty much be building on the base of undergrad research experience. Yeah, the school is a tough one, and my math background is rather sparse. lots of catching up to do on the maths front.
Choice B: PhD advisor does work in graphics. mostly interactive graphics, lighting models and all that. These are topics i am vaguely familiar with, never having taken a graphics course during undergrad. Nor did any research project on that. Its a fresh topic for me, but I am not qualified enough to judge whether to pursue this or not.

If you start by thinking about what's safe as an undergrad/grad, I think you may experience (unpleasant) surprises down the road. Do what you like best! Grad school is not an easy path, and motivation is sometimes hard to maintain throughout, so the best way to help your chances of success is actually to do something that you enjoy (and hopefully will enjoy for the next few years).

Personally, I think grad school is as much about learning than it is about doing research. Don't be afraid to learn new things and expand into new fields - grad school is exactly the time do that. My main regret from my own graduate studies is that I focused too much on doing research and not enough on learning. Of course it requires hard work, but if you don't want to work hard I would say grad school is probably not the right choice for you.
As Fx writes in his answer, you should pursue whatever interests you the most. Of course it is also important to have a good advisor - so if you have no knowledge of the field you might like to ask around.


text:
Is it viable to pay for MS if your future goal is a Ph.D
I am currently working as a software developer. I have a degree in computer science. However, my country, Turkey, is not a technology favoring country, and research in the fields I am interested in is very rare, and only available at a few select schools. From job, location and opportunity perspective (too many applicants for too few places), getting an advanced degree at these schools is next to impossible for me.
I want pursue Ph.D. badly but I need a MS degree first because I don't have any research experience. So I have decided to apply for US schools and do some research there applying for a Ph.D.
Is paying for a master's degree a good idea and will I be able to do quality research there? Do master's students convert their degrees to Ph.D., if so is it easy or difficult? What to expect from a MS for getting good research experience?

I would, you never know if you'll finish the PhD.  But a lot depends on your own situation, family, country/culture, how much money you have, and so forth.  Buf if you want a yes/no answer, I'd say YES.

In principle, yes, that's a viable plan.  But there are a few stumbling blocks to be aware of.
First: There are two types of MS degrees in computer science in the US.  Research master's degrees have a significant research component, usually ending with a formal thesis.  Professional master's degrees require only taking classes; this is no expectation and little opportunity to get involved in research.  A successful research MS is good preparation for a PhD program, and many CS PhDs started by getting a master's degree first.  (I'm one of them.)  But a professional MS is generally considered a terminal degree, even with a 4.0 GPA.
Second: PhD applicants with MS degrees are held to higher standards than PhD applicants with only undergraduate degrees, because they have had an extra year to build up a research portfolio.  In my department, for example, strong applicants with master's degrees but no formal publications are usually rejected.  See the previous point.
Third: Strong graduate programs in the US also get too many applicants for too few positions.  Competition at the top departments is fierce.  Even getting a research MS is no guarantee of being admitted to a PhD program.
To address the first three points, I strongly recommend asking the following question of any MS program you apply to:

What fraction of graduates from your program go on to get a PhD?

Fourth: If you don't have any research experience, how do you know that you want a PhD?  Getting a PhD is not like getting an undergraduate degree; doing research is not like taking classes — it is much more open-ended, much more self-directed, and much much riskier.  This is not a question to answer here, but definitely something to address in your application statement.

I don't have research experience but I independently carried out some small projects by myself for small problems. I love thinking on problems.

Enjoying thinking about problems is a good start. What makes research different is that the problems are open-ended (i.e there's no solution to look up).

In principle, a masters degree is the first steps towards a scientific career. At least in my studies it was the first time I really did a major scientific project:

Defining a research question
Coming up with a plan how to answer the research question
Doing the actual research
Writing it down in a scientific report

In a lot of countries, excluding the UK, it is obligatory to get a Master degree before you are admitted to a PhD position. So, in answer to your first question, if you want to get into science, you need to do a MS. Depending on your financial situation, and how badly you want a career in science, paying for your MS might or might not be a good idea.
Your next question deals with difficulty. In general, if you really enjoyed your Masters research this is a good indicator you would like a PhD position. If you like doing research, a PhD is a nice job, but certainly not an easy job. However, if you enjoy it, it should generally be possible to finish your PhD.
In regard to if a masters is a good preparation for a PhD, it heavily depends on where you do your masters. But in general they train you in being a scientist.