Whether to exclude standard deviation in plot of outcomes of a series of experiments? I have performed 21 different experiments, which I have repeated 3 times in total (63 samples gathered).
I plan to compare data using a bar plot. For bar plotting, I initially decided that I will calculate the mean over every 3 samples, and I will graph this value. However, along with the mean an important thing to state is also the standard deviation. I really do not want to include standard deviation on my graph as it will blur the results to the reader.

Of course, I can just put standard deviation into table, but this will be completely useless to regular reader.

Seeing other papers I sometimes spot that researchers do not really state how the values was gathered. Should I then assume they have conducted measurement only once?

Would it be ethical to not inform the reader that I plot the mean on my graphs? Any other suggestions are welcome.

Don't do this.

Here is some random data with 21 experiments A-U, each one repeated 3 times. In both cases, the experimentwise means (indicated using red crosses) are identical, but the within-experiment standard deviations are very different (1.0 in the top graph and 0.2 in the bottom one). R code is below.

Just seeing the experimentwise means is very misleading. In the bottom case, the experiments seem to be pretty different, and you could start interpreting the differences between them. In the top case, it's rather obvious that the difference between experiments is dominated by the variance within experiments. Put differently: the proportion of variance explained by the experiments is very different between the two cases.

This is a crucial piece of information. Do not leave it out. Leaving the variability out does not "blur the results to the reader" - the variability may be more important than the means.

In particular, remember that most readers will only look at your graphics, and even if they do read the text, the main thing they will remember will be the graphic. If you only put the means there, readers will remember the means. They won't remember whether the standard deviations were large or small compared to the differences in means.

So: look for a way to visualize both means and variability. For starters, don't use bar plots. Use, for example, dotcharts as I did. With your small dataset, you can without problems plot all your data, plus means.

If you want to emphasize the means, you can do all kinds of things involving colors, shapes or sizes. For instance, I used smaller grey dots for the observations so the means (larger red crosses) stood out more. And I used vertical lines to indicate experiments, and these lines are a lighter shade of grey than the dots.

Note that the human brain is better at interpreting positions (as in a dot chart) than lengths (as in a barplot). Nor should you use so-called "dynamite plots", that is, bar plot with "whiskers" that indicate standard deviations (or standard errors of estimated means - one problem with dynamite plots is that it is not always indicated whether whiskers give SDs or SEMs, and these are very different things).

See here and here for more on dynamite plots. This earlier answer of mine gives a few more options for visualizing data.

R code:

experiments <- LETTERS[1:21]
set.seed(1); means <- runif(21)
obs <- list()
set.seed(1); obs[[1]] <- matrix(rnorm(63,0,1),ncol=3,byrow=FALSE)
set.seed(1); obs[[2]] <- matrix(rnorm(63,0,0.2),ncol=3,byrow=FALSE)

opar <- par(mfrow=c(2,1),mai=c(.8,.8,.1,.1))
    for ( ii in 1:2 ) {
        obs[[ii]] <- obs[[ii]]+means-rowMeans(obs[[ii]])
        plot(c(1,21),range(unlist(obs)),type="n",xlab="Experiment",ylab="Observation",xaxt="n")
        abline(v=1:21,col="lightgrey")
        points(rep(1:21,3),as.vector(obs[[ii]]),pch=19,col="darkgrey",cex=0.8)
        points(1:21,rowMeans(obs[[ii]]),pch="+",col="red",cex=1.5,font=2)
        axis(1,1:21,experiments)
    }
par(opar)


Avoiding "Zoom bombing" in virtual conferences and seminars With travel restricted by the COVID-19 pandemic, many academics are organizing online seminars and conferences as a substitute for regular in-person university seminars, colloquia, and research conferences.

In real life, seminars are usually open to anyone who wants to drop in, and every attendee can be seen and heard and may ask questions.  So an obvious approach is to organize the event using video meeting software such as Zoom, and simply post the link on a public website so that any interested person can participate.  However, this also opens the event to "Zoom bombers", random people who just want to disrupt the proceedings with annoying or offensive video / audio / text chat - such abuse has unfortunately become very common in public Zoom meetings.

What best practices exist to keep such an event as open as possible to legitimate participants, and let them interact with each other and the speaker in a reasonable way, while reducing the risk of disruption and abuse?

What are the pros and cons of these strategies?

Strategies could be general, or involve specific features of certain software.

Some strategies I've thought of, and their drawbacks:

Create a password for the meeting.  Then the question is, to whom should the organizer give the password?  If they only give it to people they know, it excludes people who might be interested but whom they happen not to know.  If they distribute it to large mailing lists of interested academics, it raises the chance that it will fall into the wrong hands.
Offer to share the password by email upon request.  This requires extra time from the organizer to respond to those emails, and to manually verify the credentials of each requester.
Require a nominal registration fee, as real-life conferences often do.  This requires setting up an online payment system, which can be a lot of work, and may exclude people who are only casually interested, or who don't have funding, or who work in less wealthy parts of the world.  It may also involve the organizer in a lot of bureaucracy with their university as to how the fees will be managed and spent.
Use a "waiting room" feature, where participants must be approved immediately before joining.  However, as far as I know, the host only sees the participant's name.  If they see an unfamiliar name, how can they tell whether it is a troll, or a legitimate researcher whom they just happen not to know?  Conversely, I don't think there is anything to stop a troll from masquerading under the name of a famous academic.

I am wondering if people have thought of better solutions, that are specifically appropriate to academia.  Such strategies might take advantage of specific features of the academic community, e.g. to authenticate genuine researchers (.edu addresses? accounts on preprint servers? ORCid IDs?).  Answers could also address the pros and cons of such strategies as they apply to academia in particular, and how well they fit with people's existing expectations for academic conferences.

How about using something other than Zoom? Other softwares support features that can help with this. Moreover there are some serious security and privacy concerns about Zoom (see e.g. this statement by the FBI and this investigation by the NY attorney general; Bruce Schneier has written an overview of the concerns here).

In our department we use BigBlueButton (website, Wikipedia) for our classrooms and seminars. It's a completely open-source and free web conferencing system. There are a few services out there that host servers but they're completely overloaded at the moment. I'd say your best bet would be to get your IT services to host a server for your department. With BBB by default new users don't have their webcams activated, and you can prevent them from doing so. You can even prevent them from using their microphone and require them to virtually "raise their hand" before a moderator allows them to speak. That should cut down a lot of the abuse. You can also set up the service so that an account is required before accessing the meeting. Unless the abuser is very dedicated, they probably won't bother creating dozens of accounts to continue bothering people after being kicked out, I hope.

Also, something obvious: many abusers are specifically targeting Zoom and going into random Zoom meetings. Unless you've somehow attracted abusers who are specifically targeting you, if you use something else (especially something hosted by your own department), you probably won't have any problems.

Note: I'm only recommending BBB because that's what we use at our department, but there are other services out there. I know another department has set up something called "Panopto" for example, and another something called "Classilio" - you'll have to look that up, I don't know much about it. For informal meetings we use Jitsi but it doesn't seem adequate for hosting a seminar. But in any case, if a software doesn't meet your requirements, you should definitely look into switching to something else, especially with the privacy concerns...


How to react to unfair reviewer comments? I'm in a situation where my paper is accepted conditionally, thus I need to revise it in some way as stated by the reviewers. While two reviews were encouraging and mostly constructive, the third review is way off from the other reviewers in their judgement and included sources that I "forgot" to cite and should mention.

Yet, there is a problem since the sources listed by the reviewer were published just ONE day AFTER the hand-in deadline of the paper. I was not able to anyhow know about them. I feel in a dilemma right now between acting "independent" as a researcher but also having to follow the comments made by the reviewer to have a positive outcome.

Am I obliged to follow their comments?
Should I react in the "review log" that I need to upload, that the "status quo" on which research performed is not based upon these sources (although they might be relevant), therefore I will ignore the sources named by the reviewer? I feel that I should at least mention it from a moral standpoint.
How should I behave for a positive outcome? I feel the review was written with negative intentions in mind.

Take a very deep breath. The only way to react to a review that you believe to be in bad faith is to act as the bigger person. You can definitely mention that the reviewer disagrees with the other reviewers, but don't say anything about motives to the editor - there is no way that it can benefit you. The editor will have noted a difference in tone themselves and decided what they think about it. If you complain, and the editor has decided the review is valid, you just look defensive and bitter. If they have already decided that the third review is unfair, then you'll make no difference.

If its possible implement the reviewers suggestions, do so unless you think it seriously harms the paper. Whether you think they are fair or not, as long as they don't hurt the paper, do it. This goes double for citing papers if they relevant; 90% of citations in a paper will be read after the work it done.

"How should I behave for a positive outcome?" Open a bottle of champagne, celebrate your paper, be thankful you got through it despite the reviewer and forget about it. There is nothing you can do about this sort of thing. If you really want to do something support movements for open peer review and next time submit to a journal that practices it.


When describing a joint effort, refer to colleague by name or by their title? If another developer was involved in the research process for a task, should I say that "Bob and I worked on this" or that "another developer and I worked on this"?

Of course, others should be acknowledged in general, but I am asking about how to cite them in the context of the in-line text itself, rather than an explicit acknowledgements chapter.

Written Texts

In the context of a written text I usually use the person's title letters (Mr. Dr. Etc.) and state their affiliation if it actually adds something to the point I'm trying to make. Say for example I wish to point out the collaborations I have set up with other institutions, then I'd probably be verbose about it.

Of course it doesn't make sense to explicitly mention collaborators in all written texts. Neither it is customary to do so. For example in a paper the collaborators are listed as authors, and this collaboration relationship is therefore very explicit. In your thesis you should probably concentrate on your work. That doesn't necessary mean you shouldn't explicitly acknowledge collaborators, but that's the type of scenario in which I'd err on the verbose side.

Oral Presentations

In case you are referring to an oral presentation, you could state their title and position the first time you introduce them, and subsequently refer to them by their name whenever you mention them again. Something like:

  I conducted this work with Joe Rnano who is Distinguished Professor at the University of Academia.SE. Joe and I demonstrated that ...

I just came out of a conference and that's what most speakers did.


How to get free programmatic access to citations counts for a given paper? What databases allow free, programmatic access to cited-by counts for papers?

Google Scholar doesn't have an API, and they block crawling attempts.
SCOPUS only seems to allows you to retrieve a branded, watermarked image of the number.

If you are an R user, you can use the scholar package. This package allows you to analyze data from Google Scholar and obtain citations, publication list and even perform predictions of the h-index. An example R code:

library(scholar)
id = "xJaxiEEAAAAJ" # Isaac Newton's id
cit=get_citation_history(id)
barplot(cit[,2],names.arg = cit[,1])


My human subjects research is "exempt" under US regulations. Does that mean I can skip ethics review? This question was inspired by some wrong information on this site.

Human subjects research usually requires review by an ethics committee (IRB).  Some research is "exempt" under US law.  If my research is "exempt," can I skip the ethics process?

Regulation
No, you cannot skip all the process.  The word "exempt" is misleading.  The exemption is from most regulatory requirements, not institutional or journal requirements.  Exemption is specific to the regulations of the United States.
Regulations do not require IRB review of exempt research.  Regulations do require determination.  Depending on your institution's policy, the determination might not be conducted by the IRB.  But usually it is.  If your institution permits it (which is highly unlikely), you may be able to conduct the determination yourself.

The regulations do not specify who at an institution may determine that research is exempt under 45 CFR 46.101(b). However, OHRP recommends that, because of the potential for conflict of interest, investigators not be given the authority to make an independent determination that human subjects research is exempt.
The regulations do not require that someone other than the investigator be involved in making a determination that a research study is exempt. What they do require is that there be accurate determinations so that non-exempt research ends up being reviewed by an IRB. Because of the potential for conflict of interest in this situation, OHRP's long-standing recommendation is that investigators not be given the authority to make an independent determination that human subjects research is exempt.

Source
Note that ethics processes which are permitted under United States regulation may be a crime in other countries.
Journal Policy
Furthermore, reputable journals require IRB approval for publication.  The Helsinki Declaration §23 says,

The research protocol must be submitted for consideration, comment, guidance and approval to the concerned research ethics committee before the study begins.

While the Helsinki Declaration is specific to medical research, journal policies typically apply the same requirement to non-medical, human subjects research.  For example, Nature and Science.
How do I avoid the process?
You can avoid the process if you are not doing research or if you do not involve human subjects.


Dilemma: Where to publish? I am an early career researcher from India. I had earned a PhD from a top European University four years ago and then I moved to my home country early this year. I have been working on a century old problem, in the area of dielectrics, almost past five years. I believed that I had finally solved the problem and hence wrote the manuscript and submitted it to the prestigious APS journal, Physical Review Letters (PRL), as a single author. The manuscript has undergone three rounds of review and in the final round, number of reviewers were increased to six. Three of them recommended the manuscript for PRL, other two because of the specialised content of the manuscript recommended it for the journal, Physical Review E (PRE), which is another good journal from the APS family. The sixth reviewer rejected the paper without giving any reason.
I was elated to see the reviewers comments and almost majority of them were in my favour. It would have been great for my career if as a single author I had published the manuscript in the PRL. However, the editor said that the manuscript warrants publication but PRL may not be a good venue for it. He recommended Physical Review Research (PRR), a new open access journal from the APS family. I had then resubmitted the paper to PRR, but they rejected the paper claiming that it does not fit into their journal. I then transferred the paper to the PRE and explained the history of the manuscript in my cover letter. However the editors of PRE rejected the paper citing that a manuscript that has been rejected by PRL and PRR, cannot be published in the PRE, though the editor suggested that I could make an appeal against their decision. If I do, an editorial committee will be set up to look into the matter.
After I had uploaded the paper on Arxiv, I had received emails from well known researchers of the field praising my work. I am not sure what is wrong? My theory predicts experimental observations quite well. This has been almost heart-breaking for me. Why they do not want to publish it?
In the last two weeks, I have received two emails from an Editor of an open access journal, Condensed Matter, MDPI publisher. I had not contacted them at all, I believed someone informed them about my paper, or they themselves found it on Arxiv. The editor has offered me to publish the paper without any publication charges. Normally, they charge around 1500 USD as article processing charge (APC). The journal "Condensed Matter" is indexed by ESCI (since 2017) and Scopus (since 2020). Its a new journal (2016), and has published only 265 papers so far in last 4 years. The editorial board has got Profs from Universities of British Columbia, Oxford, Max Planck, MIT, Rome, Penn State, Tel Aviv, Tokyo, Minnesota, Waterloo, Los Alamos. But, they have not released the impact factor yet.
So which direction I should go?
Please share your opinion.

Usually appeals are not a good idea, but in this case it might be your best choice.  It is very odd for an editor to "suggest" appeal.
https://journals.aps.org/authors/editorial-appeal-procedures
Appeals can only be on the basis of procedure (not science!).  The procedure says decisions are based on review by referees.  Five of six referees said the paper should be published in a physical review journal.  Therefore at least one of the three rejections is in error.
If your appeal is not successful, find a good journal elsewhere to try.


What are the first names of S. F. Buck? What are the first names of S. F. Buck? He/She has several publications 1,2,3,4,5,6,7. I tried to find the author on the pages listed and also in articles citing him/her, but in vain. General strategies on how to find first names are welcomed too.

According to Google Scholar, the author's first name is Samuel.

To find this, I did the following:

Do a Google Scholar search for one of S. F. Buck's papers; I chose the following paper which was linked in a comment above: A Method of Estimation of Missing Values in Multivariate Data Suitable for use with an Electronic Computer
Click on the "cite" link (quote symbol) at the Google Scholar result for the above paper
The MLA and Chicago citation style formats both list the author's first name as Samuel


Can PhD students take a semester or two to study abroad, similar in nature to a sabbatical? I know that it is common for professors to take sabbaticals and conduct research at other institutions, but I was wondering if this is something that is available to PhD students as well?
I ask because there is a professor at another university that I would like to collaborate with at some point in Australia (I'm coming from Canada) who works in my field of interest. I think that given the interconnection between research areas may have a direct benefit to my own dissertation or other research projects, but at the same time it could be easily just become a distraction from the dissertation.
I'd be curious to know if this is something that could happen while working on my dissertation (assuming proper discipline can be maintained to balance priorities) or if it is something that requires patience for later on in ones career?
For context, the field would be in mathematical biology / applied mathematics / bioeconomics / wildlife resources (from a math / modelling perspective)

This is really commonplace in my field (computer science). I spent every summer of my PhD interning somewhere.
I think that this is ultimately up to you and your advisor to figure out, as well as for your university/the host university to agree to (universities have rules regarding how much time you need to be on campus, and about double enrollments). If it's one semester then it should probably be fine. I don't know about the standards in other fields, but spending a whole year away is less commonplace (I would probably not agree to it myself as an advisor).


Providers of fake DOIs? How to find and check providers of fake Digital Object Identifier (DOI) numbers? What are the consequences of using fake DOI numbers? How can I know is DOI number actually fake?

DOIs are registered and managed by Registration Agencies appointed by the International DOI Foundation. All registered DOI numbers resolve through https://doi.org/ - if it doesn't resolve it's not a DOI. A DOI can be applied to many different things so the fact that content has a DOI doesn't say anything about the quality or validity of the content. There's a blog post about this - https://www.crossref.org/blog/dois-unambiguously-and-persistently-identify-published-trustworthy-citable-online-scholarly-literature-right/


Accepted conference paper but changing job before the conference I am a researcher at a company C and I'm going to submit a paper as main author in the next few days for a conference next spring. The thing is, I applied to a University U for a PHD and still waiting for an answer. So in spring, I might not be in the company anymore and they will have no reason to pay me the trip and the conference. So if the paper is accepted, I can guess 5 scenarios:

C still pays me the conference (very unlikely I guess)
U pays me the conference (However this team never published to this conference so it is unlikely)
I pay for it (I don't think I would, it is really too expensive (other side of the planet))
C pays for the second author to go and present the paper at my place
My submission is cancelled

What do you think is the more probable scenario. How does Universities and Companies usually handle this? C doesn't know yet that I am looking for another position. Should I renounce publishing this paper? I have been working on that for more than a year and this is a good journal.

The only thing that can be said for sure is that the conference is unlikely to cancel the submission. I don't know of any conferences that would do such a thing.

But whether anyone wants to pay for attendance is another question altogether. It can be explored with the company and with the university. In many cases either would be happy to help you attend as it increases their own visibility. In other cases they would not. In some situations the institution (company or university) won't pay anyway depending on the paper and the cost.

The safest thing for you is to assume that if you want to attend then you will have to pay yourself and to hope that, upon asking, either the company or the university will pay instead. It isn't then end of the world if a co-author presents in your stead. You still have the publication on your record.

Withdrawing your name from authorship seems to me to be the worst option as you have done the work but won't get credit.

It is also possible that you can submit something in addition to the conference and have the university pay on the basis of that, instead.


Am I allowed to my article to researchGate which is so far only published at arXiv? I understand that in general, it depends on the publishing license of the journal if I am allowed to distribute my article further. However, I want to know if I can upload an article, which I submitted to arXiv prior to publication in any journal (which is allowed by the journal I will send it to in the end), to researchGate?

arXiv uses a default license that does not transfer copyright but rather only grants arXiv a perpetual, non-exclusive license to redistribute the work, similar to, but less restrictive than commonly used Creative Commons Licenses, which arXiv also accepts as alternative licensing for submission.  That means you retain the copyright on any articles you submit, while providing a perpetual license to arXiv to do redistribute it.

Since you still hold the copyright on your article, you may do anything you wish with it, including submit it to researchGate.

The issue you need to be concerned about is whether the journal you wish to eventually submit the article to considers submissions to arXiv and/or researchGate to be "prior publication".  Some journals only accept articles that have "never previously been published" and different journals define what constitutes "published" in different ways.  Some journals exclude arXiv, researchGate and others (along with conference presentations, etc.).  Other journals will not accept papers that were previously on those (or other) archives.  Check the policies of the journal in which you wish to eventually publish the paper to ensure that you will still be able to after submitting it to researchGate.


Papers differing primarily by examined dataset, not analysis technique I am considering a specific topic in research paper within data mining field. I just found that my idea is being implemented and published in arXiv in the last month. So far, the published paper matches the flow that I was planning to follow but the author has considered the study with Twitter data. My question is: If I want to do the same experiments but with a different data set like facebook data set will it be considered a new contribution in that field ?

Ps: Row data crawled from Twitter API is way different from row data crawled from Facebook API, and the also different in structure and body.

In fact, the main contributions in your field are "algorithms", however, data sets are just a bunch of inputs for testing those algorithms and assessing their functionality or efficiency. If the outcomes of your new tests with data set A are exactly the same as dataset B's ones, you might not claim it as a new contribution. But if the results acquired from dataset B lead to some different interpretations about your algorithm's computational capabilities or something, you can consider it as a new contribution.


Two months to go on my masters programme and I want to drop out what should I do? I've been struggling with my MSc in political science since the start of the programme. The programme isn't what I expected. And I did a undergraduate degree in finance and already hold an offer from a top financial services firm. I now have two months to finish my dissertation and I want to quit.

I hated my programme with a passion. and I had 0 political knowledge before I applied so I've been struggling since day 1. I've already failed two modules which I'll have to resit after November. I failed because I didn't understand the content. These two modules were about advanced quantitative research and EU politics. And I jumped in with no foundamental knowledge whatsoever. Moreover, with work and professional exams which I will have to study for, I won't have time to study for the resits.

I also hate my dissertation topic. I addressed this issue with my two supervisors but they didn't seem to think it was a concern. Again I came up with the topic with very little background knowledge and without knowing it's actually not something I'd like to do.

I've been trying to re concentrate on my dissertation for a week with no success. The more I read for my dissertation, the more I dislike it.

I've already contacted my firm and my school to discuss any potential consequences of dropping out and I'm still waiting for a response. I don't want to quit but I struggle to continue. It's affected my life severely and I have pre existing depression for years which my school knows about.
Please give me advice

My heart goes out to you, it sounds like you're really unhappy with your current situation and feeling very conflicted.

It's hard to give someone advice on a topic like this because it's so personal so instead I'll give you a few of the questions that I might ask if we were able to sit down and have a chat about this.

What initially led you to apply into this masters? Is it your specific experience that is creating problems or is it that this masters does not align with your interests/goals?
What is the appeal of this job offer? Can you really see yourself doing that kind of work or is it that it represents a face-saving alternative to completing your masters?
What would have to change for you to be comfortable completing your program? Is it a change of dissertation topic? Is it extending by a term or a year to take the pressure off? Changing supervisors? All of the above?
Are there jobs that you want, now or in the future, that you can't have without this degree? How important are they to you?
Do you really hate your program/subject or do you hate the situation you are in?

Think on these on these until you hear back from your school and your potential employer. Once you have answers to them, take a break and step away from it for a little while; when you come back to it see if you still feel the same way about your answers or if your thoughts have changed.

There's no right or wrong way to do this - I personally trudged through a degree when I knew it wasn't right for me because I was so close to the finish line. Finishing that degree proved to me that I could see something through to completion (something I had always struggled with) but also kept me from finding my true path for another year. I'm still not sure what the right choice was, but I'm happy with where I am now.


If tenured staff are virtually unsackable, why is the drive to find funding so strong? Tenured staff are virtually impossible to fire, why is the urge to find funding so strong? For post-docs and other untentured scientific staff I can understand, for their job depends on it. For a tenured professor it would rather be the joy and honour of doing important research. Apart from a reduction in joy and honour, are there any consequences if a tenured professor fails to get grants?

In many departments, tenured professors can use bringing in external funds to the department as a means of "buying" their way out of some of their teaching and administrative commitments. Similarly, other departments might use additional committee assignments and teaching loads to "punish" people who don't bring in grants. They may also have less flexibility in selecting teaching assignments.

In other countries, such as Germany, a long-term shortage in funding can lead to the consequence of a chair not being "succeeded" when the holder retires; in that case, the institute (equivalent to a US group) the professor is in charge of is wound down rather than finding a new leader for the group.


For NSF proposal and grant purposes, do graduate students meet the definition of "investigator"? I recently received an email from a department administrator that NSF rules have been changed (link here), such that all investigators must fill out a conflict of interest (COI) form.  They then go on to list a cadre of examples which meet the definition of investigator and a statement that all investigators must fill out this form.  Our university has the definition of investigator here.

My question is, are graduate students typically considered investigators by the NSF?  If so, we certainly do not receive the recognition that PIs and other listed investigators get.

Actually, the NSF, in its Grant Proposal Guide, does not actually define the concept of an "investigator." Instead, it chooses to define the different categories as "senior personnel" and "other personnel." Typically, postdoctoral fellows and graduate students fall under "other personnel."

Personally, in such matters, I would opt on the side of caution and just have the graduate students fill out the conflict of interest form. It doesn't take very long, and having it in place makes life easier for everyone.


Unclear referee's message I receive a message from a referee, but I didn't understand what was required of me exactly. The message is:

  please check again the typeset text of these lines

What kind of error do they refer to?

The message is vague, but check the text the referee has highlighted. Chances are you can see something wrong. The word "typeset" here could indicate a typesetting error - for example, perhaps you forgot to include a reference that the text cites (this makes LaTeX go [??]). Or it could just mean there's a spelling error, an ambiguous sentence, etc.

Either way, the reviewer pointed out which lines they're referring to, which should help you solve the issue.


Obtaining a non-digitized thesis I have been trying for a few weeks now to obtain a published thesis (this one, if you're wondering), but have had no luck in doing so.

There currently exists only one copy of this thesis, at the Lewis Library of Princeton. It has not been digitized. I have contacted the library to enquire about obtaining it, but not being currently affiliated with any university, the best they could offer me was to ask local libraries about inter-library loan programs. I have done so, and discovered that people were amazed that inter-library loans were still a thing, and after ferreting out the person in charge of it, discovered that they would not even consider an ILL from the US (I am in France).

Are there any other process I can try to obtain a copy of that thesis?

You can try contacting Robert Marzke himself. There is a chance he has a digitized version of his own that he is willing to share.


Correctly formulate Figure caption: refer the reader to the web version of the paper? I have included a pretty complex map with about 10 different colors in my scientific paper in forest ecology. I am looking for a standard formule which is applied in this case, something as : For interpretation of the references to color in this figure caption, the reader is referred to the web version of this paper.

However, in my caption I do not use the description i.e., red represent rats and green ~ herb, thus I do not want to start with For interpretation of the references to colour in this figure caption...

How can I correctly write: please, for color representation of the figure, refer to the web version of the paper?

I am not an English native speaker.

Could be the following formulation correct?

The reader is referred to the web version of this paper for the color representation of this figure.

If not, do you have some better suggestions?

thank you !

Do I understand correctly that you just want to tell the reader that the colored figure is available online (in case they printed it b/w)?

If so, then the usual approach is to do the following:

  Figure 1: (Color online) This is the caption and there is some stuff here.

This may depend on your field, but the American Physical Society (APS) recommends this.


Can I put into Acknowledgments someone who is no longer living? I am finishing a paper which was created thanks to my inspiration of Erik Erikson's work on psychological developement. The paper is, however, in the field of thermodynamics and complexity-science. I, therefore, feel grateful that such a great theory was created many years ago, and now is capable to push exact sciences step forward. I named two terms following Erikson's theory. I would like to note this somewhere, or state in general that I was inspired by the theory.

Do you think that it is OK to do this? Maybe I should hold back for some time, I can always state the "thank you" in the subsequent papers?

I would reserve the acknowledgments section for people or organizations that directly contributed to the paper.  For example, if you talked with Erikson while he was still alive and he offered advice or suggestions, then it would be appropriate to thank him in the acknowledgments.  If you were just inspired by his papers, then it is better to discuss that elsewhere in the paper.  For example, you could note in the introduction that your approach is inspired by Erikson's work on psychological development, or you could mention this background when you define the terms based on his theory.  But if you thank him in the acknowledgments section, then people will assume there was a more personal connection unless you clearly specify otherwise ("Although I was never lucky enough to discuss this work with him in person, I owe Erik Erikson a great debt for...").

The main thing you should not do when thanking a deceased person is to attribute opinions to them, because they are not around to contradict you.  For example, you should not thank them in a way that suggests they supported your work, even if it's true, unless you have some documented proof.  For example, it's awkward to write "I am deeply grateful to Erik Erikson for his steadfast belief in my theory."


Post-doc independent money/grant (astrophysics/computer science) in the US (travel expense/workshop)? I am currently a postdoc in a US University (I'm French).

I am in between astrophysics and computer science.

My work is currently funded by NSF (work related to the Dark Energy Survey).

Are there some program/award/grant out there I could apply to, to gain some autonomy (additional funding I could use in the way I want to for travel expenses/collaborations/organizing workshop).

Because my problem is that most program I've found are either for PhD students or for professors. What about post-docs?

Due to their (traditionally) short terms, postdocs are usually limited in what they can apply for. There are NSF Postdoctoral Fellowhips in your area, as well as almost every other area NSF funds. The other funding agencies in the US (DoE, NIH, etc.) also have fellowships available for postdocs. You should search the Internet more carefully for other opportunities.

That being said, whatever grant is funding your work almost certainly has travel funding included in it. Have you talked with your supervisor or PI about the kind of travel you'd like to do? You should.


What are the benefits of becoming an academic administrator? Why do some professors choose to go into academic administration (e.g., become associate deans, etc.)? I've always assumed the main attraction is that they get paid more.

But I've also thought that if I wanted to make more money than I do as a professor, I'd just leave academia entirely and take a job in industry, where I could probably earn 30-40 percent more. I'd have less flexibility in industry than I have as a professor in terms of what I research and what my work hours are. But the same would be true if I went into administration at a university (which would probably still not pay as well as industry).

So I've never seen a real benefit of going into administration, given that the extra pay does not (to me) offset the extra responsibilities (especially when the best-paying jobs are outside of academia entirely). Are there other benefits of being an academic administrator that I'm overlooking?

I feel like I'm pointing out the glaringly obvious, but many people actually want to make their institution a better place, design policies that benefit future students and colleagues, etc.


Is it ethical to withdraw a paper after reviews? I have a submitted a paper to a IEEE letter. Unfortunately, at a later stage I noticed that letter is still in process to have an impact factor.
I already received reviews from reviewers and the journal is willing to
accept the paper after minor revision.
Is it ethical to withdraw the paper at this stage?

There is nothing to do with ethics as question asks. This is simple professionalism. The journal has devoted enough time for reviewing the manuscript. The reviewers have put in their efforts.

If you are really fixed about not go ahead with submission of revised manuscript, then do the following:

Don't submit the revised manuscript to the journal.
If the journal editor asks about the revision, then say that you are extending the article in various ways and would not submit the manuscript. But, thank them for their efforts.

But, I would suggest that you had made a mistake not looking at the journal statistics, you should go ahead with this journal with the publication.


Does taking a long time to graduate impact my Ms/PhD admission? I need some advice on my career. I study in Brazil and I'm one year away from obtaining my bachelor in Mathematics. Here the duration is 4 years.

In 2016 I had to start working two jobs (unrelated to Math) to help my family and that made my 4-year journey into a 5 and a half years journey in which during the process I've failed a couple of classes due to attendance. I was able to quit the job this month and from now on I'll be able to focus only on my studies.

My question: is there still a chance for me to work on my Master's, Doctorate and so on? And also how much does the fact that it took me 5 and a half years counts? Despite not being able to attend the classes, I consider myself a good student and I know for sure I'm dedicated.

As a rule of thumb, the time you took wont matter, but the failing grade will.

However, if your goal is to get into a masters course in Brazil, many of them won't look at your undergraduate marks (I've served on graduate committees on two top brazilian math departments).

In these cases, you can be admitted by doing well on an admitting summer course, or on an admission exam (many of them nowadays use the Extramuros examination, or a local exam).

Even for institutions that will judge your undergraduate marks, it's not uncommon that a student with a failing mark get accepted. Usually they would indicate in their statement why they failed and how they did well on this course on the next time. The fact that you had to work is enough justification, if that's a localized problem and you have strong marks otherwise.

After doing well in your masters, your undergraduate marks will have a negligible impact on your PhD admission.


Can a single co-authored paper be part of two stapled dissertations (by two people)? Two friends of mine, Alice and Bob, enrolled in two different Ph.D. programs, have been collaborating in a research project and writing a paper together.  They have submitted the abstract to a certain conference and hope to publish the paper in the future (the conference allows this).  Alice, expecting to graduate sooner than Bob will, asked Bob by email if she could include the paper into her "staple" dissertation.  Bob is completely fine with that, but he is confused at the same time, since her email was lengthy for the seemingly simple favor.  He thinks that perhaps the favor would have consequences according to some customs in the academia; he is worried that the decision might make it impossible to use the paper as part of his own dissertation.

Question: Can a single co-authored paper be part of two stapled dissertations (by two people)?

(Alice is in the Netherlands, and Bob is in the U.S.  They both are enrolled in interdisciplinary programs, but the closest fields include mathematics and theoretical computer science.)

Every university should have guidelines around how publications can be incorporated into a PhD thesis. The correct advice (as @Andreas notes) is to consult these guidelines. Furthermore, it seems that PhD by publication is becoming more popular and guidelines are evolving.

I'm familiar with various models of "PhD by publication". At my institution in Australia, the PhD student is expected to be first author on any major publication that forms part of a PhD by publication submission. They also need to attach a form for each publication outlining their contribution and the contribution of the other authors. The form needs to be signed by the other authors. Non-first-author publications can be included but they are intended more as supplementary contributions. Exactly what this means is a little open to interpretation.

By way of a concrete example, here is an example of such a policy (the policy at your university may differ):

  It is expected that the student will be the first author on the papers, as per 1 above; the number of co-authors is limitless. Students may be second or later authors on additional papers.

Thus, to answer your specific question, at my institution, a paper could be included in more than one PhD. However, the student who is first author would have a stronger inherent case for it being seen as an integral part of their thesis. Furthermore, the contributions of all authors would have to be explained.

You may want to consider practical alternatives such as thinking about how the work could form two papers where you each drive one paper as reflected in being first-author on that paper.


Walk up and talk to random people at academic conferences - is that appropriate? As a graduate student, I am relatively new to my community. From my point of view, the best approach to get to know new people is randomly walking around and start conversations (with anyone, no matter what age or known/unknown). But is that appropriate at academic conferences? How do established researchers think about that?

I am asking because in my previous conference visits, I often felt that people are annoyed or not interested when I just walked up and started a conversation. What would be better approaches for getting to know the community?

Absolutely. It helps, though, to be a little context sensitive.

If you've just come from an amazing presentation and want to talk about it to someone else, then "did you just hear that great talk by/about X?" is a good way to start the conversation, better than just "Hello" or "Great conference, eh?"

If you know who the person is (they're speaking, you recognize them, etc), then greeting them ("Hi Kate," or "good morning, Dr. Gregory," according to your industry norms) and introducing yourself with context ("I'm Susan, I really enjoyed your book") is a fine first sentence but please, have a second sentence ready. After the person says "thankyou, that's very kind," what will happen next? A question is good here - perhaps there's something you've always wanted to ask - or you could go back to your opener for a complete stranger, "did you just hear that great talk by/about X?"

Never open with something negative - "were you in that stinker of a session? Wasn't it the most boring thing ever?" - is right up there with the friend of mine who asked someone at a wedding "who is that obnoxious fat woman in the flowered dress and why is she even here?" only to be told "that's my mother."

My biggest problem with conference conversations is when someone wants to have a conversation with me but doesn't actually have anything to say. That puts all the conversational effort on me and it's hard work. Should you find yourself in this situation, have a selection of questions you can ask:

is this your first time at [this conference]? (don't ask an industry luminary, or a speaker, this question)
are you enjoying the conference so far?
what is your favourite talk so far? (not good the morning of Day 1)
is there a particular session you're really looking forward to?

It's a little trickier to ask questions outside the scope of the conference, like "where are you from" or "where do you work?" because they often contain assumptions - you might assume someone is a student who has graduated, or is a prof when they aren't yet, or is in a lab when they are not, and it's possible to offend someone. So don't lead off with these. Often, stating your own circumstances is a way to prompt the other person to respond in kind: "I flew here from just outside Toronto. You?" or "I'm doing/finishing a Ph.D/postdoc/intership at ABC. You?" though again be careful if the person thinks you should know this thing about them, or if it's on their badge. You usually want to get a paragraph or two into conversation before discussing "real life" rather than the conference.

Well chosen questions not only move the conversation along, they can meet your other goals. Maybe you'll decide to attend a session you hadn't planned to. Maybe you'll learn about a great book or other resource related to something you enjoyed. Maybe you'll be invited to something, or exchange business cards, or al those other benefits of networking at conferences. None of those things can happen if you just say "hi" and leave it at that, the other person says "hi" and then the two of you stand there awkwardly, wondering why you're not having a conversation.

I read and enjoyed a book called How to Work a Room that emphasizes knowing what you want from encounters like this. Are you trying to find a job? Hire someone? Learn more about something? Tell people what you've discovered? For every want you bring to that conference, someone else brings the matching one and if you two find each other you will both be happy - but only if you tell them what you're looking for and what you have to offer. This is a skill you can learn, and marching up to strangers and saying "hi" is only the first step.


How to justify motivations for a second master? I have already graduate from a master degree in Europe (Software Engineering) , and applied for another master degree (Informatic) in Germany (TUM).

I have applied with my BSc. degree diploma and transcripts to the German university. My scores in bachelor is quit good, and convincing. The issue is they have invited me to an interview. I guess they want to know why i am still motivated for another master, while i have one?

Here are my motivations:

The focus of my first master was Software engineering, meanwhile now i am interested to learn about distributed systems, networks.
I am looking for a careers which needs both the  programming and network, and i think this master programme would help me. I am already good as a developer but i need to improve my skills in network.
I have some raw idea over the Bitcoin, Blockchain , and Internet of Things, and i need to be in touch with some experienced teachers who have deep knowledge in this fields.
Germany is an awesome country. I love the language and culture, and i think there are lot's of job opportunities for IT people.I have some basic command in German, and i am going to advance them during the programe.

Do you think these motivations make sense for them?

I don't find your justification wise enough for a second master degree in distributed systems and networks. Moreover, I don't find a real target behind the second master degree other than getting associated with professors and the country.

If your prime purpose is to learn new stuff, you don't need a second academic degree which is very similar to the one that you already have. You can learn on your own. Moreover, you could directly apply for a research degree (say Ph.D.) in Germany instead. This would definitely make more sense. Unless you have some serious career goals to pursue on the specified courses, you should not do it. In my university, my colleagues who have Ph.D. in software engineering are now doing serious research in IoT, Distributed Systems, and Network security.

Ask yourself this question: If you get interested in computational economics after 2 years, would you again apply for a masters degree in the same field?


To what extent might a non-faculty staff member expect -- or demand -- academic freedom? Faculty and students are generally regarded as having some degree of academic freedom (tenured faculty sometimes having more than non-tenured).

Non-faculty staff seem to be a different matter. Specific institutions might have policies addressing this, but I'm asking more from a general / philosophical standpoint: is there any basis upon which a non-faculty staff member at a university might expect -- or demand -- academic freedom? Or should non-faculty staff basically assume they do not have academic freedom?

The American Association of University Professors (AAUP) has a set of Recommended Institutional Regulations concerning Academic Freedom and Tenure, which has the following to say about academic freedom for staff:

Other Academic Staff

a. In no case will a member of the academic staff who is not otherwise protected by the preceding regulations that relate to dismissal proceedings be dismissed without having been provided with a statement of reasons and an opportunity to be heard before a duly constituted committee.21 (A dismissal is a termination before the end of the period of appointment.)
b. With respect to the nonreappointment of a member of such academic staff who establishes a prima facie case to the satisfaction of a duly constituted committee that considerations that violate academic freedom, or of governing policies against improper discrimination as stated in Regulation 10, significantly contributed to the nonreappointment, the academic staff member will be given a statement of reasons by those responsible for the nonreappointment and an opportunity to be heard by the committee.
...
21 Each institution should define with particularity who are members of the academic staff.

Essentially:  those staff that an institution chooses to define as "academic staff" should be able to bring grievance against a "duly constituted committee" if they believe they have been terminated (or not reappointed) in retaliation for speech or actions that should be protected under the umbrella of academic freedom.


spending time to get into top school PhD vs getting done with PhD I have a funded PhD offer from a R1 university in texas but its ranked in the 180s based on USNews, the advisor and myself click very well, he is nice, open-minded, and a young motivated and driven advisor always searching for new collaborations and the research area is in my area of interest. His background is in the sciences and I want to focus on engineering which isn't an issue as there are professors in other depts that I could collaborate with. Finally I will be his only student, he occasionally has undergraduates and his last PhD student will be graduating by the time I get in.

My research focus is in neuroengineering and rehabilitation for movement related disorders - focusing on restoration of grasping and posture. The main difference from top universities is the prestige, level of work (more translational and more grants), will have a better contact base when starting off, many professors working in the area.

Due to having a low uGPA from India ~ 55%, which is why I applied to mostly masters programs despite having around 2 years of research experience during my undergrad. I feel like I was lucky that the prof had an interest in my profile and asked me to switch to PhD and then I got it (as mentioned in the 1st para). I have also got an MS offer from a 40s ranked university based on USNews with funding only for stipend (would most probably have to take loan for tuition).

In the hypothetical situation that I take the MS offer I would have to apply for PhDs at the end of my 1st year @ around sept/oct of 2021 and I feel that I would only have a slightly better chance to get into top universities with professors that do amazing work in my area of interest like northwestern, ucsb, rice, university of chicago, and upenn. But at the same time I feel that my horribly low GPA in undergrad will hold me back as I would have to get exceptional grades and do good research; good research seems like an impossible goal in 8 months. Though I may be able to get something useful at the end of my masters but most probably not within 2 semesters. If this scenario of getting into the universities mentioned seems impossible at this point, another option would be to apply to these universities the next year 2022. When I would have finished my masters, but would have to use another extra year working in a research lab and then join the university for PhD.

My question has two parts:
1. The likelihood of getting into the mentioned universities for PhD after 1 year of masters and after 2 years of masters.
2. Is it worth using the 2-3 years to just work towards doing a PhD at these top schools with amazing professors or should I go ahead with PhD straight away and probably think about post-doc with those professors. I just feel that I may miss out on the environment and opportunities that I may get as a student.

Please do not take into consideration about what I want to do in the future like industry, academia etc. as I am set on doing research with these intellectual people and am driven to produce and make an impact on both human knowledge and the patient population (i know this seems like a child's fantasy but this is something that I like to think about) at the end of the day I may go into industry as I am a high-maintanenece person or I may chose to stay in academia as the gratification may overwhelm my needs.

I think you are vastly overestimating the value of ratings from a popular magazine as they apply to doctoral education and vastly underestimating the quality of doctoral education at any R1 in Texas.

Frankly the real difference, in an individual field between a school rated 180 and one rated, say, 40 is likely to be a mix of random and the value of a given helpful advisor.

Frankly, I think you would be wasting your time to do much of anything but take what looks like a very nice offer. You'd be halfway through a doctorate at the Texas place before you had a chance to start if you go another route. If you read a lot of questions on this site you'd notice how lucky you would be to have found a good and supportive advisor. Many are not so lucky. Who can say whether you'd have a better time of it if you look elsewhere?

And it is you that makes your career, not the journalist/researchers at US News rating places on general criteria.


Non academic career options for PhD in Math I am thinking of getting my M.S. in Computer Science. I chose C.S. because I enjoy programming and because its a solid choice, career wise.  Low unemployment, good pay, all that jazz.

But my real passions has always been math and lately I have been thinking about swapping and going for my graduate degree in Math. If I went the math route I would probably go full PhD (since I don't think there is much you can do with just a Masters in math).

But as much as I love math, I can't see myself being a math teacher. I would want to work in research or industry, applying math to solve real world problems.

What kind of non-academic jobs are there for someone with a PhD in math (or what is the best resource to see what jobs are out there)?

It really depends on the kind of mathematics you do. For example, if your work involved probability/statistics, or even certain kinds of topology, you could get a job at pretty much any tech company doing machine learning. If you were doing stochastics, then Wall street will beckon.

If your Ph.D has a computational side to it (say in numerical methods for example) the national labs in the US are interested in your expertise.

And so on and so forth. The fact that you're doing an MS in Computer science makes your profile look even stronger.

While this might be viewed as a strongly biased suggestion, you might consider a Ph.D in Computer Science: there are many parts of computer science that are all mathematics, and you'd get to do what you love, as well as getting the CS branding that will make getting an industry job way easier.


Choosing full time vs part time on a PhD application, is one necessarily better than the other for increasing chances of admission? Don't know if relevant, but I'm applying for PhD programs in math.

In general for grad school apps*, if I'm asked if I want full time or part time, I choose both if I am allowed to do that.

Is there necessarily a better choice if I am not allowed to tick both or pick either?

I mean:

Does part time indicate I'm open to working at the university as a grad/teaching assistant (and hence full time indicates not being open to such work?) ?
Or does part time indicate that I would have other commitments and so would not be seen as a whole hearted student (and hence full time means that I would be a whole hearted student)?

There may be some other things I'm not considering. Please answer in general. Which option, if I have to choose only one, gives an applicant a better chance of getting in the university?

If this depends on the program, please give examples of programs where indicating full time is a better choice and examples of programs where indicating part time is a better choice

To make this clear, I'm not asking if it's better to take a PhD full time instead of part time or vice-versa. I'm asking which is better in applications assuming I am open to either and am allowed to pick only one.

*or for example databases in ETS or QS Grad School Tours

Or does part time indicate that I would have other commitments and so would not be seen as a whole hearted student (and hence full time means that I would be a whole hearted student)?

Yes, this is my understanding of how it would be interpreted.  It would definitely not mean working as a TA or RA.

Unless you have a job you'd like to keep, or other comparable responsibilities outside of studying, I'd recommend checking only the full-time box.  I don't think expressing an openness to part-time study would help get admitted to a math PhD program, while it might look odd or worrisome.

In particular, in the math PhD programs I've studied or taught in, there have been essentially no part-time students.  (It might have been a theoretical option, but I can't think of any actual part-time students.)  For programs like this, the application might ask about it, but the expectation would be that everyone is a full-time student.

I think this is standard in U.S. math PhD programs, but some programs may run differently, so I can't say this advice is necessarily universal.  (The biggest variance would be that some applied math programs may be more open to having part-time students.)


Why don't grants from publicly-funded organizations systematically demand code and data to be released? I wonder why publicly-funded grants do not systematically demand from the recipients that code and data to be released, and results/papers to be publicly accessible. (put aside data that raise privacy issues)

Because there has not been a strong enough push to require it and some researchers prefer to keep code/data confidential. This is currently a topic of discussion at the national level led by organizations such as EFF. This is hopefully a situation that will soon change for the better.


Pros and cons on commenting on public review papers Journals such as AMTD and ACPD contain an open discussion where anybody can comment on papers under review. The peer-reviewers are still anonymous, but other people commenting are not. If I'm reading a paper and have questions about it, what are the pros and cons on posting them as public comments versus writing an e-mail to the author directly? On the one hand my comments may improve the paper; on the other hand, if I write something stupid or step on somebody's toe, that may harm my future career.

What do others think?

(Edit: I might add that in the case I have in mind, I am already in contact with the author)

I would try to answer this from the standpoint of a cost-benefit analysis.

A private conversation with the author will benefit you in that you now know the answer, and can harm you in that if your question is completely boneheaded the author will think you're an idiot.

A public conversation has the added benefit that you and other people both benefit. This is somewhat of a questionable added benefit, as oftentimes the question being asked isn't relevant to most people, but still, added discourse is often a good thing. Public discussion also has the added cost that more people can see your boneheadedness. While typically this wouldn't be a problem, as most people wouldn't ever encounter the discussion, anything on the internet can go viral, even if only within a smaller community (such as your research field). Personally, that cost strongly outweights the potential benefit. I would definitely stick with personal correspondence.


What does it mean if a committee chair asks if I applied to many similar jobs and if I plan to fly back and forth? I am currently working at Europe and applying for tenure track positions in US. I will attend an interview that is held by a school.
The committee chair told me to research on the air tickets.

Also, in her message she asked if I applied many schools in US and if I plan to fly back and forth.

I do not know how to answer this question because I am not sure what she meant. Does she want other schools to share the international fare? If so should I contact other schools about it (that was the first school offering me interview)?

Unfortunately there are budget constraints at all institutions, and interviewing faculty can be an expensive affair.  Most likely, this is a polite way of trying to figure out whether you'll already be state side during a date range they'd want to interview you. No reason to have you hop the pond repeatedly if the timing works out.

No, you should not preempt the question and ask other schools about sharing airfare.

I am tempted to think this school is reluctant to spend the money to bring people from abroad over.  It is somewhat strange they would have you research airfare. In my experience, there is staff that takes care of that. I, for one, would mark this in the 'con' column, because if they skimp on airfare for desirable faculty, what else might they skimp on?


How to automatically link LaTeX .bib references to a set of pdf full-text articles? I have a huge collection of PDFs of research papers. Many of these have valuable annotations. I also have a huge .bib file containing citations for these and many other works. Is there a reference manager software where I could import the .bib file and the collection of PDFs and somehow the entries in the .bib file could be magically linked to the corresponding PDFs? I would then like to use that tool to access my PDFs (of research papers).
I think this was a feature request for mendeley long back
http://feedback.mendeley.com/forums/4941-general/suggestions/80946-automatically-find-pdfs-link-them-to-imported-me .
As of today, I don't think that it has been implemented.
I tried Quiqqa (http://www.qiqqa.com/) , but had no luck.

Here is one nearly automatic way to do it using Zotero (https://www.zotero.org/):

1) import the PDFs in Zotero. One way is to select multiple PDFs and drag them into a collection (in the LHS pane) of Zotero.

2) Select the PDF items (CTRL click in Windows for multiple selections), right click and select "Retrieve metadata from PDF". Note that this step searches online databases for missing information and seems fairly robust.

3) import the .bib file in Zotero

4) Go to the duplicates collection in the LHS panel and merge all the duplicates.

Issues:

1) In step 4, there may be false negatives if the automatically retrieved metadata (in step 2) is too different from the corresponding entry in the .bib file (step 3)

2) Step 2 might fail on old scanned PDFs.


How should we cite a MOOC? How should one cite materials taken from a Massively Open Online Course (MOOC)? This may be a specific case of the more general, "How should one cite a university course?"

For a concrete example, consider how I should cite the "Resampling Wheel" algorithm for implementing a particle filter, taken from Sebastian Thrun's Artificial Intelligence for Robotics course on Udacity?

In many fields, it is common practice to look up the original publication in which a concept/algorithm was introduced, and to cite that. Many courses will give some literature pointers to help you with the search for it.

The reason is that citations are also meant to distribute credit for novel findings, so in this way, the researchers who came up with the algorithm get the credit.


How to promote young researchers at a conference designed for young researchers? I am currently co-organizing a conference targeted at young researchers (mostly PhD or post-doctoral people). All talks are to be done by these younglings. However, there are only around 10-15 scheduled talks, while we expect at least twice as many people.

What kind of activity can we set up so that the attendees who don't get to talk still get an opportunity to share their research (with other attendees and more senior researchers)?

Our go-to option is a poster session. However, I have been at the same kind of conference before, and these tend not to be very successful. I think this is because the conference is rather small, which means few people by poster. Posters also don't seem to promote discussing with other attendees (people tend to stay beside their poster, to speak with the occasionnal interested bystander).

A few years ago, somebody organized on the fly a "research speed dating" event: from what I have understood, everybody gets five minutes to explain their reasearch head-to-head with another attendee, then the people mix up and start again. It was quite successful, or so I have heard, but the details are fuzzy and I have no experience whatsoever in organizing this kind of thing.

Our default option is still a poster session, but what other possibilities are there? Or, if nothing else, how may we run a good poster session?

Edit: the conference was last week, so I have some feedback. There were few posters, so we did a little introductory session for people not among the plenary speakers (some who submitted a poster, some who didn't). I think it was successful in fostering discussions for those who submitted posters. Thanks for all who answered here, and who helped us choose this option.

This reminds me of maybe relevant idea. When I went to a summer-school on mathematical physics in Heidelberg, the organizers made a "Gong show". The idea was that everyone had to stand up before the auditorium and introduce themselves, both professionally and personally. The point of the gong was that you got only something like 2 minutes to do so, then the organizer hit the "gong" (he hit a glass with a spoon I guess) meaning you should finish. After that came 2nd gong and after the 3rd you had to go off stage. This was very nice as even the speakers attended this event and introduced themselves.

Moreover it really helped that we were given as a part of the conference materials printed list of names and email addresses so we could take notes on who is who.


Applied vs Pure Math for an Engineering Student I'm an electrical engineering student specializing in communications. I decided 1 year into my undergraduate studies to pursue a degree in mathematics alongside my engineering degree. I plan on going to engineering research (PhD) and possibly working in the industry after a while. I know that applied math would make more sense but I'm asking whether it would make that much of a difference if I went with Pure instead.

One reason I'm asking this is that Pure Math has more "beautiful" courses that made me decide on math in the first place. Moreover, the two degrees aren't that different in terms of required courses. Finally, Applied would take me more time to complete because my math course choices in that my 2nd year were oriented towards Pure. I'm completely willing to spend that extra time pursuing applied. I'm just wondering wether it would make a difference.

Believe it or not, following the "pure" track might help you out more.

I used to have an "applied concentration" to my math major, which meant I had to take mathematical modeling classes, graph theory, operations research I & II, etc. on top of my core classes. When I decided to go the PhD route (applied), my advisor recommended I drop the applied concentration in favor of the pure, reason being that the pure classes will give me more breadth and better preparation for grad school.

Ultimately, this meant that I had to take abstract algebra, adv. Calc I & II (also known as elem. real analysis), a proof writing class, etc. I did end up taking the modeling class as an elective.

From the point of view of my advisor (who is on the grad. Admissions committee at my school) these aforementioned classes show capacity and mathematical maturity to a greater extent than the applied courses, which is what departments would like to see when considering your PhD application. Plus, they give you a foundation to build upon once in grad school.

So, I'd say take the pure classes and cherry pick (smartly) the applied ones as electives. This will ensure you're more prepared for the rigor you'll encounter wherever you decide to go.

Best of luck!


How to sign your email to students, so to avoid their immature behavior? Or how would you like to be addressed?

As a graduate TA, I went by my first name. But I thought that some students were becoming too friendly. They took things for granted (for example, asking for a homework extension every week without even bothering to make up an excuse, or showing up to my office hours and interjecting with comments meant to be funny but came out sounding obnoxious).

I will be an assistant professor next year, and I am wondering whether asking my students to call me Dr. LASTNAME would resolve some of the rudeness that I've encountered.

But how do you ask? Sign my email Dr. LASTNAME? That sounds pretentious. Should I just use initials (FL for FIRSTNAME LASTNAME)? I sign all my emails with my first name, but doing that for students is an open invitation to call them by my first name. How do people transition from a graduate TA to someone with a PhD in front of a class full of undergraduate students?

**EDIT: I have had several students be truly rude to me, but in keeping with the spirit of anonymity, I did not describe in detail what happened. But My colleagues were shocked and appalled at some of the behaviors that I have encountered.

That said, I do very well with evaluations, often nearing perfect score, and my students score well above average in multi-section calculus classes. As you might imagine, my classes are fairly well-attended with high level of  participation. Of course there are pros and cons of familiarity, but I am somewhat puzzled at this display of lack of authority in my classroom, as all of my colleagues also go by their first names. I hope this is more information.**

Like JeffE's comment, I always prefer students to call me by my first name. My male and female, Asian and white colleagues also prefer to be called by their first name. There are some exceptions where they insist on some title according to local custom for showing respect. However, I do not have the problem you describe (students expecting unreasonable things and acting in completely unprofessional ways). The reasons that I do not have to deal with these problems is because I simply do not accept them.

Actually, I am fairly strict but also fair and I always try to be open, transparent, and predictable to my students. They know if they arrive to class late, they are absent. If they submit late, they fail. They want more time, they won't get it.

I do not see how what I allow them to call me (excluding rude names) would result in overly familiar behavior. Indeed, many of my Asian colleagues are far closer to students than I would ever allow myself to become. The ones who demand more formal forms of address are the ones who seem to get the closest with students. Perhaps this is how they remind students that they are still the teacher.

In short, student behavior is driven by your attitude towards them and you can convey a tone of seriousness in the relationship without requiring formal salutations.


How to remove the "Text Overlap" comment from arxiv Recently I have submitted an article in arxiv. But unfortunately, an indication of text overlap has been added in the comment section. It is to be noted that, the overlapped paper is also my other paper. Now I would like to remove that comment ("Text overlap"). Can I remove this comment by replacing this paper with a revised and corrected copy?

Yes, updating the paper will remove the comment. (From the new version - it will still be there with the old version.)
Note that https://arxiv.org/help/overlap (linked by AnonymousPhysicist) also lists ways to avoid having such a comment added, by proactively pointing out the related work.


Why is the two-column format so popular? At least in the field of computer science, I have noticed this to be a common practice.

Why exactly is this done? I find it harder to read and follow.

There are some established standards for page layout in publications. One that I'm familiar with is a set of patterns for desktop (that is, personal) publishing by Andreas Rüping, published in the EuroPloP 1999 proceedings (University of Konstanz).

One of the patterns says that a page should be no more than about half text. A fair amount of white space, margins, and other elements besides text.

Another pattern says that a line of text should be no more than about twice the length of the alphabet used, so around 52 lower case letters in English. This isn't applicable to Chinese, of course. This limit is "imposed" by the physiology of how the eye works. Among other things, if a line is too long, then it is harder to pick up the start of the next line when scanning back.

But a full line of text in a reasonable font can be nearly twice that limit.

So, just those two patterns suggest two column format or some other accommodation.

And note that, if you are young, you have an easier time reading long lines than someone older with poorer eyesight.


How to decline a potential PhD supervisor? I have seen something similar has been asked but I seriously don't know what to do.
I applied to 3 PhD programs all from quite good Universities. For all of them I contacted a potential supervisor, and they agreed to supervise me after a skype interview. Recently I finally got an answer from the best of the 3 Unis and after three interviews and a small project, the professor agreed on supervising me.

Due to some life events I had to wait one month to complete one of the applications, which I think it already pissed off one of the professors.

Obviously, I would like to go for the best University, not only for its ranking but also because of the city itself, the people I know in that city, and the research field which is closer to mine and more interesting for me.

All the professors agreed to supervise me after meeting me for an interview and after deciding a research topic. I have already applied to all 3 of them and I am waiting to know anything about the funding.

I did not want to take the risk of getting no scolarship for the position and missing the deadlines for others possibilities (which would then force me to wait up to one full year, which is really not a good option).

Now I may win more than one scolarship, so:

How can I decline the other two offers? I wasted their time and possibly affected their chance to accept other PhD students. I don't want to sound rude, but the PhD it's a very important choice in my life. I know they invested some time in me and my application.

From the way the talked to me, it looked like they did not consider the idea of me applying to other Universities (some of them even introduced me to the research group). I feel incredibly embarassed to be honest.

I wouldn't say you 'wasted' their time. All supervisors are well aware that most applicants apply to more than one institution at a time; wisely so, especially that PhD admissions for good universities are highly competitive, and one shouldn't risk their chances applying only for one place.

Unless you made a promise or commitments to be working with them, you've been an applicant and have acted as such. As an applicant you have the option to decline an offer, so this is totally normal.

Therefore, you can contact the other supervisors; the sooner the better so that they can consider their other options too. You can thank them for their time and the interest they had in you, and explain your situation like you did here. They will likely understand the situation (TBH this should be happening a lot for them).


Feeling like a failure because of a class I am a PhD student in the area of CS/math. My dream (for a long time) is to develop an academic career, and I work really hard (like any of us) to achieve that.

This semester I am taking a class which is semi relevant to my area. This class made me feel like a complete idiot. I have been spending hours on HW questions which other students solved quickly, it takes me a while to even understand parts of the solutions/concepts presented. This is very different from a struggle in research, where sometimes nothing works but at least you know that you are trying to solve something yet unsolved.

I know that the academic career path has so many struggles to come. However, this class kinda made me think that maybe I am not good enough for this type of theoretical research. How come other students invested so much less effort on that?

I guess I am looking for advice on this. Should I take that as a hint for actually not being able to do that type of research? Should I just forget about it? Have you been in such a situation?

What you may be experiencing is the fact that insight into some areas of mathematics don't translate into insight into others. I had a lot of insight into Analysis (my field) and General Topology, but little in Abstract Algebra. I once took a course (grad level) in discrete math and did terribly, experiencing much of what you describe.

To be successful you need a fairly general understanding of much (but not all) of mathematics and a deep understanding of one or two narrow areas. If you can achieve that then you can be a success.

It hasn't been possible for an individual to understand (at any deep level) all of mathematics for about 100 years. There are likely only a few living computer science professionals that understand all of CS, if that is even possible at all anymore, given what has gone on in the last 10 years or so.

If you are early in your studies then work on breadth. If you are mid to late, then it is time for a deep dive.


How many postdocs should one usually do before it is realistically possible to get a faculty position? I am interested in the amount of postdocs one usually has to do before one gets a "good" faculty position while considering the apparent differences in various academic disciplines.

If you mean a tenure track position at an R1 school, the simple answer is "one" (no more, no less).  And often you will have had preliminary interest (e.g. invited for talks) with some R1 target schools even before the start of the one post doc.  IOW, people already know you are "in the mix" for plum positions.  And you know it, too.

Of course, if you can get such a position with zero postdocs, go you.  But this is still rare, even for superstars.

If you are heading to your second postdoc, the bloom is "realistically" off your rose.  Look for teaching school positions at best.  Or move to industry or government.  You have too much to offer to wander around doing postdocs for your life.  Academia is a "tournament" job system (Google it) and you are one of the vast numbers of "many are called but few are chosen".

[Note for pedants, the word "realistic" in the question title...]


How are scientific papers uniquely identified? Some papers have the Digital Object Identifier (DOI) which uniquely identify them, some other have an oai identifier (e.g. oai:arXiv.org:1402.3722). Even though I inspected the metadata of different sources like core, microsoft academic, and semantic scholar I couldn't find a unique identifier which is used among all sources of research papers.

How are all scientific publications uniquely identified?

Research publications predate the digital age, so only a fraction has a digital identifier. The unique identifier traditionally used is the full citation, of which various formats exist to suit discipline-specific needs. It is very likely for a full citation to be unique.

(However, automatic data analysis may not be able to recognize the identity of diffently formated citations of the same publication. That's DOI's strong suit.)


How economically efficient is the grant system? I wonder if someone (or eventually some country, organisation, etc ...) already evaluated the costs of the system of grants.

It costs at least the salary of the researcher who writes and gets the grant
but also the salary of all the researchers who didn’t get it, and could have done something else than writing a proposal
plus the costs in administration (e.g. the National Contact Point(s) in Europe at several places in each country)
plus the cost of organising the referral (travels, meetings, ...)
plus the cost of the grant itself, of course.

On the positive side, of course the entire society benefits from a completed grant.

So my questions are:

Are there some studies about the economical efficiency of the grant system?
What are their conclusions?
How much does the granting costs?
Are there other system evaluated?

Partially related questions :

How much time do researchers spend on writing grants?
How to quantify the loss in productivity due to time spent on writing proposals

but this question is really about the economy of research and factual investigations about the system of grants, not about feeling from researchers.

I know of one such study: Cost of the NSERC Science Grant Peer Review System Exceeds the Cost of Giving Every Qualified Researcher a Baseline Grant.

The authors examine the full costs of the process used by the Natural Sciences and Engineering Research Council of Canada (NSERC) and conclude that it would be more efficient to simply give a base amount to every researcher who meets the requirements to submit a proposal. The costs they consider include the time spent preparing and peer-reviewing grant proposals. In addition, the authors argue that the current system is ineffective, in that it rewards mediocrity and safe bets over curiosity and innovation.

The same journal later published a rebuttal (The Real Cost of the NSERC Peer Review is Less than 5% of a Proposed Baseline Grant) and a reply to the rebuttal (Indeed: Cost of the NSERC Science Grant Peer Review System Exceeds the Cost of Giving Every Qualified Researcher a Baseline Grant).


What is the value of participating in proposal-writing efforts, for a postdoc researcher? I am a young researcher already having published several papers, and in the same time I have participated several times in bids for national and European (fp7, h2020) projects. So I could say I have some experience in proposal-writing.

I am now preparing my cv to apply for a lecturer position in UK. The question is: should I highlight this experience in my cv (i.e. provide more details about the bids in which I participated, my role, the outcome etc), or hiring committees are mostly focused on publications? How important is fund attraction at a lecturer level? I am asking because I see that this kind of experience is often mentioned in the desired (not the essential) qualifications of the applicant.

An other point of view over the same issue is this: If I have the chance to avoid being involved in proposal-writing efforts, should I? That is, of course, in order to continue with my research (i.e. focus on papers).

Moreover, how can one's claims be verified? How do you prove that you are telling the truth and not over-selling yourself, regarding your participation and experience? Isn't this part of your cv a part that is less verifiable?

First, your titular question:

  What is the value of participating in proposal-writing efforts, for a postdoc researcher?

Especially in Europe, and when applying for faculty positions, the value is huge. Successfully playing the grant game is nowadays what keeps the lights on in many European universities, at least research-wise. Having a track record in this dimension can easily be viewed as even more desirable than a great research track record (although, of course, you will still need at least good publications).

  should I highlight this experience in my cv (i.e. provide more details about the bids in which I participated, my role, the outcome etc)

Yes, you should definitely highlight this somewhere in your application (not sure if the CV is the right place, though). Your letters may or may not be a good place, if LoR are considered important for the job you are applying to.

  If I have the chance to avoid being involved in proposal-writing efforts, should I?

This is an interesting question, and mainly depends on what your grant and research track records look like at the moment. If you have not actually been involved in grant proposals, I would certainly recommend getting this experience. If your research track record is lacking, I would focus on research. Realistically, you will need a good record in both dimensions to be competitive for faculty positions.

  Moreover, how can one's claims be verified? How do you prove that you are telling the truth and not over-selling yourself, regarding your participation and experience? Isn't this part of your cv a part that is less verifiable?

In the optimal case, you have won some grants in your own name. But even if this is not the case, the experienced recruiter knows what to look for and who to ask to figure out whether you are overselling yourself. Keep in mind that researchers are connected and EU projects are large - somebody in the hiring faculty will know somebody who was involved in your project and give them a ring to ask them whether you actually did what you claim you did. If that's also not possible, the recruiting faculty will just ask you a few questions regarding the claim they are interested in, and observe your reaction.


Fighting for academic fairness: My authorship is unaffected but my PhD advisor pushed up authorship of a co-author at the expense of other co-authors I’m Nick, a postdoc currently working on publication of my PhD work. There are several authors on the paper - two former graduate students as co-first authors (myself and Aubrey), followed by five undergraduates (all of who have graduated now) and another younger current graduate student as the last author (Pax, who overlapped with Aubrey and me during our PhD years) before the PI's name (i.e. PI is senior/corresponding author).
We are preparing a submission to a journal after three failed submissions.
In this version, our advisor moved up the position of Pax to be second author, after myself and Aubrey. We only noticed from looking at the manuscript version she sent to us with comments. In other words, she didn't discuss the change with us.
After several days of contemplation and looking through the manuscript to see if Pax really added so much to the changes in the manuscript, both Aubrey and I decided that Pax didn’t deserve to be second author - and the answer is pretty obvious because all the remaining authors contributed intellectually and experimentally to the paper. Pax, on the other hand, has never added much to manuscript meetings and doesn’t know the data from the paper as well either. Despite that, my advisor decided to move up the position of Pax to be second author.
When we questioned my advisor on this, she said that Pax contributed intellectually to the current layout of the paper (which didn’t change significantly from the last version) and gave another unconvincing answer about how intellectual contribution is difficult to assess (which in this case, I feel the answer is pretty black and white).
Aubrey and I really think there is a hidden reason that my PI is unwilling to admit, but what bothers us is that our PI is being non-transparent. I figured this is academia and the PI gets the final say in what she does.
Neither my or Aubrey’s authorship position is affected. But I know that since I am the first author on this paper, I can fight for the authorship positions of undergraduate authors all of who have really contributed a significant amount of work to the paper. This way I can learn to fight for fairness within academia.
What shall I do? Pursue this issue further with my PI or resign myself to the situation?

Let it go. Maybe decide to not publish with this PI in the future. But this particular hill is not important enough for you to die on.