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How do I deal with the vast number of research papers on a topic? (for non-academics)
As someone not in academia but beginning professional work in science outreach and communication, I'd like to stay well-versed and abreast of the research. However, upon performing rudimentary searches on these topics, I'm blown away by the number of results.
For instance, a Google Scholar search on "science communication" (in quotes) yields about 298,000 results, and a Mendeley search yields thousands also.
So, any words of wisdom on how to go about this? I'd like to dig in and do my homework over time, but I'm not sure how to work with the obvious limitations. I don't feel I have the benefit of specificity of a topic or previous familiarity with the research due to not being in academia also (to narrow down my concerns). I'm also not satisfied with simply reading popular accounts, as I would like to be able to back up my perspective with research when needed (and ideally in a less ad-hoc fashion).

Is your question about how academics deal with such challenges?

It's actually a very relevant question as well for academics who need to understand a new field.

Not a really related, but when I'm looking for professors to follow in a new field, I asked on Reddit in relevant subreddit.

Antonio, it's for advice from academics or other related parties on how a non-academic might go about such.

What's wrong with asking an academic at your local university?  Most I've encountered would love to share this knowledge with anyone who'd listen.

Not a duplicate, but quite relevant and overlapping: http://academia.stackexchange.com/questions/30719/how-to-build-a-list-of-seminal-papers-in-a-field/30725#30725

The snowball method is always a good one to get an overview of the more relevant papers in any given field that you're not an expert in.

The situation for academics is actually quite similar to that of non-academics, when faced with any discipline where they are not already an expert.  In cross-disciplinary interactions, we are all the laypersons for the other disciplines.
I find that when I am trying to learn about a new area, often the first problem is even just to figure out what the right words are to search for.  Every discipline has its own specialized vocabulary, and often the words have unexpected meanings.
As such, my approach tends to be as follows:

Start with Wikipedia or textbooks or some other similar popular (but well referenced!) source.
Identify key terms and key sources, and use those to find some good scientific review papers to read.
That will often be enough, since I'm often less interested in bleeding-edge theories or origins than in the current community consensus.  If not, however, then the review papers generally give enough context that I can follow references forward and back from the review papers, search key words I learn from those articles, or look for other papers authored by key players.

+1. In many topics wikipedia cites some good review papers, they're also worth a start.

There's a lot of exceptional advice here (most of which I upvoted), though I accepted this answer due to acknowledgement of having a sort of cut-off point in a sense. Review papers is also an excellent suggestion, and if anyone knows other repositories that focus on such, I would be interested.

298,000 search hits indicates a mature field that has attracted significant attention. There should be textbooks, and, yes, repeating the search on Amazon gets hits. Begin with one or two well-reviewed books.
After reading a textbook or two you should have the general outline of the field, and some questions about it. The next step is to pick a sub-area, defined by terminology you learned from the books. Do more focused searches for papers.
The ideal type of publication at this stage is either a survey paper or the "related work" section of a doctoral dissertation. Either will give you references to foundation papers in the subarea of interest. Now look for recent papers referencing those foundation papers, with additional keywords related to your current question. You should get a feel for who is doing, or at least supervising, research that may interest you. Pick out some of the papers for which they are a co-author.

Excellent suggestions. My concern with books though is navigating bias. Especially in fields where theories are not as easily empirically differentiated. Even with a good review, I might feel like I'm getting a perspective in line with consensus, but it instead end up being narrow or popular for other reasons.

@Josh Don't treat any book as the last word - for one thing, publication delays ensure that it won't contain the latest information. The books are just to get an overall feel and help find some questions.

+1 to both Alexsandr's and jakebeal's answers, especially jakebeal's recommendation to look at review articles, i.e., articles that review the state of the art in a particular topic, summarizing many individual contributions and articles. Reviews are definitely something to look out for.
Depending on your specific field(s), there may be entire journals set up to publish nothing but reviews. These are the journals you want to find and set up alerts for, as per Aleksandr's answer.

Three things I'd like to add:

First, try to attend a conference once in a while if your budget permits. It's a lot easier to figure out who the central people in a field are when you see who is on a conference organizing committee, who is invited for keynote talks, and who generally makes insightful comments at others' presentations. Get their cards, google their names, find out what they do, and follow them as appropriate, by subscribing to blogs or Twitter feeds, friending them on Facebook, or following them on ResearchGate or Academia.edu.
Second, develop the art of skimming. You simply won't be able to read everything, even if you restrict yourself to review articles. With any paper, start by reading the abstract. If that does not appear to be useful, don't feel guilty about putting the entire article aside and focusing on a different article that is helpful.
However, do also develop the art of not only checking what's immediately relevant, but also what is only tangentially related to your main focus, because this is how you acquire breadth, as opposed to depth. I'll save any article that sounds even vaguely interesting and have made it a habit to at least skim one of those on a daily basis. (Yes, I do need to explicitly track this, because otherwise this daily reading will be crowded out by short-term issues, and I'll never get around to reducing my "unread" pile. YMMV.)

Edit: Regarding my first point, on conferences, @Josh comments that it might be difficult to network one's way into those.
At least in my field, you can simply attend a conference without presenting anything, so there is nothing to stop you from attending. I don't know whether there are conferences that only allow you to attend if you present something, but I would be surprised if such restrictions were common.
Conversely, large conferences will eagerly welcome new attendees. For instance, the American Statistical Association, at their Joint Statistical Meetings, have "docents", long-time attendees that are available to show first-timers how to navigate a convention center full of thousands of statisticians.
I agree that there is a bit of a chicken-and-egg problem in finding the right conferences to attend, if you want to attend to get an overview of a field... because looking for an overview by definition means you don't know enough about the field to choose a good conference. You will likely need to do some homework about this.

Look for good publications, check which academic societies sponsor those publications, look whether they organize conferences.
If you found someone who does good work, see what conferences he or she tweets about attending.
In computer science specifically, where most of the science is done via conferences rather than via journals, once you find a good publication, check what conference it was published in, and more importantly, what conferences its references were published in.

The entire "find a good conference to find good researchers to get an overview of a field to find a good conference" loop will likely need a few iterations. But there is positive feedback involved: the more high quality people/journals/conferences you know, the more new high quality people/journals/conferences you will get to know, because your network will gain dynamics and traction!

In fact, I started out in my now current field as a blank slate in 2006, with a completely unrelated Ph.D. and no academic connections to this field whatsoever. So I simply googled around, found some papers, then a journal, then the journal's sponsoring association, then its conference, simply attended this conference in 2006 without knowing anyone whatsoever, chatted up everyone I met, contributed a little to the associated practitioners' publication and pretty soon felt very welcome indeed in this particular community, although I am of course not an academic per se. The approach I propose works.

Thank you for kind words, Stephan. +1 from me to all answers, as they provide partially intersecting, but complementary and useful points. +1 to the OP as well, as this question is a rather important one.

Great suggestions and upvoted. I hadn't even thought about conferences. If one is not in academia though, networking one's way into those might be difficult. Any suggestions there?

@Josh: thanks, good comment. I edited my answer to address it.

One good way to "use" conferences without actually attending: have a look at the program and the abstract book online - it should give you quite some information on the latest topics and who is working on what. Make sure to have a look at the people to give the keynote.

Generally, there are no easy solutions to that and the underlying problem, which is usually referred to as information overload. Having said that, I can think of various approaches to the problem that you have described, including the following ones.

Mastering the use of keywords and corresponding databases' search engine syntax, when performing direct search of research papers on a specific topic. This approach includes using alerts, which I find as quite an effective tool to fight information overload in academia.
Using various citation indices and citation impact indices, with my personal preference being the open (non-commercial) ones, such as Google Scholar, CiteSeerX, RePEc and SSRN (obviously, I mean here indexing and ranking functionality of the corresponding services).
Using professional curated sources, in particular, research- and science-focused online portals (including ones, affiliated with major professional societies and research journals), where popular, significant or promising research if often featured.
Using, similarly to the above-mentioned curation services, personal curated sources, such as thematic or topical websites, blogs, discipline-focused social media and other online resources.
Last, but not least, using the power of professional networking (both online and offline), tailored to your research or professional interests, IMHO promises to increase chances in staying up-to-date on important classical and emerging scientific trends and discoveries.

These are some excellent specific suggestions, and I appreciate listing the sites (and I've upvoted). You mention citation indices which I think holds some interesting options. For instance, should I intentionally search for papers that are cited more than others? Or does this risk a sort of popularity bias?

@Josh: You're very welcome. Thank you for kind words and upvote. In regard to citation and impact indices, I wouldn't consider that approach independently from the others, as doing so increases the risk of missing important, but overlooked, as well as emerging research (I guess, this represents the popularity bias you've mentioned). I think that it is best to use that approach in combination with the other ones, mentioned in my and others' answers.

The answers you have been given are pretty comprehensive, but an additional avenue you might find beneficial is to ask an academic librarian.
Whilst not all are experts on the field (or even have a qualification in that particular area), their profession is to deal with information. As such they might be able to help you navigate resources and construct search queries to refine your result sets.
They are often well placed to suggest resources or databases to help manage your research that you might not be aware of.
Most university libraries are pretty accommodating to visitors (the University I work at allows free access and limited access to some e-resources, with a paid option for borrowing entitlements) especially at this time of year as the exam period draws to a close.

The question is concerned about how to deal with large number of research papers in order to stay up-to-date on a topic. This is different from searching literature on a topic, for which your suggestion is valid (but, IMHO, more applicable to students, than researchers, who are expected to know how to perform literature (re)search).

Then, perhaps, your suggestion can be used by the OP, assuming that he or she has access to an academic librarian. +1.

@aleksandr-blekh Thanks for the +1. Messed up my comment by trying to edit it. Below is the comment I removed so your reply isn't out of context.
The question does indeed begin 'How do I deal... ' but the OP then goes on to say:
"As someone not in academia but beginning professional work in science outreach and communication, I'd like to stay well-versed and abreast of the research"


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Review a paper with recent coauthors
I got a request to review a paper from a journal. I know the topic area well, but I've had some recent collaborations with some of the authors. Should I decline the request because of this? What is the common practice here?

It's potentially a conflict of interest, but some fields are small and have few competent reviewers. Tell the editors, and let them decide. They can offset a bias in their final decision in an informed way, or take you off the review if they believe this poses a problem.

There are separate links to accept or reject the request, so I'm not sure if this is a possibility.

@user11550 Presumably you know the name of the editor though, so can make direct contact with them?

Isn't there an email through which it was sent? A "reply" usually works.

When you submit the review, you may be able to write "confidential comments to the editor", which the authors don't see. You can mention recent collaborations there. Of course, that presupposes that you have already written the review...

Given that any time that the editor spends waiting to find out that they can't use the review is time they've not used for finding a new reviewer, it would always be best to clarify this with the editor as soon as possible. Hopefully this should be obvious, but I wouldn't want any reader misunderstanding @StephanKolassa's comment as a suggestion to write the review and then notify the editor of the potential conflict of interest.

@Ian_Fin: I was thinking more along the lines of writing the review, since the OP presumably is an expert on the topic, but then informing the editor of anything that could motivate him to take the review with a tiny grain of salt.

From personal experience, I would suggest directly e-mailing the editor who was named in the request to review, or the editor-in-chief if there wasn't one.  The "reply" may go to an editorial assistant who doesn't know what to do with your question.  (If you can't get a reply from them about this question, I might suggest these are not editors you want to review for (or submit papers to!))

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Am I allowed to process personal data on a cloud server?
I have gathered some fMRI and eye tracking data, from several subjects. I can process them using the server in our lab, but I would like to take advantage of my own cloud servers on Linode and DigitalOcean, even EC2.
Before these data were gathered, in the consent form we did not mention the possibilities that data might be processed/stored in the cloud.
Am I allowed to use cloud servers to process these data under current regulations? Does it makes any difference if these servers were purchased/rented under my lab's name?

I don't know what "regulations" would exist to govern this. It sounds more  like something your IRB would have to approve.

+1 to @NateEldredge's comment. It would be very good if your data were first anonymized suitably.

Good question, anyway, +1. I took the liberty of editing it a bit to emphasize that we are talking about personal data in the title. Feel free to roll back or improve my edits.

@NateEldredge, HIPAA in the US coould be construed to cover this very easily. Unless the cloud provider has a BAA in place with Quan's university to guarantee the correct data protection, there could be trouble.

@BillBarth but eye tracking and to an extent fMRI data are not PHI so HIPAA compliance should not be an issue.

@StrongBad, since when is an fMRI not PHI?

Data protection law varies by country. What country are you in? Are the cloud servers in the same country? (or if you're in the EU, are the servers also within the EU?)

I wrote a paper covering this. I don't recall what section. When I look over it again I'll point it out. http://albertkung.com/files/RP_IA_18Aug2013.pdf for the U.S. specifically

@AE: This is a very crucial point. Where you are in the world makes a huge difference. For instance, it's technically not allowed for German researchers to share their results via Dropbox, because the servers are not based in Germany. No way would you be able to put personal data on a cloud server not based in Germany—and even then you'd have a hard time getting around privacy laws.

To some extent, the answer depends on location. In the US, IRBs tend to be concerned with Protected Health Information (PHI). There are 18 things that are considered PHI and generally these can be easily stripped from research data. For fMRI and eye tracking data, you need to be a little concerned about two components of PHI

Biometric identifiers, including finger, retinal and voice prints
Full face photographic images and any comparable images

In the UK the term is Personal Data and the definition is:

Personal data means data which relate to a living individual who can be identified –
(a) from those data, or
(b) from those data and other information which is in the possession of, or is likely to come into the possession of, the data controller

Most people provide a data storage and archiving plan that outlines how they protect PHI/Personal Data in their IRB ethics application. Most IRBs that I am familiar with do not consider fMRI to be comparable to a full face photograph or allow the individual to be identified. This is despite fMRI researchers often being able to recognize each other's brains. Most eye tracking data that I am familiar with do not include high resolution images of the retina and would not be classified at PHI/Personal Data. People publish pictures of fMRI slices and eye tracking traces all the time. Prior to uploading data onto the cloud, you will want to confirm with your IRB what they consider PHI/Personal Data.

The applicable regulations don't directly apply to you as an individual, they apply to your institution. The institution in turn states what is and is not allowed. My former institution had a policy (stemming from FERPA) which required any email to or about a student to be encrypted, and could only be sent from a university-owned computer on-campus. This is well above the requirements actually imposed by FERPA -- it's erring on the side of caution.
You may be able to determine that there is a policy prohibiting or allowing such data storage, and I would bet that it is prohibited. The university has to be certain that personal data is secure, so except for a monumental oversight on the university's part, they surely would be some policy. You need to trace through the policy documents and see if, for example, they say that restricted data can only be put out there via a university-sponsored Box account.

I have never heard of fMRI or eye tracking data as being consider personal since it is, by it nature, anonymous. The data don't even need to be anonymised, since there is nothing personal in them.

Nameless voice data is "personal" since it can theoretically identify an individual, even if there is no name associated with it. The data do need to be anonymized, unless you have obtained consent from subjects to be identified. It doesn't matter if it's not anything you would personally care about, it's about informed consent. If the server data is anonymized you (she) are probably okay, save for a quirky interpretation of policy by the institution.

@StrongBad, fMRI data is not anonymous unless it has been anonymized. If a scan of your brain with your name on it exists, that's PHI.

@BillBarth your name is PHI, the fMRI data are not. If the name is included in the fMRI data set, the data set needs to be anonymised. Many research scanners either do not use names and/or produce "clean" data sets. I have never seen eye tracking data with a name or ID number embedded.

@StrongBad, none of what you say is in evidence here. We don't know the provenance of the data except that OP did the scanning. It could be from a clinical scanner at a university associated hospital, etc. Given the level of statutory fines, I would consult with my university's HIPAA compliance officer rather that just assume you can anonymize it or that it is already sufficiently anonymized. Further consultation with the IRB is probably also required.

"The applicable regulations don't directly apply to you as an individual, they apply to your institution. The institution in turn states what is and is not allowed." - [citation (for the general validity of this statement) needed]

42 USC 289: “The Secretary shall by regulation require that each entity which applies for a grant… to review biomedical and behavioral research involving human subjects conducted at or supported by such entity…”. It's more involved, but that is the core statute. 45 CFR 46.101(a) recognises the scope limitation to research supported the federal government -- see subsequently 103 "Each institution ... shall provide written assurance...".

@user6726, how do you know OP is in the USA? Here in the EU this would be a matter of law, some of which does apply to individuals as well as to institutions.

I don't know: this is why people need to give appropriate context when asking questions. Otherwise, people will supply whatever seems appropriate to a question about "current regulations".

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Breaking an axis - is it ever a good idea?
I know that using an origin other than 0 for numeric data is considered misleading. But for plots in academic publications, is it ever a good idea to break an axis so that patterns and outliers can be more easily seen?
Or would you always try to find an alternative (e.g., using a logarithmic scale, faceting, using multiple plots with different scales)? I'm looking for a general rule of thumb.

A long as it is not bar plot and it is not misleading.

Honestly, I'm tempted to vote to close as off-topic. This question would be much better at UX.SE, or possibly CV.SE (who also do visualization). There really is nothing very academic about this - this question makes sense for anyone who visualizes data, whether high school student, undergrad, business person or volunteer for a charity. Then again, I just submitted an answer, so I can't very well VTC...

see http://stats.stackexchange.com/questions/1764/what-are-alternatives-to-broken-axes: this question has been answered on CrossValidated.

I'm voting to close this question as off-topic because it is a duplicate of http://stats.stackexchange.com/questions/1764/what-are-alternatives-to-broken-axes

It's perfectly acceptable to break an axis and use a different origin, I see it all the time in physics papers and it's actually the default behaviour of Mathematica.

I think this should be reopened. The question it supposedly "duplicates" asks about ways to not break an axis, not about situations when it's OK to break an axis. I'm also not sure closing questions just because they have been asked (in a different way) on another SE site is a good idea, either. If they're off topic here, fine, close them, but I don't think on topic questions should be closed just because someone else asked them in a different way on another SE site.

"I know that using an origin other than 0 for numeric data is considered misleading.": No, absolutely not. Misleading is plotting data with scales and ranges that hide the data's significant characters.

In my own experience, the time when it makes sense to break an axis is when you have a mixture of two distributions, such that neither a linear nor a logarithmic scale can represent things clearly.  For example, I have done this when dealing with an independent variable in which there was an exponential distribution of conditions, and also zero. (e.g., 0, 1, 10, 100, 1000): this is poorly represented
in either log (where zero flies off the chart) or linear (where the lower values are compressed), but well represented by zero, then a break to logarithmic.
For a dependent variable, however, I have found that it is usually better to use two charts with different scales, or a "detail inset," because it is important to give the reader a sense of the full range of the observed values, and a break reduces the visual impact.

I would add that it also depends on how many things go off the charts. If it is only one, it can be more acceptable.

William Cleveland gives pretty much the same advice, see this same question and my answer at the UX site.

Today's xkcd is a good example for this :-)

I used to be a "don't break the axis" purist. I like to think that I have learned better. Nowadays, whenever I know that zero does not make sense for the data I am visualizing, I don't hesitate to break the axis.
A little example: I recently started recording my weight (in kg) and reducing my calorie intake. Here is the time series. Does anyone think that the plot on the right is more informative? It isn't. Because zero is not a possible weight for a healthy 39 year old male.

It's missing errorbars though ;-)

@gerrit they are there, they are just obscured by the symbols.

I know that using an origin other than 0 for numeric data is considered misleading

You've been told wrong. That's just nonsense. Do use a zero baseline when you're using area to indicate quantity, and a zero baseline gives you an area that's proportional to the quantity. That's typically bar charts, column charts and area charts.
But for line graphs, scatter graphs, sparklines, and any other charts where quantity is indicated by position rather than area, you're absolutely fine with a non-zero baseline.
Have a look at plots of external temperature produced by meteorological organisations: how many of them have a baseline of zero Kelvin? None. Obviously.

And note that the zero baseline for logarithmic data (changes are better described as multiples than as difference) is at 1.

Sometimes, breaking an axis is the least bad alternative.
In one of my publications, reviewers were complaining that some of my lines were off the graph.  But I didn't want to compress the y-axis so much that the lower values would be harder to tell apart.  So, somewhat reluctantly, the final version of my graph looked like this:

Source: Holl et al. (2014)
Note the unusual discontinuity around the value of 300%.
Is it ever a good idea?  It is not ideal.  But in context, it might be a better choice than any other alternative.  In the figure above, I had the choice between (1) extending the entire y-axis normally up to 500% (rendering the difference between 100% and 125% hard to see), cutting off the graph at 300% (with one line going out of the graph), or by stacking two graphs with different y-scales as shown.  I originally chose to cut off the graph, but after a reviewer complained, I opted for the solution above.
As long as you make sure that it is entirely unambiguous what set of values each location in the axes relate to, it should be acceptable.  As ff524 points out in a comment, you should also point out the discontinuity or break in the figure caption.

+1 great example! It's also important that you pointed out the discontinuity and the different scales in the caption, you might want to mention that in the answer.

I think your reviewers helped you out in this case. :^)

@gerrit The plot above looks like pgfplots output. If it is, could you share what keys you specified to get two different scales?

@WChargin It is indeed made with pgfplots. I used the groupplots library with a groupplot, group style={group size=1 by 2,xticklabels at=edge bottom,vertical sep=0pt}, then the first \nextgroupplot with axis x line*=top.  See the pgfplots documentation, section 5.5 Grouping plots.

@gerrit cool—thanks for the section reference! That seems like a very versatile feature.

It also depends on the variation of the data. If you know, from theory, that your data will change from 10 to 20 and the changes there are the ones you are interested in, you can break the axis and focus on that range. Wherever 0 is is irrelevant, as you know that your data lies between 10 and 20.


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Are there any examples for an ArXiv publication nurturing or preventing plagiarism?
First of all, this is about plagiarism in the sense of stealing ideas. Copy-and-paste plagiarism is included but not likely to happen in the cases relevant for this question.
Considering the publication of a paper prior to peer-reviewed publication on the ArXiv (or another preprint server), there are usually two main positions considering a possible theft of the idea (or somebody coming up with the same idea):

If somebody manages to publish your idea in a peer-reviewed journal before you do, you can prove that you came up with the idea first or at least independently if you have published your paper on the ArXiv. Therefore it is a good idea to publish papers on the ArXiv before they have been published in a peer-reviewed journal.
If you publish your paper on ArXiv before it is published in a peer-reviewed journal, others may steal your work and publish it peer-reviewed before you do and thus take the scientific credit. It’s difficult to attack those people since the ArXiv is not peer-reviewed. Somebody could make a living of plagiarising ArXiv papers. Therefore it is a bad idea to publish papers on the ArXiv before they have been published in a peer-reviewed journal.

Are there any example cases (or even studies) supporting either of these statements? Such examples would include, but are not limited to:

Has a peer-reviewed journal ever withdrawn a paper because it plagiarised an ArXiv paper?
Are there well-known cases of “unpunished” plagiarism of ArXiv papers?
Has anybody ever successfully resolved a priority dispute with a publication on ArXiv?
Has anybody ever accused somebody of plagiarising an ArXiv article (with the fact that the plagiarised article was published on ArXiv affecting the outcome).

Note that it is really examples and not a theoretical analysis of the statements, I am looking for. (Neither of the two positions fully reflect my opinion and some of the soft premises¹ are debatable. However, debating about these viewpoints on a theoretical basis or attacking some of the premises is usually futile.)

¹ e.g., that scientific credit is only decided by peer-reviewed publication

To quote Howard Aiken: "Don't worry about people stealing your ideas. If your ideas are any good, you'll have to ram them down people's throats."

Totally bounty-worthy. If we could get a list of examples, there is a fair chance that this could end up developing into a showcase/stock question for the site. :)

The third position: since nobody has come up with any examples, just post your preprint to the arxiv and stop worrying. ;-)

Has anyone who has any experience with arxiv and academic publishing ever held the second position? I find it completely irrational. How can you make a living out of stealing publicly timestamped content...

@SashoNikolov: I have heard professors (from fields that are served by ArXiv) make this claim (not that I support it). I think that should be sufficient reason to motivate this question. Also remember that you might consider this question remaining essentially unanswered a noteworthy evidence on its own.

@Wrzlprmft I am not sure what that evidence suggests. These are rare events anyways, and I doubt they are ever well documented when caught by journal editors, at least not publicly. If it's hard to find cases of plagiarized arxiv papers I think that suggests that the system works by deterring plagiarism or stopping priority disputes in early stages. There certainly are plenty of cases where "independent work" is established by arxiv dates, as suggested in the answers.

If you publish your paper on ArXiv before it is published in a peer-reviewed journal, others may steal your work and publish it peer-reviewed before you do and thus take the scientific credit. It’s difficult to attack those people since the ArXiv is not peer-reviewed.

This assumes that peer-reviewed publications determine scientific credit, which may be true in some fields but isn't universal.  In mathematics, it is not relevant at all for assigning credit.  Peer-reviewed papers are of course more thoroughly checked, but they do not give you any additional intellectual credit, so this difficulty does not even arise.  (In particular, for assigning credit an arXiv paper beats a published paper with a nontrivially later submission date.)

For example, has a peer-reviewed journal ever withdrawn a paper because it plagiarised an ArXiv paper? Or are there well-known cases of “unpunished” plagiarism of ArXiv papers?

This is a difficult question to answer, because how could you tell?  If the plagiarist doesn't copy any text, but rather just takes ideas, then it's virtually impossible to prove that anything was stolen.
In mathematics, it works like this.  If someone publicly circulates a paper, then there's a brief window in which people who have made the same discovery independently have a chance to announce this fact and claim a share of the credit.  They should do so more or less immediately upon learning about it.
By contrast, if too much time elapses, then the community doesn't count it as simultaneous discovery, but rather at best rediscovering something that was already known (which gives far less credit to the rediscoverer).  There's not a clear cut-off for the timing, but I see it as follows: days later is definitely OK, weeks later might be OK, months later is generally not OK, a year later is definitely not OK.
The biggest weakness in this system is that there's a window in which it's possible to steal someone's ideas and claim you came up with them independently.  This is certainly uncommon (indeed, claims of independent discovery are uncommon, regardless of whether they are true or false), but it's hard to know for sure how rare it is because of the difficulty of proving plagiarism of ideas.  Most claims of independent discovery are obviously true (because there's a manuscript that couldn't have been written so quickly, or there's a history of talks or discussions with other researchers, or there are nontrivial variations on the ideas and applications), but every once in a while someone makes such a claim without clear evidence.
Even when there isn't much documentation, I'm inclined to believe claims of independent discovery.  Faking this takes a lot of chutzpah and effort, it's not something you can get away with repeatedly, and it's an awkward situation you wouldn't want to put yourself in unnecessarily, so it seems reasonable to give people the benefit of the doubt.
In practice, I don't think the real danger is outright theft, where someone who wasn't working on this topic at all notices a new paper and says "That looks nice!  I think I'll steal it."  Instead, the most worrisome situation is when someone was actually working on similar ideas, but hadn't really finished sorting out the details.  When they see the paper, they immediately recognize some of their ideas, and the remaining details feel so natural that they say "Yes, that's exactly what I had in mind.  This paper is merely fleshing out my ideas."  They honestly believe that they had practically completed this work, when they might have been somewhat further than they thought.  There's a whole continuum here, from people who are basically right in their beliefs to those who are completely wrong, and it's not clear where to draw the line.
Of course I have no idea how often someone claims independent discovery based on exaggerated beliefs (again it's basically unprovable), but I imagine it happens occasionally.  It's certainly unfortunate if it takes place, but it's not nearly as bad as outright theft.  The worst-case scenario is having to share credit with someone who is less deserving.

Though this is a very nice answer, it sort of answers another question – see my edit to the question.

@Martin: Thanks! Wrzlprmft: Good point, I don't give any concrete examples, but I think it will be hard to produce good examples.

There are difficult parts in your question, but it is easy to find examples where posting in arXiv did establish priority. In fact, you can open random published papers, and find that a decent proportion of them cite arXiv preprints (I found one at my second random try).
To give a famous example, Grigori Perelman published his groundbreaking papers only on arXiv, and was credited for them to the extent that he was offered the Fields medal and the Clay prize of one million dollars (as is well-known, he declined them both).
These papers were digested by the community over several years, giving rise to several sets of notes by different groups of mathematicians, all of which of course credited Perelman for solving the geometrization and Poincaré conjectures; some of these notes, containing clarifications, details or alternative proofs of part of Perelman's work were published, sometimes in top journals. This part also provides an interesting example of online publishing (on a web page, not on arXiv, but seems to the point) establishing precedent, see the following erratum. In short, the authors of a published paper wrote an erratum to acknowledge that they failed to properly cite a preprint which was only circulated online and not formally published, while they used some of the ideas contained in it. This is the way any reasonable journal and authors are expected to treat such cases, at least in mathematics.

Note that while your answer made me notice that I phrased one of my examples too broad, this does not invalidate your answer in my opinion.

A similar story, albeit less glamorous, surrounds Alex Postnikov's work on the totally positive Grassmannian. The only paper is an incomplete preprint published on the arXiv. Some of the unwritten chapters have been completed by other authors and published in very good journals.

Has a peer-reviewed journal ever withdrawn a paper because it
plagiarised an ArXiv paper?

Here is an example for this:
Paper A was retracted, because it plagiarized paper B which had previously appeared on the arxiv.
Paper B was submitted to the arxiv on 7 May 2018 and submitted to Physical Review D on 9 May 2018. Paper A was submitted to Nuclear Instruments and Methods in Physics Research Section A on 8 May 2018.
This timeline shows paper A must have plagiarized from the arxiv version of paper B, and did so before paper B had been submitted for peer review. Presumably, the arxiv timestamp will have helped making this an open-and-shut case of plagiarism, although other avenues of proof may have been available.
This example was found by scouring Retraction Watch entries related to high energy physics (one of the oldest and most prolific fields to use arxiv). A secondary conclusion from this exercise is that retraction due to plagiarism are rare in this field.

Nice answer @TimRias :-) How is it possible that the paper B was submitted to arXiv on the 7th of May 2018, while the retracted paper A was received by the journal the 8th of May 2018? I mean how is it possible that just in 1 day that person plagiarized paper B? Did he/she use some AI tool (e.g. chatGBT) to re-write or at least re-organise the manuscript?

According to Stephen J. Blundell (in Superconductivity: a Very Short Introduction) dealing with priority and plagiarism was exactly the reason people started circulating and indexing preprints online in the first place.

I have found this link. It seems that arXiv itself has a plagiarism policy.
Also a paper describes "large-scale application of methods for
finding plagiarism and self-plagiarism in research document
collections." entitled as "Plagiarism Detection in arXiv".

If I am not very mistaken, both sources are about plagiarised content that has been posted on ArXiv, not about publications that plagiarised ArXiv publications.

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


text:
Is there documentation on how long it takes before publications are indexed by Scopus and Web of Science?
The two major bibliographic databases - Scopus and Web of Science\Web of Knowledge - have one very badly-documented limitation; their update lag. While the majority of papers are added quickly, it can take several months for individual papers to be added.
As an example, I ran a search in Web of Science looking for all papers published by my institute in 2014. In November 2015, it reported 290 papers. In January 2016, 293. In February, 305.
In other words, a few percent of the papers took a year or more to be added to the database, which startled me - I was expecting a lag of perhaps three months. Some of these delayed entries are from relatively obscure journals (specialist Australian publications) or book series, and it seems reasonable that these might take longer, but most are from mainstream titles - one is even from Philosophical Transactions of the Royal Society, as established a journal as it's possible to get.
Scopus is comparable. In November 2015, it reported 340 2014 papers, 356 2013 ones and 351 2012. Running an identical search three months on brings us to 341, 367 (!), and 353 respectively - so a few papers are still being added up to three years after publication. (Unfortunately, Scopus doesn't expose the date items added to the database, so it's not possible to identify which ones were added most recently - it's possible that some were due to journals being added to Scopus for the first time along with their back-issues.)
This is, of course, something of a headache for producing stats. But more practically, it could be a real problem for disseminating science - something being unintentionally missed or delayed from one of the big indexing services can make it much less discoverable and much less likely to be read, built upon, or cited, especially in that important first year.
So, the core question: does anyone know of documentation (or research) into how substantial these delays are; how they're distributed; and whether they're getting better or worse?
(I've spent some hours searching for this but to no avail. I'm wondering if I may just be looking in all the wrong places.)

My experience is few weeks for Scopus and few (3) months for WoS.

They might sample randomly.

Since your search did not return any satisfactory answer to your question, did you try contacting Elsevier's 'Support and Contact' directly about Scopus? Their answer - absence thereof - might be very illuminating.

@G-E by odd coincidence, I actually had a chance recently to speak to someone from Scopus about this. There isn't a single clear answer, since it can depend on unpredictable things like when publishers submit metadata to them, but from memory they said they would expect ~95% coverage after five or six months. (I'll check this in my notes and update if needed)

@Andrew would you please post your comment as an answer? :)

This is a really interesting question!!
According to Clairvate Analytics WebofScience/WebofKnowledge), updating of the WOS collection occurs daily on Monday through Friday. This revelation, paired with @Andrew 's comment about Scopus, suggests that the lag time exists with the publisher and not the database compilers (i.e., how long before the publisher submits (or makes available) the DOI and metadata). Here is an interesting op-ed on these lag times.
It is also important to note that articles which are published in non-indexed journal will not appear in most collections/databases, however, GoogleScholar will may pick up more grey literature (e.g., government articles, theses), and potentially some of the non-indexed journals. This article suggests provides 'optimal' updating frequency compared to GS and WOS in their field.
If the article is available online as either an early print or post-print, then it should have a DOI (I assume), and therefore should be searchable via Google. It follows that Google Scholar should pick up articles faster than human-curated databases (Scopus, WOS).
In a brief search (using GoogleScholar), I came across a preprint by Haustein et al. When is an article actually published? An analysis of online
availability, publication, and indexation dates.. The authors found that in some fields lag time has decreased but has increased (!) in others:

Various studies have analyzed publication delays and found differences
  between scientific fields, journals, and publishers (e.g., Abt, 1992;
  Amat, 2008; Björk & Solomon, 2013; Das & Das, 2006; Diospatonyi,
  Horvai, & Braun, 2001; Dong et al., 2006). Since long delays interfere
  with priority claims and slow down scientific discourse, publication
  speed plays an important role for authors and scholarly communication
  (Rowlands & Nicholas, 2006; Schauder, 1994; Tenopir & King, 2000).
  Short publication delays can therefore be considered as a quality
  indicator reflecting the up-to-dateness of scientific journals
  (Haustein, 2012). Publishers have begun to reduce delays by making
  so-called early view, in press, ahead of print or online first
  versions of accepted papers available before they appear in an (print)
  issue. It has been shown for food research journals that online ahead
  of print publication has reduced publication delay by 29% (Amat,
  2008), while Das and Das (2006) reported for 127 journals in 2005
  average lags of three months between online and print issues
  publications with particular differences between publishers. Tort,
  Targino, and Amaral (2012) showed that this lag increased
  significantly over time for six neuroscience journals. Online dates
  are now being recorded in bibliometric databases like Scopus, which
  impacts bibliometric analyses (Gorraiz, Gumpenberger, & Schlögl, 2014;
  Heneberg, 2013).

Various distributions are made available in Table 2 of the aforementioned paper.
An aside: it may be worth checking out some of the works citing Haustein et al.


text:
How can I make my master's thesis more widely accessible online?
I published a master's thesis through some online system through my university. They said they would post it online, but I'm not able to find it online.
For a few months, it was hosted on my personal page on the university domain, so it was downloadable in Google Scholar, but that's no longer the case.
How can I make my paper more accessible to people searching for the topic? Is this a common thing to do?

Have you considered uploading the thesis to arXiv? I did that for my B.Sc. thesis because for some reason my school repository allows downloading B.Sc. theses only by employees of the school.

arXiv is the de facto way of publishing papers online. Considering that arXiv allows publishing theses as well (see Is it advisable to upload theses to the arXiv?), I would consider arXiv a good option for long-term public storage of your thesis.
However, you have to be aware of certain things.
Firstly, things posted to arXiv are public forever. This means you cannot remove your thesis from there once it is published. I would consider this to be the case for all information posted to the Internet (it is theoretically possible someone has a copy), but it may be the case that nobody is interested enough in your thesis to have a copy.
Secondly, your must be aware of your university policy. Some universities may not allow posting your thesis online. However, I wouldn't choose to attend such a university if I had a choice.
Thirdly, arXiv requires you to post the full LaTeX source code if your thesis is made in LaTeX. This means all of your university's LaTeX style files that may be copyrighted by your university need to be posted too.
Fourthly, arXiv covers only some fields. I was lucky to have my thesis in the field that arXiv covers. If your thesis isn't within arXiv's scope, you have to find a suitable repository from elsewhere.
I'm not sure if the LaTeX source requirement is valid anymore, but it was valid when I posted my thesis in 2014. I actually just was lazy and didn't check with the university if posting the university's .sty files is permitted. I don't expect to be sued because of this. With some amount of work, you could eliminate the use of your university's .sty files, but then the thesis wouldn't look like a thesis made in your university.

This is pretty accurate in the fields which arXiv covers.  But it only covers a few specific fields.

Answer edited to note that arXiv covers only some fields. I actually forgot that, because I uploaded my thesis over two years ago.

A friend of mine has recently posted his PhD thesis on the arxiv without providing a latex source due to the fact that it wouldn't compile with the arxiv version of tikZ (which appears to be outdated with no clear expectation of update). But that required some back-and-forth with arxiv moderators.

You can create a simple home page for yourself, for example at wordpress.com, and publish your thesis there.  You can link to your home page from various other places.  For example, if you have a google profile, you can link from that.  Also, if your department or group lists former students, it may be possible to include a link.  Finally, you can create a Google Scholar profile page.


text:
While applying for PhD in mathematics, am I better off dropping a course I'm performing poorly in?
I may or may not 'drop' my Point Set Topology course since I performed very poorly in it (also I am partially inclined to 'drop' the course so as to avoid a low GPA ),  but I do not have any idea whether it will be a problem during my PhD application or interview. I want to know how much it matters.

How poorly is poorly?  Are we talking about a B+ or a D or something in between?  What other courses are you currently taking?  Can you give us an idea what factors have contributed to your not doing well in this class?  What are you planning to take in the spring semester?

Why was my comment deleted? It was a legitimate comment and adhered to stackexchange comment guidelines.

(I am the graduate coordinator of the math department at UGA.)
Point set topology is a good course to take for an undergraduate hoping to go to graduate school in mathematics, but it is not a required one for admission to any program that I know of.
If you are asking whether it looks better to have a transcript containing point set topology with a poor grade vs. a transcript not containing point set topology at all, I would say: if it doesn't appear at all, it looks much better.  Point set topology is an introduction to the abstraction / generality of graduate level mathematics, perhaps more so than any other undergraduate course because nowadays we don't really have separate undergraduate versus graduate offerings in the subject: the point set topology that you learn as an undergraduate is in many cases the point set topology that you take with you through your graduate career.  So doing well in that course looks like a good predictor of success in graduate level coursework.  Thus by doing badly in it, you're showing a clear data point which is not in your favor.
I should say though that dropping the course is not helping out your education or graduate preparedness at all: at best, it's papering over the problem.  Are you sure you can't redouble your efforts and actually do well in this important course?  Or the flip side of the same question: are you sure that you can truly drop it with no stigma whatsoever?  E.g., will it show up on your transcript as a withdrawn course?  Will faculty who write your letters know that you really struggled in this important course and responded by dropping it?  (If I were writing a letter for such a student and had this knowledge, I would probably feel honorbound to mention it.)  These are things to think carefully about and discuss with faculty advisors.

A "W" appearing on the transcript for this course would (in my opinion at least) look worse than an A, B, or even a C in the course.  My experience in advising students on this is that for some reason many students think they're better off with a "W" than a "B" in a course.

I appreciate @BrianBorchers' opinion about a W, although mine is different. If I saw a W on a transcript, I would not hold it against a student, since I've seen so many students withdraw from courses for external or neutral reasons, such as health problems or having taken on too large a course load. Also, some schools allow students to drop a course very late in the semester, while others would call it a withdrawal.

Does time permit retaking the course?  I remember from my undergraduate days that I failed Calc II, but when I repeated the class the next semester I got an A.  Clearly you need a little more time and effort to master the course material.
So much of mathematics is foundational: you have to master A before moving on to B, and so forth.  If you think you understand foundational topics early in a course, and then find out in mid-course that nothing is making sense, then you know you're in trouble; I've been in that situation myself.
My advice, then, is to repeat the course if you can, and do what you have to do to ace it.


text:
Is it possible to be paid by a company for research and also use this research towards a Ph.D.?
The question in this link makes the assumption that the work you do at a private company and the work you do at a university for a Ph.D. do not intersect (or have very little in common), thus the person asks if "it is too much work or stress" to do both.  This question (and its answer) got me to think of another related question.
My Question: I'm wondering if the research you do for a private company can be used towards a Ph.D.? For example, suppose I work for a private company X and I have been accepted into the Ph.D. program at university Y.
Is it possible to be paid by company X for your research work, but at the same time use that research work to publish a paper along with your advisor at university Y?
I think I already know the answer to the question: It's possibly only if your advisor at university Y and your supervisor at company X have a strong relationship of many years and trust each other.
But I'm wondering if there are other answers?
Some background information about me: I have 10+ years of software engineering experience. I have a two B.S. degrees (Computer Engineering and Mathematics), one M.S. degree (Software Engineering), and a 2nd M.S. on the way in 2020 (Electrical Engineering).  My plan is indeed to pursue a Ph.D. in Electrical Engineering in 2020.

Country/region matters a lot, so it would help to obtain more useful answers if you add that information. In Germany working for a company to do research towards a PhD is the norm (or at least common) in many fields, especially engineering/computing-related, and often the work done for a thesis is specifically done for the company and primarily only written up explicitly for the University. In the US it is not the norm, but is also not prohibited - I'd roughly say "somewhat rare".

Yes it can happen, I knew of several theses that were effectively classified as "secret" and not published as it was work done for the Armed Forces... Graded by both sides the students passed no problem, but you won't find those in the library...

Yes, you can do this, but use caution. There are situations in which you can do research at a company but be prohibited from writing about it or using it outside the company. Contracts rule in this area.
There are other situations in which you can do such research and have the university involved so that you can use the research to obtain a degree, but your dissertation disappears into the void and you can't publish anything, again for contractual reasons.
If the work you do can be patented, there may be additional restrictions on who owns the patents (likely not you) and who can benefit from it (possibly you, but not necessarily).
Other places there are no issues.
So, before you contemplate doing this, just be aware of any restrictions on your results and what you can do with them after your relationships to both company and university end.
And, if you have a contractual obligation, be sure to honor it as companies can be ruthless if you expose proprietary work or trade secrets.

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


text:
Admission offer deadline extension
I received an admit (tuition fee waiver + TA) from a university for PhD in Physics. I was offered in the last month, and I replied the graduate admission director that I will inform him regarding 'accepting or declining' the offer around end of the march.
(the deadline for accepting the offer on April 15)
I thought I will get maximum decisions in March but few of the universities have put me on their waiting lists and probably they will decide by April 15.
Should I email the graduate admission  director  to extend the days? I mean, I will ask him that I inform him by April 15.
OR, as the deadline is 15th April, it is not necessary to email him to extend the date?

Related: http://academia.stackexchange.com/q/16004/19607

I think a very short email saying you are going to wait until the deadline for accepting the offer, with no further explanation, would be enough. You are not doing anything wrong and April 15th is the original deadline.
Perhaps it wouldn't even be necessary to explain anything. However my suggestion is that it is always better to be wrong on the well-mannered/ cautious side, than thinking "it is not necessary" and then find out it actually was.

So you are suggesting to email him rather than no emailing, though it could create a little bit bad image?


text:
What is the meaning of the official transcript?
I am going to apply for graduate admission in the US universities. Most of the universities require official transcript  which  must be sent from my institute with official envelope and seal.
I went to my university to send the offical transcript to the US universities. The controller of the examiner asked me that which one I want. New transcript or copy of my transcript verified by the controller with envelope seal.
More precisely, they asked me to give them photocopy of my original transcript. After I give them the copy, they will sign and pul offcial seal to send to the university I wanted to send.
My question is that,,

will the US universities consider the  copy of the main transcripts(verified by the exam controller with enveloped and seal) as official?

or

US universities  are expecting original transcripts (with seal and
  enveloped) like I have a copy with me?

I would think either would be okay.

If I want to get the original one from my department (like the one I have) they will give but it requires a lot of verification and it takes time too.

We can't really answer... ask directly. If in doubt, send the not-so-official one, and promise to send the one with seal and signature and notarized by the embassy and all later.

I think we can't really answer AND that likely either is ok.

If this is about graduate admission, universities normally require an official transcript (i.e. NOT a copy). An official transcript normally carries the signature of the Registrar, is in color, and is put in an sealed envelop prepared by the Registrar's office.
Some US universities require that your transcript comes directly from the Registrar's office of your institution, while some would accept one that you send in as long as it's inside the sealed envelop prepared by the registrar's office.

In order for your incoming school to accept your official transcript, it must be ordered from your previous school and must be sealed. They will not accept photographs, copies, open transcript packages. Contact your department of student affairs.
"will the US universities consider the copy of the main transcripts(verified by the exam controller with enveloped and seal) as official?"
Your school has an administration dedicated to supervising the transfer of international students. My educated guess is yes, it will be acceptable. Contact your student affairs department for more information.

You write as though this is a universal condition for all schools: is this in fact the case?


text:
Unofficial documents for admission process
I have applied  few universities for the graduate admission (PhD in physics) in this fall. Maximum of the universities require all of the official documents for the admission and review process.
Before applying these universities I emailed the graduate coordinator and the admin of the department to know if they allow the scanned copy (I upload the scanned copy of my transcripts and  students copy  of GRE/TEFL score cards.) They replied that the review process can be done without the offical copies but final decision will be made after the official copy they have with them.
My intention is that I want to send the official  copies to the department after hearing the review results from them because if I send the official scores  before the decision I may loose some amount of money and also I may not get an admission  offer (my financial status is not that great).
My question is that, will it create any problem if I send the offical copies after I get any  positive news (admission offer) from any of the university?
"If you uploaded your documents with the application, you do not need to mail anything at this time. If you are admitted, you will then be asked for official documents." this was from University of Tennessee.
Do I have to send official transcripts?
"For the sake of evaluation purposes, no, you do not have to submit official transcripts. You are welcome to upload unofficial transcripts to the on line application website. If you are admitted, you will be required to submit finalized official documents".it is from the Washington state University

Have you asked whether they will tell you a tentative decision based on the copies?

No I haven't asked them but  they have said that the review process can be done without official copies.

one of the admin wrote this "the department can review your application without the official scores from ETS.  But UIC will not admit you until they have the official TOEFL scores.  Then I will not give the Office of International Services (OIS) your I-20 information until I have your official GRE scores."

"If you uploaded your documents with the application, you do not need to mail anything at this time. If you are admitted, you will then be asked for official documents." this was from University of Tennessee.

I would bet that the postgrad admission process at most universities involves at least the following steps:

You send in scanned copies of your transcripts (I am assuming here that these days most of the admissions procedure is handled electronically, in particular for international students)
Someone checks to which degrees from "well-known" institutions your degree is roughly equivalent to and convert your grades into the local scale (e.g. GPA). On this basis, a first assessment is done whether you satisfy admission criteria.
In my institution the previous two steps are handled centrally, but the next step involves academics: assuming your grades are good enough to satisfy requirements of the department (which for highly attractive departments might be higher than the regulations say), it is checked whether your profile and interests align well enough with one or more academics to be sure that a supervisor can be found, and (if applicable) whether sufficient funds are available to support you.
Only if all of this is checked positively will the university make an offer to you.
When you accept the offer, you have to supply the formal (perhaps) transcripts and have to provide evidence that these are indeed proper certificates (i have heard of cases where this has to be duly apostilled). Clearly, there is a strong expectation that your official transcripts match the ones from the first step.

Universities have a strong interest in getting students (and their tuition fees) so they want to make the first few steps as easy for the "customer" as they possibly can and "lure him in". The onerous part only comes with the last step.


text:
How to email Graduate Director that I will not attend (F1 student)
I have made some wrong decisions during my PhD studies in a US university (let's call it University X). One year ago, I got another admit(let consider this University Y)  when I got admit to University X. I didn't have fund to join university Y, thats why I got accepted the offer from university X.
Now university Y offered me admission plus funds  and I accepted it, even the admission procedure has been completed. I have not transferred my sevis  no yet.
After a lot of thinking I have decided that I will not transfer to another university, rather I will complete my PhD here.
How can I email to the graduate director of University Y that I want to cancel my admission there and I do not want to join their program?

"After a lot of thinking I have decided that I will not transfer after all; rather, I will complete my PhD here.  Nevertheless I would like to thank you and the admissions committee for the offer."

Are you asking how to write the email, or are you asking about something else in the process? If it's just about writing the email, then the comment from @aparente001 is a good example of how to be clear and professional.

So you have already accepted the new offer but now you want to reverse the decision?

@Dawn yes, And the admission procedure is completed too.

I feel like in this case it helps to give a more compelling reason than "I changed my mind." Also, I would challenge you to make sure your first and second instincts to apply to the new school and accept their offer are not better than this new "cold feet" feeling.

@Dawn I did it because of financial reasons and a little better reputations. Now I find that the financial supports are same rather I would lose a year. What should I write?

You would lose a year because they won't count the classes you have already taken? Did you try to negotiate this with them?

Nope I didn't. I also passed the qualifying exam here. They don't know that i will be a transfer student, its because i got the admission at the two universities same time.

Agree - you have to tell Y. I agree with the above but add capitals to Admissions Committed.
Dear Professor X
Thank you very much for the offer of funding to complete my PhD with [name of uni]/your Faculty/Department [match to the Director's level of appointment].    After some thought, I have decided, respectfully, not to accept the offer.
I remain though very grateful for your consideration and I would like, through you, to convey my thanks to the Admissions Committee for their support.
With kind regards,
Sincerely,
ZZ

You could add something like "I have learned (belatedly) that my current courses/work will not transfer to your program, and so I must regretfully withdraw my earlier acceptance." This would possibly replace the second line of the first paragraph, or go at the end of the first paragraph.


text:
How were the figures in old pre-TeX research papers and books created?
If you see old pre-TeX-era classic research papers, technical articles and books the figures still look pretty good. They seem to be hand drawn but with some components of computerization.
For example see this CRAY-1 document: http://bitsavers.org/pdf/cray/CRAY-1/CRAY-1_Brochure_1975.pdf
How were these figures created? What tools did folks use to create and then place them into the paper or book?

When my father was a student (in the late 1930's), one of his classes was "descriptive geometry", which was about making accurate drawings of mathematical structures. He told me once that he was required to draw an accurate 2-dimensional projection of a regular dodecahedron.

The figures in the Cray manual seem pretty clearly completely hand drawn, at least to me.  Zoom in and look at the irregular arrowheads and squiggles on page 2, and the wobbly curved lines on the "tube" things on 4.  Of course, they had T-squares to draw straight lines and right angles, and so on.  People can be quite good at making neat drawings when they are experienced and careful.

This depends on the age in which the papers were developed. In the computer age there have been graphics programs going back to somewhere in the 1950's so it is possible that they were created on a computer. Possibly using vector graphics.
But note that the machines on which early programs ran were large and expensive.
Earlier than that, and overlapping with the computer age, artists were employed by publishers to create graphics using the same sort of tools that architects and "draftsmen" used. The French Curve was common and every student in a course in mechanics (physics) had one to help prepare homework. Actually artists may still be employed, but they tend to use computer tools now, rather than manual ones.
Math and physics undergraduates needed to be quite adept at graphing functions by hand, but these were a bit too crude for publishing. Hence artists.
To extend it a bit, even in the 1970's mathematics papers needing formulae and equations with any complexity were prepared by hand by skilled typists using specialized typewriters. The special symbols, hundreds of them, were on individual wands that were inserted into the typewriter under the striker. The glyph was struck and then the wand removed so the next one could be inserted. The typists worked from hand written papers prepared by the author.
For publishing, pages were prepared in sets of, say, 16 and printed using something like the lithographic process. The 16 (or whatever) pages printed together became a "signature" and these were prepared and the sewn together to make a volume. High quality books often still use sewn signatures, which you can see by looking at a closed book from the top or bottom - the "spine". You can also see the threads used to sew the signatures. See Book Binding for example.

This question has an implicit assumption that TeX graphics are the only form of computer graphics. They are not now (for the vast majority of office workers) nor have they been so traditionally.  It would be better to say how were figures done, pre computer graphics, not pre-TeX.
FYI: I do all my figures in Excel, PPT or specific programs like an Xray or NMR program.  I've never bothered with LaTeX.  I think the math/CS/physics mafia assumes everyone else uses it.  But many biologists, chemists, etc. like MS Office.
Prior to mid 80s, I assume the figures were hand drafted.  (As an engineer, I saw half our large MEP firm still doing hand drafting construction drawings as late as mid 90s.  In 94 or 95, it changed like a light switch and we went to 98% CAD (just revisions of old stuff on a drafting table).  A good draftsman can produce stuff that is hard to differentiate from computer drawings.

An upvote from me, because the CRAY-1 document looks like it contains drawings produced by a draftsman

TeX was really at the fore-front of main stream computer usage. Sure there were plotters before then, but they were run by professionals and really expensive. Prior to TeX and PLT and Postscript (basically the early 80s), figures were produced by draftsman. Everything in your answer is essentially 90s and beyond.

In the early 80's one could use graphics programs on a mainframe and get printouts. When I started grad school in the mid-80's the department still had artists and photography experts available on contract for figures and micrographs. The artists rapidly disappeared, although in certain niche areas (e.g. rendering new species in the correct style) they still are often used.


text:
Is it crass to acknowledge a colleague that passed away in my thesis?
A PhD student in our school recently passed away unexpectedly, to the shock and  grief of a large number of research students and academics, including me.
I had little to do with him on a daily basis, and he had little to nothing to do with the content of the thesis, but nonetheless it occurs to me to make a mention of his passing in the acknowledgements of my own (Honours) thesis.
Is this appropriate, or could it come off as disrespectful?

I could see this being weird or scientifically inappropriate, but how would this be disrespectful?

The question would be better asked as "Is it inappropriate..." The statement "I had little to do with him on a daily basis" doesn't answer a question on whether or not you considered him a friend or a colleague. I had a friend suddenly pass away in college who I rarely took classes with due to our different studies, but I wouldn't say that lack of daily contact made us any less friends.

What is the purpose of the acknowledgment?   As you said, you had "little to do with him" and "he had little to nothing to do with the content of the thesis."  I'm guessing there are many people who can be categorized as such, but aren't candidates for acknowledgment.  Why this person?

@Compass I considered him a colleague. Not so much a friend, but someone I had a lot of respect for.

@BrianP There are of course many people who have had little input on my thesis! I think the primary reason for this is that I had a lot of respect for him, and the School as a whole was shocked by his passing. I think the magnitude of that shock, magnified obviously by the recent timing of the event, makes me consider it. I think Pete is right in his answer that a dedication or memorial is more appropriate than an acknowledgment as such.

I certainly don't think it's "crass", and I have a hard time seeing who could be disrespected.  In general, you can acknowledge whomever you want in a thesis and the only crass thing would be to say something negative about them.
However, there is possibly a bit of room for misunderstanding here, because the ostensible purpose of the acknowledgments is to recognize people who helped you out in some way.  Based on what you write -- you were not close, and he did not help on your thesis -- it doesn't make sense to thank this person in the acknowledgements.
I might instead suggest going for a dedication or commemoration.  Some ways of wording this are given here.  You could either end the acknowledgments with a dedication, probably in its own separate paragraph (and you can dedicate the thesis to more than one person, if you like), or you could include the dedication on its own page separately in the thesis, e.g. "For X", "In memory of X (19xx - 20xx)", etc.
Speaking personally, I like the look of the latter, and I find it to be the opposite of crass to take time out to remember the departed, whether they had a special relationship with you or not.  You are doing your part to make sure that your fellow student will not be completely forgotten for some time to come.  Good for you.

@BrianP: The OP describes his fellow student's passing as "to the shock and grief of a large number of research students and academics, including me."  That's the connection.  How or whether to commemorate the deceased is one of the most personal things I can think of at the moment.   I would be careful in being too critical of this.

@BrianP Your comment cuts to the heart of what I was trying to ask here - essentially how much of a connection is needed. I've marked Pete's answer as correct though from the standpoint of remembering a fellow student. Doing what I can, in essence.

The social etiquette of acknowledgments sections vary from school to school. It would never be rude or disrespectful. I thanked family and friends in mine - and made reference to an internal lab jokee. Check previous theses to get an indication of etiquette in your school, but I don't see any reason this would be inappropriate.

I've spoken to my supervisor about the acknowledgments section, though not this question in particular, and it seems as if it's a touch of anything goes. The caveat is that you have to tick a couple of boxes in particular, and after that it doesn't 'matter' as such.

You might easily look like someone who is seeking public attention.
Dedicating a publication is a privilege you should leave to close friends or the faculty staff.
Consider your best friend died, you wanted to commemorate him in your thesis, and then found three others had done the same before you. Could feel strange, couldn't it?
Or think about the mourning parents. They might spend days to find your phone number, cause nobody they know knows it, and then call you, expecting to find someone who is as sad as they are. Do you want to risk that?

-1: "Consider your best friend died, you wanted to commemorate him in your thesis, and got beat to it by two weeks by whats-his-name-usually-sits-in- the-front-row." I'm sorry, but that's just idiotic.  Obviously one deceased person can be commemorated by multiple people.  Obviously.  Also making up such blatantly fictional scenarios in an answer to a question about an actual deceased party seems in poor taste to me.  You should not pretend to know how grieving parents will act.  I would recommend that you delete this answer.

(I've rephased that a bit.) The OP has made it clear that he had no personal relationship. The friends and family might be OK with his commemoration, but then they might feel he's forcing himself on them. I don't know, but risking it is tactless enough, imho.

By what mechanism will the family members of a deceased PhD student come to read the thesis of an undergraduate student in the same department?  Anyway, honoring the deceased is something that everyone has a right to do.  The idea that one person's practice of this takes away from another's is really perverse.

You seem to be very sure about rights and wrongs. Sorry. I'm simply recommending to tread ligthly around people's feelings here.


text:
Series of simultaneous rejections, how to advise younger fellows
I myself work as a clinician-scientist. I work in a small group and oversee several students. The current situation involves one of them who is a PhD-candidate. She is bright, fast and hard-working. Over the past two years, she wrote several good papers. Many of these papers are based on existing collections of data. Two out of six papers were published. We tried to maximize their impact and submitted to journals with good impact factors in our field. This ended up in 4 papers being under review at the same time (although one was submitted 11 months ago and the other one just a few weeks ago). Now all 4 papers got rejected within one week. For her, this is a tough issue and hard to deal with. We discussed this today but I somewhat failed in encouraging her to just resubmit her work to other journals. Although I repeatedly emphasized that publishing also involves luck, (I feel that) she left the conversation with the impression that her work is not good enough for publication.
What could I have done better?
PS: I am convinced of the quality of her work. It is super solid and will eventually get published sooner or later.
I am aware of Losing confidence after a series of paper rejections but could only find a partial answer here.

How long was the time span between the last rejection and your talk? Maybe she just needs a few days to handle the frustration, and if you talk to her again next week, the outcome will be different. (At least, that's what holds true for me...)

I think you're doing fine.
To me, the best way to convey this oddity of the academic publishing system is by sharing experiences and telling stories. If you get 20 academics in a room and tell the story "I once had 4 papers rejected in one week", I'd expect a combination of "Wow, that's great productivity to have 4 papers in submission at once!" and "Ha, that's nothing, one time I had 4 papers rejected in an hour!" It's just life in academia.
Now, I don't actually mean for you to assemble a room of 20 people to do this as some sort of intervention, but rather to reiterate this, share your own first-person and third-person stories, hopefully some that have a positive ending. And as more of a prophylactic approach, make sure there are social opportunities for your students to talk to each other and other researchers about these sorts of things. The group I work in has occasional "journal club" meetings where someone presents a paper that we all discuss, but especially in the good weather months we have these meetings outside, some people drink beer or eat ice cream, and people tend to hang out and linger afterwards. Or dinner parties. A lot of conversations about academia more broadly occur in those settings naturally.
Importantly, though, you also don't own or control anyone else's emotions. It can be difficult, especially for people with strong empathy, to be comfortable with others having negative emotions. You want to fix it! You want them to feel better! Sometimes, you can't. Having even 1 rejection at a time deserves a bit of a grieving process. As a mentor, you want to try to prevent that from becoming broader disillusionment and prevent it from turning into "giving up", but it's fine for it to hurt for a little while. Try to help set a schedule/goals for resubmission to keep a clock on it, but don't feel pressured to resolve this immediately, and don't put too much pressure on the next round needing to succeed. Also remember that you're not having an argument here, just present your own thoughts and feelings. If a student says they feel their work isn't good enough, if you disagree you don't need to tell them they're wrong. You can just say, "I'm proud of your work and proud to be your coauthor." It's fine if they roll their eyes, it'll sink in later.
Consider also some alternatives for spreading the work. Medicine is a bit slower on embracing preprints, but many journals are now okay with them: check the ones you plan to submit to, and if they allow then get your work up on medrxiv or similar, or biorxiv if the work is closer to basic science. Look for and suggest opportunities for presenting at conferences for your students: the networking opportunities are very important but they also give an opportunity to present work where you're face-to-face with the people evaluating it: that gives a better opportunity to defend the work and share the results compared to the faceless process of journal peer review. Look for opportunities for internal presentations to other students/faculty/clinicians as appropriate. These can happen before work is polished for submission, too: look for as many possibilities for feedback and sharing work as possible.

@ Bryan Krause - Thank you so much!! I am not so experienced with mentoring students (I have this role since 18 months). Would you advice me to seek follow-up contact or just let a week pass before going back to the topic?

@Dr.M I think it depends on your normal contact schedule; also hard for me to advise from afar. If a student was really struggling with it, maybe it would help to reach out sooner, otherwise your normal contact schedule seems fine (e.g., if you meet weekly). A short note along the lines of "Hey, I know the news this week has been tough, just want to reiterate that I think this work is strong, publishing decisions can be a bit arbitrary, and we aimed high on the journal targets. When we meet next Thursday we can talk next steps" could be nice, or it might feel oppressive.

Also, focus on the positive side: having two papers already published in pre-doctoral phase is per se an excellent result; and tell her that she should look at the rejections more as "in flight" work than "lost" work.

When I was a first-year undergraduate student, we were working on a topic that was genuinely interesting, but new to my supervisor. Our paper was rejected six times. Not because the quality of the work was low but because we didn't have a good network and were aiming quite high and didn't quite know which journals to aim for. After the first two rejections, I lost hope. My supervisor didn't and persisted that the work is of good quality and assured us that it was just a matter of patience. It got rejected four more times before finally getting published.
I guess in professional research it is more about the work, and not about the result. It is a game of the last man standing. Most successful researchers now are not the ones who always focus on conquering new peaks, but the ones who just hold on to the end of the cliff for a longer time. You must learn to move on and try persistently. Science and art is very similar in that sense. People create art not thinking about the amount it would fetch, but thinking about the enjoyment it offers. Many art works will remain unappreciated, and some of it might even end up in the darkest corner of an art room; but after some time you will make a masterpiece and that's when people would compete to buy even your worst works.
Forget about the result, and focus on the work, results will come automatically. All the best for your work and please ask the student to keep her head high and move on.

You did fine! I think it's more a case of what to do next rather than what you could have done better, as it would be surprising if, after 4 rejections, she didn't spend some time questioning her own abilities.
I would suggest some combination of the following, whichever appeal to you:

Keep mentioning over the long term that you believe in their abilities and work.
Point out that it is normal to feel inadequate after multiple article rejections, but that feeling passes as the work continues.
Share something like the CV of failures, or your own greatest hits of career No's, so they can see that multiple, continued rejections is the mark of the professional---only amateurs expect "genius" to be recognized first time.
Perhaps a book such as Writing Your Journal Article in Twelve Weeks would be helpful. I think it is more humanities-based, but its introduction has some good data and anecdote on how common it is for junior researchers to delay re-submitting rejected articles, and how important it is that they get the work back out there.
Start a lab or cross-lab writing group specifically aimed at revising journal articles that have already been peer-reviewed.

I wish all advisors were as supportive as you appear to be.


text:
How can I promote a published article?
My article was recently published after a long process of peer-review. I don't know how to introduce the new findings in mainstream science.
Can you advise me on the best way to promote my study?

Not by posting the link here, I am afraid. :) I have removed the link to try to make this a more general question applicable also to other users.

If is of interest for mainstream, normally it is spotted already by the journal that put emphasis on it. Of course, this doesn't suffice to send your paper really mainstream. For that, your institution might have a dedicated office or person. I main mainstream news. If you mean "mainstream science", basically it is done already by having it published. Try to go to conferences or politely send it to whom may be interested.

could try answering questions on a relevant stack-exchange (or similar forum)

There are plenty of options when it comes to promoting your work, both amongst fellow scientists and the general public.
The first and most obvious is giving talks about your work either within your own institution or at other universities. If you're really keen to do this, don't wait for an invitation to speak. It's ok to email the organiser of a department's seminar series and ask if they have any free slots in the next few months. Most seminar organisers I know are very grateful when someone volunteers to speak, as it makes their organisational job so much easier. One bonus of the pandemic is that everyone is giving talks online at the moment, so you can probably give more talks than usual and in locations that might normally be too expensive to travel to for one fifty minute seminar.
Related to this is speaking at conferences. The typical conference season is the summer, but again with everything being online at the moment, more and more conferences are happening at different times. Talking at an online conference is obviously not a good replica of meeting in person, where it's much easier to strike up casual conversation about your work in the queue for coffee, but it's better than nothing.
Furthermore, you can try using social media. In my field, it's quite common to write a Twitter thread explaining your results when you publish a new paper, so you could do something similar. This only works if most of your followers are fellow academics; if your only followers are friends from school or fellow football fans (for example), they may be less interested. Personally, I prefer to write a blog post about my work and then draw people's attention to the post on Twitter. A friend of mine makes Youtube videos. This is your chance to get creative!
Finally, if your work is sufficiently high-profile, you could get in touch with your university's press office and ask if they will write a press release for you. This is presumably a more difficult process to go through but is clearly an excellent way to promote your work to a much wider audience than just academics.

Thanks for the answer

Is there evidence that any of these actually work?  There are some studies on social media use and it is quite weakly correlated with citations.  Of course citations are a bad metric.

Plus one for the possibility to present at normally geographically and budgetary inaccessible institutions.

Are you at a university?  Some universities do press releases and other publicity for research results found by their faculty.  So find out what office at your university does this, and notify them.  At my university, the Dean would send us a request from time to time asking us to inform him of any research we may have done that should be publicized.

Thanks for the answer

One possibility is to politely send copies of your work to others in the field, v.g. people you cited, collaborators or collegues.
Remember that whomever you send this to has probably not chosen to read your work so this must be done extremely carefully and by thinking through the message that will come with the copy,  else recipients will think you are pushy or self promoting.
Such emails should be selective as anything that looks like a mass email will immediately go to the delete folder.


text:
How to not let paper rejection affect you?
At times I am really frustrated with constant rejections when the papers just fail to make it to acceptance. And if this keeps happening for quite some time, especially when your peers are moving on, how do you deal with it? I am working, trying to address the reviews but somehow at some point, it is getting too much for me.

What level are we talking about?  When you are a Ph.D. student, your advisor will be able to help you with this.  Maybe the papers are not good.  Or maybe the papers are good, but you tried the wrong journal for the paper.  Your advisor will help you figure out what is happening.

You don't say why you are being rejected. This makes it hard to give realistic advice. It would also be useful to know whether you are a doctoral student or not, and if you have an advisor/mentor.

I've suggested this is a duplicate because even though rejection is different than revision, I think the suggestions around emotional detachment may help; if you disagree, please comment and it can be reopened.

It is normal.  Even for an experienced person like myself, rejections continue to sting.    Constant rejections could simply mean you do not have the skills to publish a good paper.  This means you need the help of an experienced author.  For example, I just reviewed a paper where the authors think a frog is a lizard, and they do not seem to have read anything on frogs or lizards or realize that their problem is at least 10 years old.

It is next to impossible not to be affected emotionally by a rejection of a paper. You put in a lot of time, effort and hard work, so it is a perfectly natural reaction to have a short term issue with motivation. There is no need to suppress this, and it will include quite a bit of frustration if rejections keep happening.
One of the more important things when it comes to publishing is that you are convinced of and positive about your own work and you may have to regain this after a rejection, so that the short term effects do not turn into long term problems. This might be hard to achieve when fighting all by yourself. Everybody needs some positive feedback from time to time. So talking to other people like your advisor or your peers and asking for their feedback will help because if you keep learning from the discussions, your work and your confidence in it will improve.
Of course there is also the possibility that you are working on a dead end with a particular paper. After having overcome the initial emotional response, you should be able to figure out if this is the case, maybe with the help of others. Then it is best to move on and concentratre on other projects with a better chance of succeeding. There is no happiness in working in a dead end. It is impossible from the distance to tell if this is true in your case.