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What makes a publication (or a publishing forum) academically acceptable for inclusion in a literature review?
I'm in the process of conducting a systematic literature review and an integral part of this is the definition of inclusion and exclusion criteria for filtering the search-result-publications.
A common criteria for these reviews is that the publication is an academic publication or otherwise academically acceptable. I haven't been able to find a proper definition for this. The ones that I can think of are that the publication fora must exercise peer-review on the papers and that the fora are widely accepted by (inter)national funding agencies.
Hence, my question is what makes a publication or a publishing forum academically acceptable?

Where do you conduct your search? If you only do it on SCOPUS or Web of Science, you should already be partway there, since these already pre-filter academic publications. (And you will still need to read the publications themselves and judge their quality.)

@StephanKolassa we work on a rather new software engineering concept and as such we'd like to consider all possible databases in order to capture all research in the area. For us this means expanding from SCOPUS and WoS to e.g. Engineering Village and even Google Scholar

Acceptability is in the eye of the beholder.  You cannot get this "right" for two reasons:

Different scientific communities have conflicting opinions about about the credibility of various publication venues.
Even "good" venues publish rubbish papers.
Some important papers are published as white papers or technical reports, and will not appear on any list of journals.

To my eyes, the real question is not about what the "right" value is, but about how the boundary that you draw will affect the conclusions of your systematic review.
For example, if you are attempting to perform a meta-analysis on the data within other data sets, then you just need a wide enough scope to be sure to get good statistical validity.  Therefore, if your topic is well-studied, you can probably restrict yourself to only those publications listed in some field-appropriate major database, e.g., PubMed for biomedical literature, DBLP for computer science.  It doesn't really matter which one, because you're not actually going for comprehensiveness, just for sufficient sampling, and it's more important to get well-curated data than all data.  Moreover, the bad publications in the dataset are expected to be drowned out be the good ones in your data processing.
On the other hand, if you are attempting to summarize all of the credible thinking regarding a topic, then you would want to set a much broader criteria, e.g., any journal or conference with at least 5 years of publication history and not on Beale's list.  In this case, you can be so generous because you are going to be using a lot more personal discretion in deciding how much weight to give each paper and interesting thinking may turn up in obscure places.
These are the two main cases that I typically see for systematic review; for other cases, you may need to adjust or pick other strategies.  In all cases, however, the guiding principle is a) there is no "right" answer, and b) your choice should be driven by the effects it will have on your review.

@jakebeal while I now understand that selection of these criteria is very context and research goal specific, I think rules like "5 years of active publication history" and "not on Beale's list" are very good general candidates. Thank you

@Davidmh Right you are - I've incorporated this point into the answer.

2a. ...and even "rubbish" venues publish good papers.

The link to Beale's list is not working anymore, is there another alternative somewhere? (and thank you for your great answer!)

@Emilie Unfortunately, I have not yet found a good replacement.

I am afraid this is an impossible question to get right: An "acceptable academic publishing forum" would be one that is accepted by "acceptable academics" - and "acceptable academics" would be identified by publishing in "acceptable academic publishing fora"...
Peer-reviewed is not a bad criterion, but it falls short: There are peer-reviewed journals for creationists and homeopaths - so the value of peer-review depends crucially on who the peers are. It doesn't even work as a necessary criterion, as missing the arXiv for math-y fields or books for humanities would mean that a literature review is very incomplete.
"Acceptance by funding bodies" gets the question backwards: Funding bodies try to approximate what the academic community considers good publication venues, they don't define it.
If formal inclusion/exclusion criteria are important for you (maybe because you do some meta-statistics?), you will need to look for field-specific standards. In medical subjects, I could imagine that "listed on pubmed" would be an acceptable one. In this case, looking are published meta-studies and their criteria would be useful.

In relation to peer-review, there is also the difference of stating that peer-review is conducted and actually doing proper peer-review. Most fake, predatory journals claim that they do peer-review. So this criteria might be clear-cut in theory but harder to apply in practice (especially during a literature search)

so it is a question of what are the generally applied and hence accepted criterion for one's specific field of research?


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Can I patent a model that I described in a paper or that I adapted from a model proposed by someone else? Is a patent more prestigious than a paper?
Academic papers in engineering sometimes propose a new model to tackle  prior difficulties. These proposed models are not usually patented. For example in experimental papers and many power electronic papers, the models are fully available.
I have a published work that proposes a new model, but it is pure computer simulation and math.
So, my questions:

Can I patent my own published paper?
Can I use others' paper and patent their idea? (specifically
experimental for papers)
If the answer of 1 or 2 is not, how many modifications do I need to
apply in my model be able to patent it?
If I have an original idea to propose a new model, what should I do then: A patent or good rank ISI paper?

My understanding is, the fact that it is published means that it cannot be patented, even if it is your idea.

Thanks. How much modification do i need to apply in order to patent it? @DaveClarke

I don't know. The patent office will decide.

Thanks,  If I have an original idea to propose a new model, what should I do then? A patent or good rank ISI paper? @DaveClarke

Note that the motivation for publication and for patenting differ: one is to share knowledge freely, for the betterment of humankind; the other is to make a buck usually of some insignificant idea, without going through the effort of building a proper business idea, though also for protecting actual business intellectual property.

If my objective is to have a better reputation and resume as a graduted M.Sc who would like to achieve a  good scholarship for studying PhD abroad, what would you propose? (Note: I have 2 good rank ISI paper already) @DaveClarke

If you want to study a PhD abroad, then publications are more important. Writing patents that essentially steal someone else's idea is pretty dubious.

Good to know, thanks. Besides, I cannot steal from myself lol. @DaveClarke

Trying to patent someone's published idea isn't going to get too far, or should the patent office not do their job, it would not withstand any scrutiny in the patent courts. It is also bad form...

@Jamaisavenir Also bear in mind that filing and maintaining a patent costs money, and if you aren't making money off the patent (by exploiting or licensing it) then it is a complete waste.

If I have an original idea to propose a new model, what should I do then: A patent or good rank ISI paper?

It depends on your objectives.

If you want to make money from your model: Get a patent.
If you want to earn academic reputation: Publish a paper.

In many cases, it's actually possible to do both - assuming your "model" can be patented at all. However, note that patent fees can be quite expensive, and it is usually only worth paying if you really aim to make money from it. The academic reputation gain from a patent is mostly marginal.

The academic reputation gain from a patent is mostly marginal. Good to know. Thanks for your answer @silvado

You don't patent papers. You patent ideas.
You can't patent other people's published work because their published papers are clear evidence of prior art.
Why do you want to patent a computer model in the first place? Why do you want to restrict people's use of it? How lucrative will it be?

Do you think that  publishing a paper for your model helps more than patenting it for your reputation? Please tell me your opinion for both academia and industry @curiousdannii

I don't think a patent alone means anything - there are plenty of examples of useless / bizarre patents out there.

Adding to the other fine answers:

It costs a considerable amount of money to file a patent.
Patents are written using very specific idiom and formulations. There are commercial bureaus that rewrite your idea into a proper patent proposal, but that also costs a serious amount of money.
You can find most patents through the world intellectual property organisation (WIPO): https://patentscope.wipo.int/search/en/search.jsf
. Have a look there and read some patents in your target domain, if you want to proceed.

Don't underestimate the impact of point 2. The language of patents merges technical jargon with legalese. I have trouble reviewing my own patent applications after they have been rewritten.

Im Not A Lawyer.  Heres what I have found in my own experience.
First, this is very country specific.  Both in terms of what is 'good' for reputation and what is allowed by the patent law.
In many countries, you can publish a paper and then patent the (or some of) idea within a certain time period, usually under 1 year, of course, it must be your paper.
As for modifications, that will be up to the evaluator.  There are rules, novelty, innovative step, etc.  You need to read your specific countries rules for what qualifies an idea to pass.
In some countries and research areas, patents are well regarded.  For example, in parts of Asia, I have seen patents very admired as it helps research institutes make money that can be used outside of the normal grant allowances.
This all depends on your target audience.  If you want to join the lab of someone who is very open-source minded, having a patent might be a turn off for them.  If you join a lab that has many grants from industry, it is possible they like to have someone with experience in patents, which could lead to a better chance of getting industry funded projects if the company wants to work with people that can get patents from research funding (which can be shared IP or not, depending on location).

It is very good to know these information, thanks. I think I'm going to publish my model as only a paper like my other works. This is also easier for me as I don't need to implement my model and a computer simulation is okay. I was thinking that patent is a huge thing, but now i am convinced that papers are as (sometimes more) important as (than) patents   @user1938107

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What to do when you publish a paper that accidentally included a wrong or irrelevant citation?
My paper was published and later on I found that two references were mistakenly included with the third reference, which is the correct.
My phrase looks like this:

I am worried about this (Smith 2001; David 2006; Magnus 2007)

and this is the correct form that it had to be:

I am worried about this (Smith 2001)

so the references "David 2006" and "Magnus 2007" have nothing to do with the cited phrase and they never did that work; and were not meant to be included but maybe it was a problem with reference management software that I used at the time.
I wonder if this will cause a problem to my paper or even plagiarism/retraction.
I am really worried about this and any advice is more than welcome.

Plagiarism is the use of another author's ideas or words without proper credit.  You haven't done that, so there's no need to worry about it.  Also, people don't retract papers over trivial editing errors like this.
However, since it's something that might be confusing to a reader, it may be worth asking the journal about printing a correction.  Simply get in touch with the editor who originally handled your paper, or if they no longer work with the journal, contact the editor-in-chief.  They would typically publish a one-sentence note in some future issue of the journal, stating that the references were included by mistake and should be ignored.  Alternatively, they may decide the matter is too trivial to be worth the space to correct it.
Either way, you should post the correction on your web page, and any other place where the paper is publicly available (preprint servers, etc).
This is no big deal and happens all the time.  Just get it fixed, move on, and be more careful next time.

+1 for correcting all online versions you have access to. This is often the version people find if they search on Google scholar, so fixing it there goes a long way.

Many thanks, what about the authors of the cited papers that I put them by mistake? Do I worry about them?

@Barry: No, I can't see that they've been harmed in any significant way.

Obviously it would have been better not to commit such a silly blunder in a published paper, but I don't think it matters much. Such errors, especially when accidental, will inevitably occur, much as typographic errors. A slight embarrassment to you, yes, as any typos or errors in formulas would be, but not truly "actionable" by anyone, so far as I know. So, bottom line, "forget about it".

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/


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Is it normal for the manuscript submission date to change from the original submission date to the revisions submission date?
I submitted a paper to an ISI journal almost a year ago. The submission date of the manuscript was May 20, 2015. I received a referee report on January 15, 2016. The report was quite positive but asked for some major revision. I made all the required changes and submitted a revised version of the manuscript on March 10, 2016.
Ten days afterwards I received from the Editor a message that the manuscript would go into the refereeing process and Date received: March 10, 2016. Is it normal to change the initial submission date of the manuscript?

This is a little bit of a grey area: In some journals, if the editor feels that the revisions asked by the reviewers are major and would take a while, the editor will write something like "we cannot accept the paper at its current form, but after revising we invite you to resubmit the paper as a new manuscript". In this case you will get a new submission date.

In my field, for a time, a very brief time, the time between submission and publication was a factor for people when submitting to journals. Some journals the time between submission and publication was close to two years while for other, equally reputable, journals the time between submission to publication was less than 3 months.
When people started complaining about the time to publications, the slower journals began to cheat. The outcomes of the review process used to be Accept, Revise and Resubmit, and Reject. To "speed up" the process they changed "Revise and Resubmit" into "Reject and Resubmit". The resubmission was treated as a new revision, although you got the same reviewers, so the submission clock was reset. While this did nothing to speed up the process for authors, it reduced the time between submission and publication (it also made the journal look more selective). As I said, it is cheating.
In regards to if it matters, while it would be nice for authors to have access to meaningful statistics, it is not something the publisher needs to provide. Some might argue that "time stamping", but realistically, in fields where articles are infrequently published in the first journal they are submitted to, time stamping does not exist since I have never seen a time stamp based on the first journal an article is submitted to.
One thing to be concerned about when the submission date changes is if the process has gone awry. It is possible that the resubmission is being treated as a new submission and not a "Reject and Resubmit". If that is the case, then you may get a new batch of reviewers (and editor). Unfortunately, the way the automated systems work, sometimes it is difficult to tell what is going on. In these cases, a quick message to the editor is not out of place.

+1 It does matter, not only does it deceive potential authors about the likely review times it means that the author potentially loses priority on their discovery/method, which should depend on the date the paper was first sent to the journal.  What happens if someone else beats you to publication because their paper was accepted after one round, even though they submitted it much later than you did?

@DikranMarsupial I am not really sure what priority is, so I asked here: http://academia.stackexchange.com/questions/66052/what-do-researchers-mean-by-the-priority-of-an-idea

Basically who is deemed to have discovered/invented something typically depends on who is first to publish (goes all the way back at least as far as the Newton-Leibnitz kerfuffle) https://en.wikipedia.org/wiki/Scientific_priority

@DikranMarsupial sure, first to publish is not the same as first to submit (at least not in my field).

I think where the date of submission was given, that would be what defines priority (which is why it does matter, although I like Feynman's reported attitude ;o).  The important thing is to be able to avoid accusations of plagiarism you want to be able to show when the paper was first submitted to a journal (it would be nice if there was a formal record where it is submitted to one journal and rejected before being accepted by another).  Things like ArchivX help, but introduce other problems as well.

The current refereeing process is about the revised version of your manuscript that was submitted on March 10, 2016. This is why the editor message refers to this date and not on the initial date your first version of the paper was submitted.

But they have given a new registration number to the manuscript.


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What is the difference between Ph. D programs with coursework and those without it?
I have been looking into PhD programs in the Engineering field, and I have found different types of programs, such as some with coursework, and others without any coursework.
What is the practical difference between them? (Besides the obvious coursework) What kind of student is expected for each of them?
EDIT: To be more specific, I have been looking into Robotics PhD programs, such as:

CMU Robotics PhD (Coursework + Research).
KCL Robotics PhD (Only research).

It might be great if you were more specific about which engineering fields you are talking about and/or including links to the different types of programs you've found...

@shan23 Done, see edited question.

It seems to me that there are several advantages; none of these are suitable for every student. It's up to you whether enough of them apply to you, to make it worth doing a taught PhD:

A PhD with a bit of coursework in the first year will help those who
are crossing over into a discipline that they're not already deeply
embedded in: it will give you some hand-holding through the things
you'll need to know but don't yet;
it should (if taught well) also teach you some extra research skills;
it will give you some indication as you progress as to how well you're doing, compared to how well you should be doing if you're going to finish
it will allow you to explore different aspects of the field, to help you finalise your thesis topic
it may, depending on the country and institution, give you an intermediate degree at the end of the taught section, such as an MRes, which will count for something even if you then don't go on to do the full PhD
it lessens the culture-shock for those going straight from fully-taught study to a research degree.

Also +1 for the culture shock. Very true. Describes my situation exactly.

Coming from industry + masters, I found the class requirements annoying as they got in the way of me doing research full time. We had 9 required courses and only 2 of them provided any real value to my research. The major unseen benefit of classes is that their difficulty pushed me to make friends "in the trenches" of group projects and assignments. These friendships lasted throughout the rest of my PhD.

One thing to keep in mind is that there are international differences as well. In Germany, for instance, doctoral programs almost never require coursework as part of the research program requirements (although it may be mandated for purposes off establishing degree equivalency, if you come from a foreign country or have a degree from another field). This is because it is assumed that you have taken all the necessary courses as part of your Master's program, which is considered the follow up to the bachelor's rather than the precursor to the doctorate.
The reverse is true in the US: I don't know of any PhD programs there that don't require courses, for the reverse reason.

Does this mean that non-coursework PhD programs require that students have previously finished a Masters degree?

In Germany, it does; however, for programs in other countries, you'll need to check the admissions policy of the individual programs. These are usually available on the Internet; if not, you can always send an email or call the personnel responsible for admissions.

Also, a coursework PhD program is very useful for someone (like me) who took a break from academia to work for a couple of years - it would be invaluable in refreshing those basics that have atrophied during the time spent at industry.

Sometimes, especially in the beginning, it is easier to measure course progress than research progress, and thus good for the self-esteem.
Being able to say "I've accomplished something this semester" is crucial.

Doesn't the extra workload from courses mean that to some extent, you will only get around to start concentrating on the research in year 2 and make comparably little research progress then?


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Submitting the same research to multiple conferences
I'm aware that it's a violation of terms for most publishers to submit the same article to more than one journal, but I frequently see authors whose papers seem very similar, particularly papers released in a single year. In my field, neuroscience, this is particularly true about conference papers; one researcher will often have numerous posters/conference papers about seemingly the same topic. What are the guidelines for acceptability regarding this type of behavior?

"Same topic" does not imply "exactly the same results". This depends largely on which fields you're referring to: many journal papers in computer science would be redundant since they are journal versions of works published in the proceedings of an earlier conference. In mathematics, it's more common to talk about already published work at a conference, whereas in computer science we usually present new work. I'm sure other fields abound with their share of examples.

According to the Committee on Publication Ethics Guidelines on Good Publication Practice, the term "redundant publication" is defined this way:

"Redundant publication occurs when two or more papers, without full cross reference, share the same hypothesis, data, discussion points, or conclusions."  In addition, it states:  "(1) Published studies do not need to be repeated unless further confirmation is required.  (2) Previous publication of an abstract during the proceedings of meetings does not preclude subsequent submission for publication, but full disclosure should be made at the time of submission.  (3) Re-publication of a paper in another language is acceptable, provided that there is full and prominent disclosure of its original source at the time of submission.  (4) At the time of submission, authors should disclose details of related papers, even if in a different language, and similar papers in press."  Note that (2) states that it is generally acceptable to present a paper in a conference and then later publish exactly the same paper in a journal, as long
  as you mention to the editor that the paper has been publicly presented.

According to the paper Science journal editors’ views on publication ethics:
Results of an international survey,

"Breaches of publication ethics such as plagiarism, data fabrication and redundant publication are recognised as forms of research misconduct that can undermine the scientific literature."  It also stated that redundant publication is an unethical practice.  Of 16 ethical issues studied, redundant publication had the highest severity (that is, it caused editors the most concern---more than plagiarism or data fabrication).

Rather than asking what's acceptable, I think it's worthwhile to step back and think about the purpose of scientific publication.  Your goal in publishing should be to disseminate useful ideas, not to create a publication record.  If you have ten papers that are all very similar, it's hard for people to learn about your ideas because they won't have time to read all those papers.  Just write one good one.

While I fully agree with you, you clearly are not at a university whose administration is full of bean counters.

True.  My university really values quality over quantity.  The Provost recently advised us that it's better not to publish mediocre papers, even if the alternative is publishing less.

Alas, if only academia leaned toward quality, and not quantity!

Personally, I have no qualms with submitting the same talk to multiple conferences; however, in my field (Chemical Engineering), we don't really do conference proceedings. Therefore, it's not such a big deal to present a work more than once; it's being given to different audiences that might not otherwise see the work, and it's not going into the publication record multiple times, so there really aren't any ethical violations going on.
However, in a field where conference papers are required to give a talk, then ethical rules demand that you disclose if a paper has been accepted previously. If you've changed the material enough, or introduced enough new material, then it's a little bit more of a grey area. But it's still better to err on the side of caution than to get caught out.

Essentially the same here (chemist). Conference proceedings papers don't earn you anything in chemistry (they often take about everything, and some even try to force you to submit a proceedings paper instead of having peer review and accepting only good papers). Things are different if there's a special issue about a conference in a proper journal and has normal peer review. Consequently, that's where the field moves.

There are a few things to keep in mind:

Submitted talks vs. invited talks. Many researchers will have given many talks on a subject, but if most of them are invited talks, the reason they're duplicates is because conference organizers have essentially asked for duplicates.
I'd argue it isn't ethical to submit the same presentation, but a topic is a wide ranging thing. Heck, even a single study has a lot of aspects to it, and many conference presentations have less content than a single paper. For example, you might have a presentation at one conference that's highly technical, another for a different audience that's more practical/applied, etc. Those are different talks.
Consider what you want to get out of it. Unless your field is one of those where presentations trump papers or themselves generate papers (CS comes to mind), presentations aren't that big of a deal on a CV such that an extra one or two will really put you over the edge. In my field for example, everyone knows there's certain conferences that will essentially accept as many talks as they have spaces to fill (and they have many spaces to fill), so as long as your science isn't egregiously wrong, you're probably going to get in. What you do get out of that is good contacts, and good advice. If you keep repeating the same thing over and over, your return on "investment" starts to dive.
If your talk is going to be spun into a paper via conference proceedings or the like, be doubly cautious, and make sure if you are double-dipping in an experiment or the like that the resulting papers are clearly different as well. I don't know anyone who doesn't frown on duplicated papers, and more than one venue that will smack you down hard for trying to play a game like that.

Presentations do not trump papers in computer science; conference papers trump journal papers.


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Is it worth to switch from Bibsonomy to Mendeley?
What are the advantages of Mendeley over Bibsonomy?
Is it easy to migrate from Bibsonomy to Mendeley?
Does Mendeley offer equally powerful bibliography exportation?

In detail, the following disadvantages of Bibsonomy  are crucial for me:

you can not modify all your bibliographies at once, e.g. exchange in every URL field each # with \#
many references are not present, so I have to import the bibtex myself
search functionality could be better.

Does Mendeley solve these disadvantages?

See also http://academia.stackexchange.com/questions/36/what-citation-manager-should-i-use

You ask two questions (Bibsonomy vs Mendeley and how to migrate from Bibsonomy to Mendeley) in one thread, which is not the best suited for SE.

Sorry about that. I thought all my questions were so closely related that I should ask them in one thread.

You shouldn't replace # with \# manually in the database in the first place. Use \usepackage{url}, and enclose urls in \url{} commands, which should handle special characters automatically.

@Federico Poloni: Thanks for your comment. My bibtex-style wraps \url{} around the URL bibtex field. I still have problems with #. The URL manual says that If the argument contains any “%”, “#” or “^^”, or ends with “\”, it can’t be used in the argument to another command.

That documentation seems to be outdated: the comments in url.sty (in version 3.3, 2006) say otherwise. I can confirm that urls containing # work out-of-the-box at least with my tex distribution. Do you have version 3.3 of url? Maybe we have a question for tex.stackexchange.com.

Yes, Mendeley does offer export - BibTex, RIS, and EndNote XML.
The search is pretty decent, though I often find I use Acrobat search instead - its word-stemming seems better.
Batch replacement is very weak - the only way to do it is to go into the database yourself and tweak it. Very unsatisfactory. There is some batch update, in that you can select several papers, and add the same metadata to all in one go: but that's not the same as a batch search & replace. The one batch search & replace it does do very well is that when  you get two versions of an author's name, you can drag one name onto the other, and all the papers will get updated accordingly.
I've also found the technical support to be very slow, and often unsatisfactory.
The auto-grab of references from the web is patchy, and you may find you're often correcting it. Often, its guesses seem utterly bonkers, like it's just grabbed a few general words from the title, and gone off to find the closest match for those, in some subject that's completely alien to me.
The interface is klutzy, though I've yet to find a reference manager that had an interface I did like.
Earlier versions of Mendeley did occasionally corrupt the metadata, doing things like swapping round the lead and second author - unbelievably frustrating. This may have stopped now - I don't use Mendeley so much any more, because of this and other problems.
Mendeley does have its evangelists, and it seems to have been very slick at cultivating its fanbase - more resources seem to have been spent there than on the software. The feedback forum has now become pretty much unusable - there are plenty of important things in there that have been "planned" or awaiting assessment for 2 or 3 years.

I haven't got the chance to use Bibsonomy, since I use Mendeley since the beginning.
Concerning your questions:

You don't have to import bibtex files in Mendeley(although you can), you just simply drag and drop a pdf file to Mendeley, and Mendely will grab the title, user, publication details for you, which is the best thing about Mendeley.
Search function in Mendeley is quite satisfactory.
As for modification, I don't have the experience in doing that. Since Mendeley grab the things for you, I guess there is no need to do that.

Also after you registered in Mendely, your references will be uploaded to your account. So when you reinstall your system or something, all your references will come back.
Mendeley is quite great and has other great functions, totally worth trying!

I've got impression that Mendeley is pushing energy into something that is not the desktop software for sure. I had 2 years break from my sci efforts and after that period I've installed fresh new version of the desktop software and found few things:

my online cloud/repository was crashing desktop software immediately after start (after connection is made)
I've just created new username after realizing there is no way to reuse my old account (tried to delete all via web interface but no luck)

So the cloud argument: hm, proved not to be to reliable.
Then I noticed few bugs that blown my mind.
It was all fine before but now (LibreOffice plugin): you click "insert citation" it minimizes Mendeley Desktop (!?! yes, you are at LibreOffice but for no apparent reason, it minimizes the Mendeley Desktop even it is on the second screen), opens popup window within the LibreOffice where you have to know exactly what you want to cite - but, your cursor is not refocused to the input field (HA!). You say: ok, let's see what I was about to cite: you open Mendeley from the task bar and then: HA! the popup window is gone! Then you click "insert citation" again - and guess what: it does the same thing, with the windows again!
So, you might thought that multi-display environment is common in scientific community - but no, you're wrong: apparently 99% of Mendeley users have single screen and find this show&hide game amusing. At least, such impression I've got from low votes on this issue on their support/suggestion issue rank list.
I'm still using the Mendeley because I'm so used to. But if you're a new user, having a learning/adaptation curve to pass anyway: try something else first.
Mendeley does have very good auto-discovery solution for any PDF you put in  watched folder(s). Few fantastic features it has, in that direction like auto online search for more data for existing entry. But then some really stupid bugs make you crazy: like you manually edit a field, then open another entry and come back to the edited one: HA! you see the old data, the update you just typed in vanished. I'm still trying to understand a pattern there: because it's like every 4th modification is just ignored, at least in my case.
To me it seems they have to stop with development of new features and go back to fix the stuff that was fine before, but suddenly became buggy for no reason. I wish it is an open source project so I can jump into the code and disable this "now you see me, now you don't" game of the windows. It kills me.
(this is comment, not answer)


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Is there a generally accepted format for submitting papers to journals?
I believe in Mathematics and Computer Science journals usually accept LaTeX documents. In fact, the AMS has a number of packages and document classes for just this purpose.
What about other disciplines? I'm not particularly familiar with the humanities. Would a Microsoft Word document be unacceptable?
Does it vary from subject to subject, or even journal to journal?

In jest, all journals I know of still take physical paper copies through the mail. That is about the only similarity between journals though even in just my field (either in file types allowed or formatting of the content)!

The policies vary entirely from journal to journal about what is considered acceptable. APS journals, for instance, will accept both MS Word-based documents as well as documents formatted with RevTeX, their modified template system. ACS journals and a number of other publishers also offer their own LaTeX- and Word-specific templates for authors to use. Whether the use of the template is required or merely recommended is also a function of the journal. So, as a general rule, you should always check the homepage of a journal before you start preparing an article for submission to that journal.
To some extent, I prefer working with LaTeX in preparing manuscripts, for the simple reason that their plain-text document format makes it a lot less painful to switch back and forth between different templates, compared to a word-processing format like Word or LibreOffice or Pages.

It does indeed vary from subject to subject, and journal to journal. I once got in a short argument with some math students who had asserted "If its going to be published, it needs to be in LaTeX", a disagreement that only ended when I went and found some submission guidelines. For three fairly good journals in my field (Epidemiology), you have some considerable differences.
American Journal of Epidemiology wants everything in either Word or PDF format - LaTeX documents are compatible with this, but its certainly not doing anyone any favors in terms of already being formatted. Epidemiology will accept LaTeX documents, but warns that the odds of typesetting and other erros increases in formats besides Word. Journal of Clinical Epidemiology only requires that an editable version be available.
So the de-facto standard in my field is Word, though of course there are ways around that. And then, as mentioned, there are formatting issues beyond just "what's the file extension?" How references, the text, and figures are reported - must odds ratios be graphed on a log scale or not?. How p-values are treated. What format graphics are allowed to be in, etc. As Fabian said, submitting to a new journal often involves combing through the same content to subtly tweak formatting.

This varies a lot between journals, and probably even more between different disciplines. In the life sciences Latex is rather rare, MS Word seems to me to be the most common format in my subjective observation.
But the actual document format, be it Latex or Word, is only part of the difference between journals. The exact rules on how to format a paper vary so much that you'll have to put significant effort into adapting the same manuscript for different journals anyway. Check out the Author submission guidelines for Nature or those from JACS as an example. They often regulate details like how the axis labelling in graphs has to look like. The journals also often have different length requirements, so you might have to shorten your manuscript if you decide to switch to a different journal.


text:
How to find all of the responses to a published research paper?
While searching through various journals with my library's on-line journal search tools, I have occasionally found short articles which are simply comments on other published papers. These short articles might have various kinds of comments, but generally describe why the first paper's research or theories are flawed. In addition, sometimes I have found replies from the original author of the first paper, responding to these comments, for e.g., to clarify the meaning or perhaps to give further support to their original arguments.

Do such exchanges generally only occur within the same journal, i.e. the responses are published in the same journal, or can these occur across journals?
Are there any special tools to assist with locating all of these "replies"?

First, it may depend on your field, but at least in mine (physics and chemistry), it is rare for papers to generate comments or replies, and really extraordinary for a paper to be followed by multiple comments. (The editor usually lets the original authors reply to the comment, however.)
Some publishers provide links to the comments and replies on the webpage for the original paper. Otherwise, you can locate those comments using the following criteria:

they are published in the same journal, or in a preprint server (like arxiv)
their title includes “comment on” or “reply to” (or other such publisher-dependent prefix that you need to identify)

Finally, you should get the list of all newer papers citing the original paper, and check them out. If you're investigating a paper in depth, you’ll do that anyway :)

At least in Theoretical Physics, there are also sometimes errata fixing mathematical mishaps that are more than mere sign errors... Depending on the journal, these are often directly linked to at the paper's online presence, if they are not even included in a re-publication

In pure math, a good paper may be cited only 10 to 20 times.  An excellent paper may be cited only a 100 times or fewer.  As a result, it's fairly quick to skim the titles and abstracts of all newer papers that cite a given paper.  This is easy using MathSciNet.  I think Web of Science provides similar functionality for other fields.

I think that answer missed the question.

The point of the answer is that you don't need any special tools.  It's fairly quick to do manually, given that you have access to a decent citation database.  To say it another way, the best tool is a good citation database.


text:
Can "Feel free to contact me if you are interested in a copy of any of my publications." cause legal issues?
I know that some journals allow public archiving of publications (making them available for download) on a researcher's personal website. Some of these journals (at least in my field), however, constrict this right by saying that it is only allowed to public archive after one year following publication. EDIT: My question is concerned with the time frame of this first year or with the situation where journals do not allow public archiving.
To make a publication available to an interested reader, who is unable to obtain the article from the publisher due to institutional subscription policies, does one risk any legal problems on putting the following sentence on his/her website:

Feel free to contact me if you are interested in a copy of any of my publications.

Oh, probably.  Feel free to contact me anyway.

A related question I recently posted on [law.SE]

This will likely vary from journal to journal, but the information should be available in the "authors" section on a journal's webpage. For example, Science provides the document "License to Publish—Information for Authors" document, which clearly states:

Once the Work has been published in Science and provided the Work's first appearance in Science is properly cited, authors may:
...

Distribute photocopies of the Work to colleagues for non-commercial purposes only (providing that recipients are informed that they may not further distribute or copy the Work). Authors may distribute photocopies or download and email the Science PDF to their colleagues for their colleagues' personal use provided the recipients understand that the copy may not be further distributed or reproduced without the approval of AAAS.

This license would allow what you described, as it's non-commercial.

The link is broken. The 2023 version of the docoument is not as clear about emailing PDFs, highlighting that policies can change also with time. (I don't think an edit to the answer is necessary; it still provides a good historical example.)

Thanks for highlighting. Old article is here: https://web.archive.org/web/20130626075506/http://www.sciencemag.org/site/feature/contribinfo/prep/lic_info.pdf

With respect to the specific question of writing such a statement, there is no implication of an agreement that sending you an email will automatically lead to receiving a copy of the publication. If there are specific restraints on your distribution of preprints, then you can explain those limitations when a preprint is not available.
Alternatively, you could indicate which papers are "embargoed," and include a statement that says: "Except where noted, preprints are available by contacting the author," or something to that effect.

Short answer:
So far, I did not see a copyright transfer agreement, which did forbid an author to distribute pre-prints for his/her personal use by e-mail, or in a printed form.
Long answer:
The answer always depends on the particular publication. Whenever you submit your camera-ready copy, you usually also submit a signed copyright transfer agreement, or a document similar to it. Therein, you always have listed which rights to the work in question you are transfering to the publisher and which remain with you. Usually, in my field (CS/AI), there is a section on "Returned rights" where is explicitly stated what (publishing a preprint, distribution to colleagues, figure re-use, etc.) and how the author can, or cannot do it (obligation to include a copyright statement, etc.). Since your question is of a legal nature, I suggest contacting the publisher of the work in question and simply ask whether what you want to do is in line with copyright agreement you, or some of your co-authors signed, or whether you need to handle it differently. But before that, take a look on that publisher's website, all the major ones have these policies quite explicitly, and often including FAQs and other guidelines, listed on their websites.

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


text:
Should writers give credit to reference librarians?
The reference librarians at my school are often very helpful. If I tell them my topic, they will help me find many resources which I might not have otherwise found and generally tend to save me a lot of time. Is it common practice to credit them in someway, especially when publishing a paper? If so, what is the common format?

Yes, the acknowledgements section of your paper is an appropriate place to thank anyone who provided valuable assistance.  Depending on the circumstances, you could phrase it pretty generally ("I thank the reference librarians at University X for their assistance in conducting a literature search"), you could thank specific people, or you could even identify particular contributions ("I am grateful to Y for bringing the literature on Z to my attention").

Yes, the acknowledgements section would be the place to acknowledge the hard work librarians do, especially the subject librarian tasked with your field of study, or, any other librarian who you'd like to acknowledge. And, as a librarian (although not a reference librarian), I thank you for recognizing the hard work of your campus' librarians!

In general, I tend to give acknowledgments quite liberally.  In particular, if anyone spent more than 3 or 4 hours doing anything that helped improve the paper, I like to thank them by name.  I see it as a no-lose decision.  It really doesn't cost you anything to acknowledge someone (none of your readers will think less of you or your paper), and I know that I always appreciate being acknowledged (so I assume that most others do to).


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Should I Cite a Journal's Page Number, or an Article's?
When I'm citing a page in a journal, and the article has an independent page numbering system, should I cite the page number of the journal or the article?

Each journal has it's own rules. Look for the Author's guide for your specific journal. If nothing is mentioned - look at previous published articles in that journal to see what is common.

Beyond each journal having it's own rules, different bibliographic styles have different generic rules. For example, the Chicago Manual of Style generally wants all references to cite specific individual pages referenced. Similarly, APA style wants you to include or not include volume numbers based on if journal uses continuous pagination.

Both! Easy enough to give both... no downside. Just be honest, straightforward! :)

I'm not certain what you mean by an article with an independent page numbering system, but I assume you mean the following.  The published journal article is, say, on pages 25-48 of the journal, but there is also a preprint available online with different formatting, and it is numbered from 1-23.  Not only the page divisions, but even the number of pages differ, so there's no easy way to transfer a reference between these numberings except approximately.
The most important rule is to be clear and correct: you should leave no doubt or ambiguity about which numbering system you are using.  If you cite only one version of the paper, then you should use the same numbering used there.  If you cite several versions, then you need to make sure your references are clear.
The second rule is that you should focus on the "most official" version of the paper, whatever that is.  In most cases, a journal paper is more official than a conference paper, which is more official than a numbered technical report in a series, which is more official than a random preprint.  You want to cite the most final, complete, and authoritative version, and the one most likely to be accessible to future readers.  There may occasionally be subtle cases (for example, a paper that has been reprinted in books with corrections or additions), but this generally means the journal version.
P.S.  The only other interpretation of the question I can think of is for journals like Physical Review, where an article has its own page number (like 032326) and then the individual pages are given subsidiary numbers (like 032326-1 through 032326-8).  In that case, if you want to cite a specific page you could refer to it as 032326-3, or maybe just 3 if the context is clear.  In the bibliography, you would write 032326:1-8 or just 032326, depending on your bibliography style.

Yes, your initial interpretation of the question was correct.


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In a thesis, which comes first - Abstract or Acknowledgements?
I am writing my masters thesis now. I saw some theses with the acknowledgement chapter after the abstract, in other cases it's the other way around.
I think the acknowledgement chapter is not related to the scientific work in the thesis, and thus should not be put between the abstract and the introduction. An abstract could be nice in the beginning if we're looking at a paper for example, but for a thesis (usually >80 pages) the reader would have to turn the pages anyway.

You should check the guidelines from your university. I'd assume that they would have requirements for the order. If not, I always prefer the acknowledgements should come first, that way the non-scientific stuff is out of the way.

Highly country dependent. In Germany, at least at my University, we had 0 (that is, literally zero) requirements, nor guidelines.

@KonradRudolph lucky man.

@Zenon No guidelines is not necessarily lucky, because you are still judged on your choices.

Just to illustrate how strange requirements can get, my doctoral thesis had to have the abstract first. I don't just mean before the acknowledgements, but before the title page.

Actually, under normal circumstances, I would expect the abstract to be as close to the front of a thesis as possible. The reason for this is to make the job of cataloging and searching easier. Abstracts of theses are indexed by services such as ProQuest, and having to wade through additional pages of material makes their work harder.
That said, scientifics is correct in that you should follow whatever regulations your university has. But in general, in the absence of such guidelines, I would put the abstract before the acknowledgments—readers want to know as soon as possible if they should bother to read the rest of your thesis. Burying it after the front matter makes it less likely for them to invest the time.

Just adding my two cents: around me, people commonly print out and bind their thesis in such a way that the one-page abstract is on the back cover. I think it makes a lot of sense, and allows one to get an idea of what the thesis is about without flipping pages (literally).

I would prefer to put acknowledgement before the Abstract so that I will be done with the preliminaries first, so that when one reads Abstract he will have started looking at the actual content. To me acknowledgement coming between the Abstract and the introduction is a disruption. But the guidelines of the University are to be followed.


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What are the various designations/stages in the academic career of the person
In context of a person's academic profile in a web application, I need to broadly classify the various degree/designations/stages in the academic career of the person.
For example I would like to clearly know what is the current stage the person , in his academic career path starting from a pre-university student & progressing ahead.
So I would like to classify something like (below) & ask user to select one of these designations:
Edited:
Pre-university student

Undergraduate(Bachelors/diploma/associate degree) student
-doing
-earned

Masters student
-doing
-earned

PhD(Doctorate) studs
-doing
-earned

Postdoc

Faculty

Scientist

Independent researcher

Does this cover most of the stages/designations in the academic career or is anything missing ? Is there a better term to represent any one ?
Update:
I don't really need a fine grained classification like assistant prof, associate prof, etc but I do want to include all the academic community & related people who have interests in academic topics(which includes scientists or self learners as well) & ranging from university student to faculty, independent researcher or whatever are the higher positions. May not be necessarily a hierarchical list but at least an exhaustive list is needed.
Update 2:
Another idea was too use classification which includes people from academia & even outside that work on/ explore  academic topics & removing ambiguity between faculty, scientist & research positions . Something like this:
    -> A Learner/ enthusiast,

    -> Pre-university student

    University/Research Students:
    ================================

        -> Undergraduate(Bachelors/diploma/associate degree) student
            -doing
            -earned

        -> Masters student
            -doing
            -earned

        -> Doctorate(PhD, DPhils, etc) student
            -doing
            -earned

    University Faculty/Research Positions:
    ==================

        ->  Professor
        ->  Associate Professor
        ->  Assistant Professor
        ->  Lecturer
        ->  Emeritus
        ->  Other

        -> PostDoc,

    -> Scientist

    -> IndependentResearcher

Did you ask Wikipedia?

@EnergyNumbers: My audience is global. Ok, Scientist does fit into the hierarchy but scientists are also part of my user community so what option would fit for them more appropriately ? Won't "Emeritus" distinguish between current faculty & retired ones!?

One could argue that a career in academics does not begin until you get a faculty position since everything before then is training.

Given the edited list, I would have no idea what to select given I have earned a Bachelors, Masters, Doctorate and have completed a postdoc and am currently faculty. I also consider myself a scientist and independent researcher.

@DanielE.Shub: Gosh, you're right. I suppose the best thing to do might be to separate highest education level earned and current position, AND say pick only 1 from each category that is the closest match.

@DanielE.Shub: the user is asked to provide the match which describes his current position best way.

@DanielE.Shub: and yes, I really dont have a clear idea about how to distinguish between faculty(which also fits into scientists category) & scientists which work outside academia in industry, as I want to include them too. A newer idea was too use classification which includes people from academia & even outside that work on/ explore  academic topics (appended to question).

@user01: Postdoc should be in research position. It is not a course/qualification but a job. And like I said in my previous comments, "scientist" doesn't really mean anything. If you're referring to commercial researchers, its better to say so. In academia, basically anyone who do research is a "scientist". And I just realized that there might be non-PhD non-postdoc university research staff (e.g. ex-masters students hired to do research).

@Legendre: Thanks again! I updated my list. About the 'scientist' term, I know you're right. So, could you suggest about how do I include those people in this list that are outside academia but do research like say scientists working in NASA or other research organisations. Sorry that I didn't made it clear in the question before but I also need to include people outside academia that work in industry or research organizations on scientific topics. Could you suggest some terms to represent such people in this list?

@user01 : Those would be commercial/professional researchers. Commercial if they are employed by firms like pharmaceutical, banks etc. Professional if they are employed by firms that are not strictly "commercial", e.g. NASA, Public Health etc.

@Legendre people who do research in the humanities do not generally consider themselves scientists.

@DanielE.Shub - My suggestion was the title "commercial/professional researcher", not scientist. "Commercial/non-academic researcher" would probably be better.

@user01 Since you have some responses below that seem to answer your question, please consider marking one of them as ‘Accepted’ by clicking on the tickmark below their vote count. This shows which answer helped you most, and it assigns reputation points to the author of the answer (and to you!).

Like EngergyNumbers said, you should tailor your classification to the culture of your targeted audience. This list of academic ranks for various countries might be helpful for that.
Also, "Scientist" and "Researcher" doesn't really mean anything. A postdoc, assistant professor, principal investigator, or someone doing research in the commercial sector can be a scientist or a researcher.
I think you know this but just in case: "postdoc" is an (often) temporary job that people take up after obtaining a PhD, and not a qualification. Some people do not do postdocs, and go directly into teaching, industry or become assistant professors after getting their PhD.
Finally, "Post Grad" can refer to both masters degree or PhD students. It is common to say "applying to graduate/grad school" to when referring to applying to a PhD course.

I don't really need a fine grained classification like assistant prof, associate prof, etc but I do want to include all the academic community & related people who have interests in academic topics(which includes scientists as well) & ranging from university student to faculty, independent researcher or whatever are the higher positions. May not be necessarily a hierarchical list but at least an exhaustive list is needed. I made a correction in my list as per your comment about postdoc not being a qualification.

This should be more or less comprehensive: preuni, undergrad, non-PhD postgrad, PhD student, postdoc, faculty, retired faculty, commercial, independent. I think "emeritus" might not be understood globally. Also, independent would cover those doing research without official affiliation (I know a few). And there are masters students (MPhils, research masters etc), who are postgrads, and doing research.

@user01 - Using your current edited list, someone who has earned a masters, did his undergrad and is an independent researcher and doing science would have 4 categories to pick. I suggest having two categories: 1) highest education level (earned or currently a student), 2) current research position (student, faculty, postdoc, commercial/professional, independent/non-affiliated/others). Pick only one that is the closest match from each group. "Scientist" really doesn't mean anything.

I see problems with your ranking.
Firstly, there is not much difference between * (Completed) and the subsequent ** (Ongoing) level - somebody who completed a post-doc probably is currently either a professor or in the industry, where having a completed post-doc experience does not matter much in terms of being an academic rank. Besides that, there are countries where being a "post-doc" does not mean anything special, the official position would be either the same as being a PhD. student, or a staff researcher.
Secondly, if you want to be too fine grained, there are several levels of professor positions missing (assistant, associate, full plus all the combinations with tenure position, or being a teaching/research specific position, etc.)
Thirdly, and perhaps most importantly, as others here wrote, the ladder is culture specific so you need to think about your target audience. In the case the audience of your website is somewhat local, go with the local tradition.
If your audience is global, my advice would be to give up the particular fine classification. Rather, you could go with a combination of 3 axes of coarse-grained classification roughly corresponding to the track the person currently follows (industry/academia) plus the highest achieved academic degree plus indication of duration of the current status. You would end up with classes such as

academic & BSc + 2 years - your ongoing undergrad student
industry & MSc + 5 years - you are probably facing an experienced professional
in an industry
academic & PhD + 3 years - either a post-doc, or an assistant professor, or lecturer, well anyway an early career researcher
academic & PhD + 20 years - somebody roughly equivalent to a more senior-level professor

Well, this way I guess you can capture more nuanced classification, than with a single ladder. You can of course add your own axes, e.g., tenure vs. pre-tenure, etc.

I take a somewhat skeptical view of the world. I see three stages:

Trainee: It doesn't matter if they are a student or a post doc or working in industry, if their goal is to acquire a set of skills and move up, then they are trainees. Generally, trainees think being an independent investigator is fun.
Research monkey: Someone who is neither attempting to acquire new skills nor is conducting independent research. Generally, research monkeys realize that independent investigator spend all their time trying to get funding to allow research monkeys to do the fun stuff.
Independent investigator: Someone who conducts their own research. Generally, when not looking for funding they are trying to figure out how they could become a research monkey.

Care to explain the downvote?


text:
How big of an advantage are publications for Applied Mathematics grad school applications?
How much of an advantage does an Applied Mathematics PhD applicant have if he/she has a publication under his/her belt?
Of course, this depends on the "prestige" of the journal that he/she published in. I suppose publishing in a top tier journal like Nature or Science would be a major advantage, but would the applicant be one of the first picks because of it?
More pertinently (I suppose seekers of such advice would not have a top tier journal publication), what about those with publication/publications in lesser journals?

A publication demonstrates your ability to do research, which is highly valued. The better published the article and the more "yours" it is, the better.

a top tier journal like Nature or Science — Careful!  Depending on what you mean by "applied mathematics", Nature and Science might not really be top-tier journals.

"About yea big" (extends arms)

To elaborate on JeffE's comment, some applied math departments are open to students simply applying math (like engineering) and some applied math departments require their students effectively be pure mathematicians that are only "applied" in the sense that they prove abstract theorems in the fields of PDEs, dynamical systems, numerics or probability. Most applied math departments fall somewhere in between: they'd like you to prove something in your thesis and would like to see some actual application, but the rest is up to you.

The question is not answerable at this level of abstraction, because grad school admission is not decided on the basis of easily described rules.  If you're a coauthor on a brilliant and important paper, you may still be rejected if the committee doubts you were a major contributor to the paper.  On the other hand, some applicants with no publications at all may be accepted.
As a general rule, nobody on the committee will read the paper itself.  That would be both time-consuming and unlikely to be fruitful, since the committee probably doesn't even have an expert in this specific area.  They may get a little information from the abstract or your personal statement, but everything else they know about the paper will come from your letters of recommendation.
The letters need to indicate why this paper should help your case for admission.  Specifically, they need to explain why the paper is interesting, what you contributed to it if you are not the only author, and why your work was impressive.
This task will be easier if the paper is really good, and that's correlated with being published in a top journal, but this is not really necessary.  For example, if an undergraduate makes a major contribution to a solid but not exceptional research paper, then that could mean a lot, even if the paper doesn't get accepted to a leading journal.  Of course the paper needs to meet at least some standards - publishing in a junk journal or vanity press doesn't count.  However, the most important issue is demonstrating that you can carry out good research, not getting your name in a prestigious venue.

"If you're a coauthor on a brilliant and important paper, you may still be rejected [...] everything else [...] will come from your letters of recommendation." Actually, it's sad. It means basically that actual accomplishments are worth less than networking, being at a prestigious university, having a recognized and diplomatic advisor, etc.

I see it as the opposite: it means you need actual accomplishments, not just the ability to attach your name to things.  Sometimes people get their names on papers because of minor contributions or networking. Letters give a way of distinguishing this from serious contributions. If you are the sole author of a paper in a top journal, then that may mean a lot by itself, but few grad school applicants are in that position. If you are one of several authors, or the quality of the paper is less obvious, then letters are crucial.

OK, you are right with this "appending risk". However, the first author in a decent-class journal is not that rare.

The answer depends on how the admissions process works. In my school you need to find someone who is willing to be your primary advisor to have any chance of being accepted. I am much more likely to spend a few extra minutes considering a candidate with a publication. In fact, I would say that I would schedule an informal phone interview with anyone with a publication nearly independent of the CV. Beyond this initial stage, which in my opinion counts for a lot, but not everything, things get too complicated to speak generally.

PhD admission works like this in the UK too: students usually have to contact a supervisor/advisor beforehand.

In applied math this is not always and often not even usually the case. Many applied math programs, like math, admit students and then they find their advisors after they have finished some coursework and passed their quals, in the meantime they are assigned a temporary advisor before hand.


text:
Identifying new references when appending to existing reference list
I am building a database from several online sources like Engineering Village. Everyday I am searching different/close/related keywords that pertains to my research topic. Then, I am (everyday) exporting and printing out the documents to do manual filtering depending on the relevance of the article/report. I also importing/appending daily search results into my cumulative list. This may lead to duplication which Reference Managers identifies and filters out in most cases. How do I have a daily reference list such that there is no duplicates? In order words, is there a way to know each time I append my references which are the new ones that I generated (through query) only today.
Please let me know if you need any clarifications. Thank you for your help.

If you are using the EndNote reference manager, it will tell you that you are importing duplicates, which references are duplicates, and then give you options for what you can do with them. It seems reasonable that other reference managers will do the same.
As an example, many journals now have adopted the practice of publishing articles online before they have been assigned to a print volume. Thus, I may want the manager to replace the old reference (without page and volume information) with the new (with that information). EndNote lets me choose to do this.


text:
Batch editing references
I imported many pdf articles into Mendeley but saw that Mendeley did not capture all the fields correctly. So, I needed to change them manually. It would be a tedious job to do so with many documents. Fortunately, many of the documents share common journal names and years. So, I needed a way to edit them together.
Is there a reference manager where we can edit selected references in one go without having to do this for each reference individually?
I have tried Endnote. Mendeley, and JabRef so far but could not find such a way. I will be grateful if someone has any idea/experience in this direction.
Edit-1:
After solving the batch editing problem, I also had a problem with getting the syntax for the authors correct.

Thanks @CharlesMorisset. This question taught me more thing than I could imagine. I realize the value of SE where you can get questions and answers either not found or hidden in guides and manuals

Mendeley does it actually. I did not try properly before.

Then I had a problem with getting the authors correct. What you need to do is put them as follows
Last Name, First Names
Last Name, First Names

and so on.
After Edit-1:Another useful thing in Mendeley is that, you just have to select the authors from the pdf and Mendeley will give suggestions on the syntax based on existing authors in the current database. See the following image.

If you use bibtex, then you can batch edit with things like sed, awk, or simple find/replace in any text editor.

In my experience, the author syntax changes if you're using DOI or PMID. In addition to the method that @Stat-R suggests, if you filter by authors, you can simply drag and drop author names onto each other and they will merge into your designated syntax.


text:
Should honorifics be included in acknowledgments?
In the “acknowledgments” section at the end of a paper, I currently have a sentence saying:

The authors thank Bob Johnson for discussions and insightful comments

However, I wonder: Bob’s full name is Robert Z. Johnson, he is a professor and a fellow of the Royal Society. Should his title be used? What about post-nominal letters? And middle initial? Finally, is it “Bob” or “Robert”?
I initially went with “Bob Johnson”, because that’s how everyone calls him (heck, his academic webpage is title “Bob Johnson”!). But is that appropriate?

In general, when in doubt, you should use the name of the author as it appears professionally. If the person in question publishes under a particular name, you should use that. The only exception is if you and the author have an existing relationship outside of this, in which case it is appropriate to use a less formal name.
You do not normally need to include honorifics ("Prof.", "Dr.", etc.) unless specifically asked to do so.
This leads to the final point: if you have any questions about how someone should be credited in an acknowledgment, ask. They'll generally be more than cooperative.


text:
Influence of Letter Submission Methods on Postdoc Hiring Outcomes
Is it common for labs with postdoc positions to ask candidates to request recommendation letters to be sent rather than directly asking from the references?
I've noticed a pattern where labs that ask for letters to be sent to them are less likely to consider me for the position seriously, i.e., either hire or decline within a timely manner and not to ghost me. I also have had PIs inviting me to their lab without asking for a letter, but I have not had luck with someone who asked to send it to them.
This trend has led me to believe that those asking for letters to be sent might not be seriously considering me and are simply collecting them as a backup. This has become problematic since repeatedly asking for letters has led to one of my references not sending the ones I ask for but sending the ones the faculty asks about me. I would appreciate your take on this as a faculty or former postdoc.

It seems plausible that the people who directly ask the references for letters would do so only after reviewing other parts of your application  and deciding that  you should be seriously considered.

I would attribute the difference to whether the person who makes the hiring decision is working in an environment where (i) hiring goes through a shared portal that allows applicants to enter the names of letter writers, and then automatically notifies these letter writers, or (ii) hiring is done on an individual basis, based on the decision of the PI, who then simply tells the appropriate administrator to hire that person.
I don't think that your inference from procedure used to outcome is valid. I'd think the two are entirely unrelated.

I think this merely illustrated some administrative differences. There are many places that first collect all candidate information, then remove unqualified persons from the list, to finally send out requests for the letters of all candidates. Only after that, the shortlisting process begins.
In other words: without knowing the system that the other places are using, we cannot know for sure, but I believe that there's an effect on the likelihood. I wouldn't read too much into it.
Good luck with your applications!

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


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Is it Beneficial for Postdocs to Give Talks to Single Research Groups?
As a postdoc applying for a second postdoc position, I frequently email potential mentors. I have a question regarding two situations where the faculty member showed interest in my work but had no openings. Instead, they invited me to give a talk to their research group via Zoom. While I appreciate the opportunity to give a presentation and have done so before for departments and multi-PI journal clubs, I don't find giving a talk to a single group beneficial. The reason is that the audience members were either required to be there and not interested or trying to impress their advisors by asking questions, and some were very forward. In addition, both occasions involved faculties who were center directors. Therefore, if my work interests them and they are not simply looking for entertainment, I expect them to expand the talk to their center to at least allow me to benefit from networking opportunities. Another view is that these groups are important enough that I should be more than happy to present in their group meeting (one at MIT).
As a faculty or postdoc, what is your position on asking a postdoc to present their work to your group, and if I should ask them to upgrade it to at least a multi-PI level meeting if they want me to give a talk?

Perhaps, also consider that this is a chance for you to interview their group. In your case it may be good to see how the group interacts. Are they providing useful feedback to each other or trying to impress their advisor as you say? This may be valuable information if/when you decide on which group to join.

As well, its possible to meet with more PI's without insisting. Maybe a response like: "Hi, (PI A) I would love to give a talk. Afterwards, maybe we could grab a drink with (PI B) as well..." In most cases you may just see other PI's afterwards and in some cases I imagine those that agree to meet after may want to attend your presentation without you insisting the presentation become larger. I think this is my last thought, otherwise I will group them into an answer.

You should probably regard this kind of thing as a pre-interview for a position that doesn't exist yet.
Let's say you email me to enquire about positions. I don't have any money now, but my postdoc Alice has been interviewing for TT positions and I expect that I'll need to fill that post again soon. And I'm hoping to hear back from the funding agency any day now. Perhaps I'll even get around to writing that other grant application over the summer...
So, while I can't offer you anything right now, I am keen to know a bit more about you in case something comes up in future. And depending on how interesting you turn out to be, I might be more (or less!) inclined to make an effort to find money for you.
So, these talks are an investment in your future. They probably don't pay off now, but they may well impact what opportunities present themselves in a year or two's time. Whether that is a worthwhile investment depends a lot on your current and future plans.

Giving a short talk at a single group's meeting has the following benefits:

Practicing your talk skills. Academia is full of terrible talk-givers. Doing good talks (preparing slides, speaking, answering questions) makes you a better academic and teacher. And the most efficient way to improve is to, well, give lots of talks to lots of different audiences.
Refining your "elevator pitch" -- that is, in a nutshell, what do you do and why should I (another researcher) care? To win grants, make collaborations, and reach wider audiences (such as for commercialization or media outreach), you need to master your marketing pitch.

"I make simulations very fast so people can efficiently model batteries, supercapacitors, and other electrical devices critical for our green future" is better than "I study matrix pre-conditioning and efficient GPU computations for dynamically charge equilibrated molecular dynamics simulations to accurately model conductive boundary conditions that can't be captured by planar dielectric approximations". It's taken me dozens of talks to get there, and I'm still improving.

Tailoring the generalist introduction to your topic. Giving lots of different talks to lots of different groups helps you gauge the "common knowledge" that you can assume, letting you skip to what makes you the best at what you do without leaving your audience in the dark.
Broadening your horizons with in-depth discussions. Giving a multi-PI talk means your subsequent discussion will remain at surface level; giving a talk to a single group will generate deep and meaningful discussion that can result in collaborations. (And if you haven't prepared for generating discussions based on the group's own expertise, you haven't prepared for the talk.)
Thickening your skin and deepening your gratitude. On one hand, an academic will always lose half their audience, simply because other academics are always distressed and harried. You might as well get used to it. On the other hand, you get the chance to share your work! You are doing something few others in the world do, and you have a chance to share your expertise with a community of like-minded people. Healthy scientific subdomains have vibrant communities where people love to share ideas and make friends -- don't ever take it for granted.

Ultimately, this is a personal decision that depends on how you value your time, but in general I would say that as an academic there is hardly a thing as giving too many talks purely from a honing your skills perspective as detailed in another answer.
On top of that, being invited to give a talk by people who are not in your network (yet), should be seen as an honour as they are interested in your work and/or you as a scientist. So each invited talk is another line on your CV, so to speak.
Third, perhaps you should lower your expectations a bit. Even as a PI I still frequently give talks to 'just' a research group. I've also given full center talks where in the end only five people from a single group showed up. As well as talks for up to 300 people in the room. Either one of these can give rise to a good discussion and new network connections and future collaborations. Strength is in interest here, not in the size of the audience.
As an aside, with the advent of zoom it is probably easier to invite people for a talk than it was before, so you may need to be selective - but keep the above in mind.

Why being selective? People inviting you are in general interested, they don't have time to listen to research that is of no interest for them.

I just meant to say that there is a limit - if this person gets 10 requests a month that's too much, but a few each year? That's what many postdocs would want!


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How to publish your research quickly when it pertains to a topical current event?
I would like to submit my very current research to some Journal. The work is related to recent hurricane in USA (Hurricane Harvey). Since the peer-review process takes months to publish a work, so I am looking for some well-known journal which can publish my research in maximum 2 weeks with no cost. Would anyone have any idea where and how to publish very current research? or already published their very current research in past?

What do you want to accomplish? What is the point of the two-week deadline?

What kind of research did you do in the last few days, given that this is something that just happened? Generally, any meaningful research undertaking (worth publishing) takes time to actually do. There are probably a few exceptions to this... but very, very few.

Yes, I understand your points. I have analyzed the tropical extreme events in past 60 years. Though I had finished all works before July, but this hurricane occured when the manuscript was supposed to submit. My boss told to include the recent one also. Thus part of the result highlights the recent hurricane. Anyway, after getting the comments and answers, it is better to get accepted my few months research through peer-review process.

Scholarly papers aren't like newspaper articles - if something is only of interest because of recent events, maybe a blog would be a better way to disseminate your results than an archival publication?

What is the intended audience of your research? If you publish too soon after the event, your audience may not see your work as they won't be expecting it. If you're trying to reach a new audience, they may not even care if your work is formally reviewed.

Quality peer review takes times: Science takes time and quality peer review takes time. Presumably, you want the stamp of approval that peer review brings. In which case, you will want to publish in a journal where the peer review has meaning. And in this case, peer review takes time. Sure, some fields and journals will get you an initial decision faster than others. But you might get rejected at the first outlet and that can take time; and you might be asked to do revisions somewhere and that takes time to get that outcome, and then for you to make the revisions, and then get an outcome on those revisions. The fastest experience that I've had from submission to in press was about 2 months. And I wouldn't expect to have the same outcome for other work submitted to the same journal.
Consider sharing a preprint: One option would be to post your work to a relevant preprint server. I don't know what discipline you are in, but OSF preprints will accept work in any discipline https://osf.io/preprints/
This would allow you to circulate and share your work immediately.
You could then engage in the more time-consuming task of getting your work published in a peer-reviewed journal.

so I am looking for some well-known journal which can publish my research in maximum 2 weeks with no cost

This is unlikely to exist. There may be well known journals that will publish slowly at no cost, or obscure journals that will publish for free quickly, or predatory journals that will publish quickly for a cost.
But peer review takes time. So a proper publication.
What are you goals? If you want knowledge to be public, you could approach a magazine or newspaper, make a blog post, or post a preprint to ArXiV. This can also help if you want to establish work as yours, so you don't get "scooped".
At the end of the day, the urgent responses to a hurricane will likely come from government scientists, publishing government reports instead of peer-reviewed articles.


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How secure is a post doc job offer in an email from the department chair prior to receiving the official written letter?
I'm in/from the US. I'm finishing my PhD this semester. I've been offered a research postdoc, via email, by the dept. chair at one of my top choices, but outside the US (would rather not give too many details). I replied to say I'm accepting the position. Everyone seems very happy: me, the chair, the professor I intend to work with. But I have nothing in writing.
In the meantime I have an offer for a teaching job at another place much closer, which I would definitely take if I were not getting the above postdoc. I don't feel comfortable turning this down until the other setup is official.
I emailed the postdoc place asking for an official letter. They said they would send it out by mail, but ignored my request for a scanned emailed copy, and I need to give a yes or no answer to the second place before their alleged letter would arrive. I emailed them again about the scanned copy and no response though it has only been a couple days.
How confident should I be that this postdoc is really happening? How common is it for informal agreements like that to be backed out of? Are scanned emailed letters less customary outside the US? It would be terrible of I turned down the teaching job and then the postdoc fell through.
Also, what should I say to the other place if I am still unsure about the postdoc by the deadline for my yes/no?
Update: I got the requested scan of the official letter today. I ran it by my adviser and he says this seals the deal and I can cancel any other interviews. Whew!!!

They said they would send it out by mail. I have a similar incident recently (nothing to do with job offer). I sent the other party a signed official document via express mail so I know when it gets there and who signs the receipt of the document.

I might be wrong, but I would guess this depends a lot of which country.

Note that there are institutions at which offer letters cannot be written for legal reasons. In such a case, the paperwork that you are expecting would be some form for starting the hiring process. This may be the reason why you are not getting a scanned copy upfront - you could not use it for anything. Since you did not write where your postdoc would be, I'm only guessing here, though.

"Are scanned emailed letters less customary outside the US?" -- Even in the U.S., use of digital communications varies widely by institution. In the early oughts I was at a college where everything was digital. Over a decade later, I'm at a college where basically everything is done on paper, and no one is in the habit of doing things by email (e.g., many people would not know how to scan a document).

This sounds like it is a real offer but I would still be wary of this. A close friend of mine was offered an assistant professor position at a good US university in such a manner and had even worked out details such as how he planned on spending his startup fund. Turned out the reason he wasn't getting the offer was because one of the professors at the department was delaying the process to try to squeeze in an interview for one of his friends and my friend never got the offer he was promised (verbally on the phone by the department head). I suggest you get an extension on your other offer.

I was talking to my mom about some of the comments from here, she is a retired high school teacher, and she could relate. She told me of 2 instances she knew of where a person was recommended by the dept. chair and the principal, which is usually a shoe-in, but the superintendent went with a personal friend instead.

An offer in this type of situation is almost always a real offer. However, this kind of delay in getting a written offer is nonetheless quite common and has to do with the way the university's internal bureaucracy works. And as the word "almost" indicates, there is always a chance that something will go wrong, so you are absolutely right to be concerned.
The way it works (in the U.S., and probably in some other countries) is this: postdoc offers are often made by a department chair, but are often subject to approval by a higher university authority such as a dean. Naturally, the dean needs to actually review the file before approving the appointment, and this takes extra time (sometimes several weeks, since deans are busy with many other things) after the department chair or search committee have already recommended making the appointment. In the meantime, the department wants to ensure that they can secure the candidate's commitment to accept the position. Waiting those extra weeks before contacting the candidate is completely impractical and means that they will almost certainly miss out on the opportunity of hiring the person.
The result of this dynamic is that the university will try to play a game whereby the department chair will contact a postdoc candidate with an email, formulated to look as formal as possible (e.g., containing salary and other details, and a response deadline) without actually entering the university into a legally binding commitment. (By the way, IANAL, but just the fact that it's an email rather than a letter is not necessarily the issue; I believe an email could very conceivably be held up in court to be just as binding as a "written" offer, and that it really all depends what the "offer" actually says, including nuances such as whether the word "offer" is used, and whether it contains weasel phrases such as "recommend your appointment to", "subject to approval by", "pending review" etc.)
Note that the way this process is designed is more or less well-intentioned and done in good faith, at least in places I'm familiar with. The goal is simply to achieve an optimal outcome under the constraints of how the university functions, while protecting the university's interests to the extent possible. In all likelihood, no one is trying to scam you into accepting an offer that they will then not offer you. At the same time, as a department chair myself I often think that this way of conducting the university's affairs is somewhat unfair and places an undue burden of worry on the candidate's shoulders. After all, there is always a chance that something will go wrong, there will be a disagreement between the chair and the dean or some other step in the process will fail and the appointment will fall through. And I wonder if when push comes to shove, the university's position of sending emails that are carefully optimized to get people to think that they have a real offer when the language of the email actually avoids making any concrete promises will really hold up in court. At least from an ethical point of view it seems problematic to me. But that's the way things work in many places, and usually things work out in the end.
The bottom line is that a lot of this comes down to a question of trust: did the hiring department manage to instill in you a feeling that they "got you covered" and are backing up their claims with concrete actions? Or are they behaving in a way that seems suspicious and alarming? The lack of willingness to email you a scanned copy certainly seems like a possible red flag (depending on whom you sent it to - never discount the possibility that that person may simply be incompetent or forgetful, so consider looking for other people in the department whom you can turn to for help). Only you can decide how risky the situation feels, and how much risk you are willing to tolerate to secure the position. The only general answer we can give is "an offer is usually a real offer, except when it's not".

I've been speaking to the dept. chair and the professor I would be working with. When I raised these concerns with the chair he said there is absolutely no need to worry and that he would expidite sending the letter by mail. As for the prof. I am certain he would be very upset if this fell through, even thanked me for accepting. Only cause for alarm is the lack of reply from the chair about the scan request.

While from the chair side of the table, you are correct that these offers are "real" and rarely fall through. The issue I have seen is when overly anxious candidates misinterpret an "expression of interest" as an offer. Candidates need to have a frank discussion about what is happening to make sure everyone is on the same page.

Don't count on an offer until you have it officially, in writing.  A verbal offer is not an offer.  An email or call saying you will get the offer is not an offer.
You say you "emailed the postdoc place".  Who did you email?  If it is an administrator they may not understand the urgency of the situation.  I would email the professor you will be working for and (politely) make it completely clear that you have a non-negotiable deadline for replying to another offer.  You should also state that if you don't have at least a scanned copy of an official offer from him/her before then, you will have no choice but to accept the teaching position, even though the postdoc is your first choice.  If they really want you, they will take the 5 minutes to scan a copy of the letter.  If they don't, maybe it's best to turn down that offer anyway.
In the meantime, I would also negotiate with the second place for an extension of the deadline.

"An email ... is not an offer" you should provide a legal citation for this. In the US, you would want to read up on the UETA and Forcelli v Gelco.

People break the law all the time. Unless the OP is ready to spend his time litigating a university in a foreign country, the details of the law do not matter.

@JørgenFogh Not to mention "burning the bridges" with those people, if the litigation gets anywhere.  - - - - - - - - Actually a police sheriff in a speech ("Don't talk to the police" is the title on youtube, i think) on a law school said that everyone has broken some law at some point.

@JørgenFogh your logic also applies to so-called "written" offers. If the details of the law truly "do not matter" because "people break the law all the time", why is a written offer any better than an email? The answer is that your premise is incorrect - the law does matter, even if not as much as we would like. corsiKa's point is valid and important.

The difference is that the counterparty is much more likely to honor a contract on paper. I agree that in the platonic world of ideals, there is no difference. In the world of reality, there is, even though my argument is technically invalid.

This whole discussion is not relevant to my answer; I did not write that "an email is not an offer".  An email very often is an offer!

David, you wrote literally "An email or call saying you will get the offer is not an offer." Yes it is. An email saying an offer is forthcoming and guaranteed is a formal, binding document as per Forcelli v Gelco.

This may seem obvious but the fact that you are asking the question implies that you are unsure as to certainty and that alone should encourage you question anything that is not a signed contract.
Personally I would approach this by contacting them directly and explaining your position. If they are 100% on their commitment then expediting the written confirmation you need will not be an issue. A little pressure will work wonders.
Good luck.

I wanted to say something like this, too.  Your immediate problem was already resolved, but if it weren't, I would not hesitate to call the place and explain (again) why a scanned copy in email would be urgently required.  Though I'm guessing their conundrum was that they didn't take a photo before putting it in the mail, and producing a scan of a newly printed second copy would seem to be of dubious utility, and possibly raise questions about forgery, even though the purpose is completely legitimate and pressing.


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Do references, notes, and tables count towards journal word count restrictions?
I'm preparing a manuscript to be submitted to a journal, but I'm struggling with the language used regarding the word count for this specific journal:

The ___________is a peer-reviewed publication. Articles
  between 4000-7000 words (double spaced pages) including tables, notes
  and references, are accepted for review. The Editors reserve the right
  to return papers to authors where they exceed this word limit.

My confusion is, does this mean that references/notes/tables contribute to the word count of the manuscript for this particular journal?

In this case, the journal is explicit in saying that the word count "includes tables, notes, and references". I suppose the more interesting question is what is meant when there is no such explicit statement.

Yes, the references/notes/tables are to be included in the word count.

Cheers. Would this include the bibliography, or just in-text references do you think?

This would typically include the bibliography.