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Withdrawing from project I am helping in
I have been assisting with a project that my friend had come up with. I am doing the entirety of the analysis for it as they have zero research experience and are not able to do anything beyond conception of the idea.
They are not letting me submit it to a conference to present a small part of the project at a very small "conference" (quotation marks because it's a one day event held at a university auditorium for medical trainees specifically), based on the fact that they would like to present first. I have been slightly annoyed by this, and am contemplating withdrawing from the project, which admittedly is a bit of a dirty move.
That being said, if I do withdraw from it, could/should I ask for any and all analysis done by me to be removed and not used?
Or should I just bite the bullet and let them just carry on.

Why are you offended about them presenting first? Especially if it was their idea. It would seem that the best overview would come from them. You can follow up with details. What is the issue, really?

So, they would like to present first.. Have they actually got a slot to present or is this wishful thinking on their part? If they don't have an actual date then you should consider what are your reasons to continue or should you move on. If they do have a date for a slot, then get written agreement that you can present your part wherever and whenever you wish. If they don't agree then you can probably use your time better elsewhere...

Tough situation and I don't know the answer.  You could consider an ultimatum.  Another approach is just to go to the conference and present.  Buddy can probably stop a publication, but I don't see how he can stop a talk.  (Not pushing these options, but just listing ideas.)

Withdrawing is a loss-loss situation and I will not recommend it. You have done your work and they seem to have the motivation to release it some day. If you withdraw now, the work is gone, tension arises, friendship threatened. These are not worthy for a short moment of revenge-induced pleasure.
If you feel your input is so instrumental then take this as a lesson to bargain better; in future when similar collaboration comes along, make "have the right to present at xxx conference [year/month/day]," or similar terms as your condition. You should also raise the issue of authorship from the get-go.
Ascending one more level, if you're indeed that much more experienced than the team in terms of how the research realm works, why not help them further? Connect them with this very meeting that you plan to attend, and propel the work forward by letting more people know about it.

Yeah. I am regretting not having set out more clearly what I am offering to help with. I underestimated how much I would have to help him, and it's basically come down to the point where I am just feeling it's not worth my time and effort to help him see this to his end.

Sometimes you have to show the whip hand.  I would cut it short.  Dude lacks a feeling of helping collaboraters.  I definitely don't understand stopping a collaborater from using something they need in their own area.  Don't bind the mouths of the cattle that grind.  Actually, you should each try to get a pub in your individual areas.  you can usually slant that especially if we are talking conference papers, not full up journal papers.  (Conf paper for one might be heavy on apparatus and light on results and vice versa.)

What you describe is indeed can be potentially annoying. I agree. The main likely reason for that is that you and your colleagues might had from the beginning different expectations. You think that without your analysis they can do nothing. But they might think that their idea is so genius and thy make you a favor inviting you to work with them. Instead of quitting due to dignity concerns, I suggest you to talk with the head of the project and to adjust the expectations. Tell him/her under which conditions you will be interested to continue the work. You cannot demand something in retrospect because you had not agreed before. But you do can say that for the future conferences you are interested in doing that (Penguin_Knight also suggested that). If what they agree do not work for you, you might quite. But I do not think that it would be fair to ask them not to use what you had already done. They also invested their time and effort. The problem of not adjusting the expectations in advance is the problem of both sides. So, it would not be fair that they suffer an extensive damage.

He has the idea that this relatively small project will be significant enough to get presented at an international conference (which... I am doubtful about). And all of these are scheduled for August-Dec, and the insistence that nothing else be done until he has finished is what has gotten me to the point above.


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FERPA and confidentiality of information when university officials contact school
I have a reason to think an official from a university I previously applied to is potentially stalking me. His previous actions and attitude had made me uncomfortable. We live in the same town and at a talk I attended recently, he asked if I am a grad student at University X now (the school I chose to attend instead). I did not answer and largely tried to avoid them but I do indeed attend university X. The thing is, I really don’t want them to contact me at my university/lab so I do not want them to know my information related to this school. I asked the office of registrar to make my directory information confidential. It took a few days and I have also been told that FERPA confidentiality has some limitations and it seems release of information to educational institution officials is one of them. As long as a university official contacts the school with an education-related interest (it would be easy to fake one, I think), apparently revealing my information is at the discretion of the school and not governed by FERPA. Is this correct?
If they were to contact my university as an official from a different university / department head, would they be told any of the following information:
- My current address and phone number
- The department and the labs I work in
- My office address and office phone number
- Dates of attendance
- Classes I am currently taking and their schedule
etc?

Some of the information you mention might be considered public information and not "educational" and so not covered by the law. Your courses, and similar are probably covered, but FERPA is more intended to cover your performance. But if you are concerned for your safety, for example, you need legal counsel. The university may be able to provide it via some office dedicated to student services. But for a serious concern you may need to contact a lawyer or even the police. In some situations, a university can bar a person from school facilities, of course.
It may be a crime for someone to use the university systems to harass or stalk you, but if they are willing to risk it, you would be at risk, so you need to take precautions. But for serious interventions, you probably need some evidence or corroboration by others. Some people are just awkward rather than creepy, but only you can really judge that.

FERPA distinguishes between directory information (generally public unless the student has requested confidentiality) and other student records such as grades that are always confidential except for university employees who need the information to perform their duties.
If you have requested confidentiality for your directory information then the only answer that should be given under FERPA is something like “I can neither confirm nor deny that Linda Mona is a student at our institution.”
In practice, information like this can often be social engineered out of staff, faculty, and other students.  If you are concerned about this, it might help to remind your advisor, department chair, and support staff that you have asked for your directory information to be confidential and that you have reason to fear a stalker.
Also, if your department maintains a web site listing graduate students in the department you can ask that your name be kept off that web site.
It is very unlikely that your registrar’s office would reveal this information if you have had it marked confidential- they are generally well trained on this issue and will only release this information in response to a request from you.
To answer your particular question, an official at another university should be treated under FERPA exactly the same as anyone else outside of your institution.  For example, if you apply to another university you will have to ask your current university to release your transcripts to that other institution.
Because this rule is strict, many students ultimately decide to make their directory information public.  For example, background checks and letters of recommendation can be difficult to get if you have confidential directory information.  Furthermore, your name won’t appear on graduation lists or lists of award winners if you’ve requested confidentiality.
Also, there are many situations under which you would have to make your affiliation and contact information public as a graduate student.  For example, if you work as a TA you would have to reveal this information to your students and they would have no obligation of confidentiality.  Similarly, if you give a conference presentation or publish a paper you’ll need to list your affiliation.  When you complete your thesis or dissertation you will most likely have to publish it in a way that makes your affiliation public.  If you ultimately go on the academic job market you will definitely want to have a professional website and profiles on services like Google Scholar.

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Can research project scholarship offers ever get retracted?
I got an offer (written) for a research project scholarship, emailed the supervisor about the start date and they asked me to come in mid December.
I sent an email back confirming that I can start on that date. In the same email I asked them where I should meet them on the said date.
I might be overly paranoid of losing my scholarship, but it's been over a week and they have not replied.
Do professors ever have second thoughts about a potential research student that they've basically already confirmed that they will be working with? I know that they may just be busy, and my question was trivial, but would it be smart to give them another nudge?

It is implausible that your scholarship offer is in any way related to professors not answering emails.

Well, probably yes, if they find out you have a "rap" sheet for dealing in x,y and z etc etc.
But I think they have just been busy so have not replied, and are still looking forward to welcoming you on that date.
You may find that you receive an email with lots of info as you are on some other mailing list to get initial information... The wheels sometimes grind slowly...
Best of luck!

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How to address the issues of not including technical contribution
Recently I defended my thesis for a master's degree in computer engineering, and internal reviewers marked it satisfactory, however, they made some comments in my report and presentation, one of them was to include the technical contribution of my research in the thesis report and presentation.
I found this comment very serious, and I couldn't get any idea on how to work around on those issues.
My research was related to some intervention on online learning (here I have used the techniques that are available through literature review) and it is based upon the use of popular psychological theory.
I used statistical methods to analyze the results. I have collected the data through a self-reported survey questionnaire. Results obtained were also somehow satisfactory(findings somehow deviated from the existing findings).
I also develop a tool to visualize the activity of the student interaction in that online learning, and which I consider as one of the contributions.
With all these things done, I am still confused about the problem of identifying my "technical contribution".
My Questions are:
What should I report as my technical contribution? How should I approach myself to identify my technical contribution? Actually, what is considered a technical contribution?
I know I need to consult my supervisor for this, but he will definitely ask the same question to me, and I will not have any answer for that.
Any help would be appreciated and thanks in advance.

What new engineering knowledge did you add to the literature? Basically, what's new.  What did you find?

I have used an existing theoretical model that has been implemented in different domains and used that same model in my domain with some changes in variables and factors. And I have tested that model and got the result out of that. And I extended the duration of the experiment up to 16 weeks and the experiment was done in a real learning context (which was not done in previous research). And the results of that previous finding did not match with the finding I have obtained.

seems trivial.   This like saying I'll now show 1+1=2 works if I replace the symbol '1' with an 'apple'.

@Prof.SantaClaus, I am stuck now, Isn't demonstrating the concept of integrating the various elements in the real learning context, and observing the long term effects, by using the existing theoretical model and validating the model not considered as my finding?

Do your thesis regulations actually mention that your contribution must be technical? Otherwise, you can argue that the type of your contribution is different. You make an empirical contribution towards deepening the knowledge about online learning (based on certain, established methodologies).

@lighthousekeeper Yes, they keep on commenting every time, if they didn't find any algorithm, machine-learning involved in the research. Now, they have commented to include the technical contribution, and they will always ask for something that looks as technical.

You didn't answer my question about the thesis regulations. It's possible that they have it wrong (because they request something that is not required) or that you have it wrong (because you did not produce what was required).

@lighthousekeeper I am ignorant about that part and couldn't say anything from the part of the thesis regulations.

Then this is now the homework that you need to do so that we can give a good answer to your question.

Computer engineering means that they expect a "computer engineering" contribution. Your work seems more of a "market study" or "psychological evaluation" kind. What is the "computer engineering" technical contribution? The visualization seems to be your main technical contribution? If so, that's what you need to improve. Is there something else that's technical?

That visualization tool is developed by my own programming knowledge and experiences (i have made that software by writing various queries and processing), but those developed tools are used to support the findings for my psychological evaluation, which shows the visualization of user interaction. And involving online learning and integrating the various technical elements(tools that support interaction) on that (but not developed by me) isn't considered as the research work technical?

Actually, from your description, it is hard to see how your work is related to Computer Engineering. Most work in that field is (probably) very technical but this seems to be about Education, not Engineering. Perhaps they are making the same point. "How is this Engineering."

This is a late answer and possibly moot now, but I'll guess that whoever wrote that was concerned that your field is engineering but your contributions are more likely to be pedagogy. Perhaps they were looking for some engineering contribution and, not finding it (or finding in insufficient) made the comment. But it seems not to be a blocking comment as you were passed.
But a "technical contribution" can be to pedagogy as well. How does your thesis contribute to the learning of engineering or some such thing. In particular, since you used an existing model, how does what you did differ in the application from what was known in other domains?
It is just possible, of course, that your results could have been expected from what was known, in which case there is little technical contribution at all. If it was otherwise sufficient, then you have done well, but it is something to keep in mind for any future academic work that you might do. Editors and reviewers of scholarly papers may be more insistent on how "innovative" a contribution is than would be an MS defense committee.


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How to set off an abbreviation from its resolution in a project title (CMS)
I am part of a team wrapping up work on a humanities project whose title is more conveniently used as an acronym. Because that acronym is not universally known but we want to encourage its use, the consensus at this point is to print the abbreviated form along with the full title in the how-to-cite recommendations for our project website. However, there are different ideas as to how such a sequence is best styled. One draft citation that crossed my desk had the format

"SODOFF = Some Online Database of Facts and Figures," ed. by ....

whereas in my documentation drafts I had entered the acronym as the title and its resolution as the subtitle in my biblatex database, yielding

"SODOFF: Some Online Database ..."

One can argue over whether the resolution can strictly be considered a subtitle, but the most apt biblatex solution that comes to mind, to enter the full form as the title and the acronym into the shorttitle field, is not intended to print both side by side but e.g. the full form on first occurrence and the short form thereafter, while the "equals"-notation printed above is not without objection either because it entails entering two distinct entities and a delimiter into a single field.
I'm curious what conventions exist, particularly in Chicago style but also more broadly in the humanities and out in the world of acronym projects specifically. Does any style guide account for such a case? Is equals-notation in fact de rigueur in actual (anglophone!) usage, is subtitle style more common, or should we abandon the side-by-side model and recommend that the full title be used on first mention and the abbreviation in subsequent citations?

Isn't parentheses the most common way to label an acronym?


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Free venue for advertising a funded PhD opportunity?
I am trying to advertise a PhD opportunity in Sciences. So far, I have tried some relevant groups and email lists, as well as my own social media accounts. As I don't have a huge number of followers, my posts have not attracted a lot of relevant candidates.
I thought of findaphd.com, but then I found that their prices are very expensive.
I was wondering if there are other similar free or cheap relevant venues for advertising my PhD project? If so, which ones?

At this level of detail and precision, the answer is "yes".

@tripleee Which ones? Sorry if I was not being precise enough for you.

It obviously depends on the field and the topic, which you have not revealed.

Have you tried your university's web site? Or your department's web site? If they don't have such, they might like to start. When I want to know about a uni their web site is often where I start.

The cheapest, and often best, venue to advertise for a PhD student is within your home institute. That way you have people that are already in the city, available to look around, probably have reliable recommendations from their teachers (your colleagues) and they are already being taught the speciality of institute X. Put fliers up around your department common areas if you have a noticeboard or something, send emails through departmental mailing lists (if your institute allows it) and try to hit groups on social media.
Also, don't underestimate personal connections. Ask colleagues if they know anyone looking to do a PhD in X.

Not only your home institute, but in particular your own circle. If you are at the point in your career, where you can advertise Phd opportunities, you will certainly have collaborators and close colleagues who currently work at other universities. So send them a short note and the advertisement. If they just put it on their local noticeboard or mailing list, this already helps advertising to the right people, but they might also know some good candidates more directly.

Great addition @mlk . I think people underestimate the power of word of mouth.


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Why did the status of my paper change from "awaiting reviewer scores" back to "under review"?
I submitted a paper to a journal that uses the ScholarOne submission system. The manuscript status has changed from "awaiting reviewer scores" back to "under review".
What does this change mean? Does it mean that one of the selected reviewers has declined the invitation? Is it a bad sign?

Thank you! But in the journal i submitted to, under review means AE is examining the paper as the first stage, while "awaiting reviewer scores" means it's actually out for review. So I just wonder why it was returned to the AE again...

It is possible that a reviewer who previously agreed to review the paper has changed his mind, therefore the paper went back to the AE who will now find a new reviewer.
But the truth is we do not really know (and should probably not care). Only the journal knows the reason for the status change and they will contact you when the reviews are in.


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How do you archive multiple versions of the same article on computer folders?
I have some articles that were accepted by different journals, translated into different languages. How do you archive your writing in those cases? By publication? So to know exactly what was sent and where, which also means duplicating images and other linked resources (I write in markdown)... or by date? Keeping everything in the same folder, which avoids duplication of files but also makes it hard to keep track of where the piece was sent?

Disk space is cheap.

Maybe use git for that

@Giulio This article "https://academia.stackexchange.com/questions/8359/archiving-papers-simulation-and-experimental-data-etc?rq=1" may be useful.

@imtaar Thanks. This is very helpful!

That's what version control is there for. I imagine that I'm not the only one who has their home directory under version control. (The other advantage of this is that my home directory looks exactly the same on all of the machines I typically use, and that's quite a few.)


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Chance of publication in top combinatorics journals after complicated submission history
(First appeared in Mathoverflow) In May 2020, I submitted a paper to a notable Combinatorics journal where a couple of earlier papers in the topic of my paper had been published. It was one of my first papers in Mathematics, and I didn't motivate the introduction as well as the referee would have liked as it turned out, and had imagined that the major result of the paper would sell itself. I received a detailed referee report in December 2020 where the referee mentions that according to them all the results are correct, and had a lot of suggestions for improving the writing of the paper and identified typos and misspellings. Then they said the paper seems insufficiently motivated and in their opinion, the paper seems borderline for publication in that journal. The referee said they would like to get contacted by the next journal where this paper may be submitted in case the editors decided to reject the paper.
The editor rejected the paper. I sent a follow up email to this editor politely asking if he could confirm that he would be able to forward the referee report to the next journal. I did not get a reply to this email.
In February 2021, I spent time trying to motivate the paper better and reworded parts of the introduction and included some examples and references to more recent work in the area, and then submitted to another new prestigious Combinatorics journal, requesting if they could use the earlier referee report. A month later, I sent a couple of emails requesting if they could let me know if the earlier referee had been contacted, but did not get a reply. In late October 2021, I sent a further email requesting for some information on the refereeing process, and got two new referee reports the next day. One of these said the paper is well motivated and well written and is suitable for publication, but that the main long proof could be written a bit better. The other detailed report said the paper is "worthy of attention" but asked for a lot of changes in the writing and that I spend time on the main theorem. The editor's message said overall this is no guarantee of eventual acceptance.
I completed the revision in December 2021, spending some time on rewriting this proof and including diagrams. I did not hear back from the editor till a couple of weeks back. I sent a couple of polite emails asking for the status, over a weekend, but didn't get a reply.
There was a follow up paper to this paper that was written up a bit poorly and ideally should have been worked on after this paper did get published. This was causing some amount of stress. I withdrew the paper two weeks back. Only then the editor emailed me saying he had a follow up referee report which noted that the paper had "improved considerably" although the "main theorem remains hard to follow, but perhaps that is a personal opinion", and lists a couple of small further typos.
The editor said he would be willing to forward these referee reports to the next journal I submit to. I replied thanking him, but also saying that if I knew it was actually close to being completely refereed here, I would not have withdrawn it.
The editor in chief of the next journal said he wanted "formal letters" from the editors in chief of the two previous journals. I wrote to both of these earlier journals about this. However, today I received a rejection saying they could not get hold of the previous referee reports.
Now I resubmitted again to the second journal, which took around a year and had two referees go through my paper. In this case, can I expect this journal again to consider this paper objectively?

There is so much here. I feel to some extent a lot of the history has become irrelevant. Is this a fair summary of the current state of affairs? You have previously submitted the paper to journals 1, 2, and 3. The paper was rejected from journal 1 after the referee reports, you withdrew the paper from journal 2 after a round of revisions with the referee (but found out after you withdrew that you had positive referee reports on the revised version), and the paper was rejected from journal 3 because they could not get the "formal letters." And you want to know what to expect now from journal 2?

Yes. Sorry I could have condensed this a bit.

It seems like the most recent feedback you've had on your paper are the positive referee reports from journal 2. (Journal 3 rejected the paper, but for administrative reasons). I would just wait and see. My experience is in physics, not pure math, so take this with a grain of salt. But it seems like you have written a nice paper. Since you have already resubmitted to journal 2, taking more action now will just confuse things further. And, the last you heard from this journal, they like your paper. If that changes, you can deal with it -- but wait for them to decide.

So waiting it out is the best thing to do? I have published a couple of elementary Physics results and also refereed for a Physics journal incidentally, and in Physics things seem to move a lot quicker; editors start to request for reports a few weeks after initially requesting you. On the flip side, probably the papers are not always read by referees as thoroughly in Physics, as in Math. But regardless of the subject, in a situation like this it just seems like the right thing would be to do everything possible to help get it published in a comparable journal.

At this point you've already resubmitted, so I think your best option is just to wait. Whatever worries you have about how journal 2 will perceive your first resubmission, will only be amplified if you withdraw and then end up to resubmit again. And, you've already tried submitting to another journal, and that didn't work -- probably better not to try it again if you don't have to. At this point, as far as I understand, the last thing you've heard from journal 2 about the content of your paper are positive referee reports. So that seems like a reason to give them a chance.

Yes the last reports sounded positive. But the very first report from the first journal was also somewhat positive, even though it had a couple of negative comments which the reports from the 2nd journal don't have and so it should be more encouraging. I should wait and see. Judging by some other questions on S.E. this type of thing is not unheard of unfortunately,

It's been now 17 days since resubmission to journal 2, the new prominent open access general Combinatorics journal that was launched last year. I have not heard back from them.

30 days and counting; no response from the journal.

65 days and counting, and still no response from the journal.

The handling editor for Combinatorial Theory rejected it after 66 further days (this is after I sent two further requests directly to the managing editors), showing no further referee reports, just stating that since the one referee stated in March the main theorem was hard to follow, he can't say for certain it is correct, so he has to reject it. I think he was not pleased I withdrew the paper under his watch.

The second journal, Combinatorial Theory, the new open access Combinatorics journal, which doesn't have any staff working on their behalf so presumably doesn't reply to any queries, didn't reply to me last year when I asked them if they could contact the previous journal where the referee had said he wanted to get contacted. In the process the time of three separate referees has been wasted.

I contacted the redoubtable Bela Bollobas a few weeks back, the editor of the first journal, if he could send that referee report to a new journal, and didn't get a reply. I am now submitting this again to another good journal which will begin a new refereeing process presumably.

https://chat.stackexchange.com/rooms/136884/math-journals

As the Editor-in-Chief of a reputable combinatorics journal, I find the story very strange or/and incomplete.
So an unmotivated paper is submitted to Editor A, who received two reports from referees B, C. I guess B's report was a "quick opinion". B noticed that the paper lacks motivation. Why was not the paper immediately rejected, is not clear. Then Editor A suggested that A sends report from C to another journal and to editor D, where the paper is going to be submitted.
Now either A will disclose the identity of referee C to Editor D and that violates the anonymity of the referee, or Editor D will use a report from a referee whose name Editor D does not know. Both options are impossible unless A and D are the same person.

You should never tell editors which referees to use, including using earlier reports, it is their job to find referees not yours. Would you conversely let journal 2 know there is already a negative report from journal 1?

Given that you have already resubmitted the paper to journal 2, and especially since the last contact you had from them about the content of your paper was a positive set of referee reports, I would just wait and see what happens.
(a) I don't think you are likely to be able to guarantee a faster process with a positive result at another journal.  Withdrawing and resubmitting will just lead to delay and more confusion.
(b) Given that you've already withdrawn and resubmitted this paper to journal 2, withdrawing again might end up causing bad feelings with the editors.
(c) Journal 2 has access to the last round of positive reports. Other journals do not, and as you have experienced, getting journals to communicate with each other is complicated. I think you have the best chance of having the previous, positive reports help your case if you stick with journal 2.


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Should you ask same professors to provide recommendation letters for different graduate program applications at the same university?
I asked some professors for recommendation letters for my MEng in Mechanical Engineering after having completed my BEng in Mechanical Engineering. I am looking to apply for an MEng in Computer Engineering at the same university. I do not have work experience in computer engineering so could I ask the same professors to ask for recommendations, since no one else other than my mechanical engineering professors is in a better position to write a recommendation letter? If they write a very similar or the same letter would it affect the chances of admission, if the admission committee realizes they are the same or from the same professors?

This is for Canada.

In the US it would be completely normal for letters to different programs to come from the same professors. Admissions committees here are looking for general indicators of success. An exact match between the letter writer and the program isn't needed or expected since it is common to switch fields after a bachelors.
While the fact that the letters come from the same people might be noticed, it wouldn't be remarkable. And, it is possible that there are different committees in any case.
In most cases identical letters wouldn't be an issue unless the letter is too tailored to one specific field.
But you could talk to the professor(s) about how they feel about their recommendation for a somewhat different field. They may have some advice for you.
I'm not sure that this advice/answer holds outside the US, however. The preceding paragraph here probably works most places. Have a conversation. "Are you comfortable also recommending me for computer engineering?"


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Editing Mendeley citations with Zotero
Elsevier have really really ruined Mendeley! The latest update has gone very disturbing, with lags, errors and citation taking too long. Mendeley Desktop was awesome! The new Mendeley is just very not worth the hassle.
Is there any way to edit a document's citations (cited with Mendeley Reference Manager 2.74) using Zotero? It used to work in documents cited with previous versions, but now I'm unable to get it edited with Zotero without re-citing everything.
I have already migrated all my libraries from Mendeley to Zotero and started using Zotero, but many documents I need to edit are cited with Mendeley. Also EndNote is an option if it would work with it.

Just to clarify, are these Word documents you're using to cite?

@CephBirk yes indeed Word document


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How to share authorship in a 2-author paper where both contributed equally
I am currently in the following situation:
Another person (not from my department) and I did a study together.
The other person is an associate professor, I am a junior researcher (medical doctor).
We performed a secondary data analysis of clinical data. The data is his and I performed the analysis. We both wrote the manuscript. When discussing about authorship my collaborator was very liberal replying "XX, it is really up to you. Take the first or last authorship, whatever you prefer and like best". We are both from different countries (in Europe). The manuscript contains an author contribution section, detailing who did what.
How would you handle such a situation? I read that this is field-specific so I was wondering what would be best for medicine / statistical science.

In mathematics, the authors just list their names in Alphabetic order. I presume that they do that because they see ranking contribution as futile. Why not just do that?

Since you seem to have a good relationship with your co-author, in addition to the answers below, I would suggest responding "To me this choice seems most appropriate because I think it signifies these contributions; can you reality-check that framing for me, since you're more experienced?"

I've seen publications where author names are additionally marked with stars which are defined below as "contributed equally" - while this is obviously somewhat awkward, it could be a way to go if in doubt.

Related: https://academia.stackexchange.com/questions/2467/what-does-first-authorship-really-mean-in-field-x

First author: The person who did most of the practical work
Last author: The supervisor - most often had the idea/data

In your situation I would think that you should go first and he should go last as senior author. Would possibly benefit you both most. As Professor he doesn't need first authorships  any more but you do (EDIT: and it might even be expected that he has primarily last authorships).

For a (senior) professor it might even be expected that they have primarily last authorships. They key role is managing a lab, not doing the lab work themselves.

In many fields (I cannot speak for the medical field, though), first author is the most coveted "spot" in the authors list.
Your professor probably has enough of a publication history amassed, so that he doesn't need another first-authored paper to enhance his reputation.
If he really doesn't mind, take the first author spot.

lordy's answer is appropriate for the medical field. The last author position is just as coveted when it indicates a supervisory role. A student or post-doc (or resident/other physician-in-training role) should accumulate first-author publications that indicate they're the primary person responsible for doing the work; a professor or other senior-role person should accumulate last-author publications that indicate they're the primary person responsible for mentoring and driving research directions.

If it is deemed appropriate for you here some journals allow a symbol which marks Authors contributed equally, making the order of the names less significant. perhaps this applies here.

I've yet to meet a journal that doesn't allow "these authors contributed equally"

While this is true, it's worth noting that I don't know any method of bibliometric data collection that can actually detect this case. Whether or not this matters is obviously dependent on the field and the situation of the authors.

You can do this, but I have never seen any benefit to it.

@MichaelMior JATS XML has an equal-contrib attribute to encode this. PubMed understands and displays this.

@AnonymousPhysicist For cases where there are equal contributions, or disputes, this is sometimes an accepted compromise. I've seen this in several papers in my field, the practice of doing this is occuring.

@AnonymousPhysicist I got my faculty position with 1 first author paper, but 5 joint-first author papers. My academic probation (similar to tenure) requirements required me to have 1xIF>10 or 2xIF>5 papers as first or last author, but joint authorship counted. Similarly for my recent promotion, I needed 2 "major" output every 2 years with first or last, but joint counted.

@user71659 Interesting! I hadn't come across JATS before and haven't seen anything similar used in my field.

Most journals implement the concept of shared first authorship, A.K.A. equal contribution. How it is indicated varies, but ultimately it signals that the two of you made equal work and should be credited equally. Mentioning this to the editor should be enough. This concept is well understood in academy, so explaining this later will always be straightforward
Which one of you goes first in such a shared authorship has only symbolic value, so it's up to you two. Don't overthink it, I'm sure two polite academics can decide on it without either of them getting hurt.


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Do mega-journals (e.g. Scientific Reports, BMJ Open, Sage Open, ...) have longer peer review durations?
We recently discussed mega journals (PLOS One, Scientific Reports, SAGE OPEN, BMJ OPEN, ...) in our group. One member argued that said journals have longer peer review and processing times than field-specific journals. He argued that said journals require more time to find field-specific editors and peer reviewers. In addition, said journals receive large amounts of manuscripts.
Would you agree on this argument?

I do not have too many data points (two with Scientific Reports, to be precise), but in these cases there was nothing special about processing and review times.

I am not sure whether it is allowed to post links to other homepages but there are several databases of review reports that undermine the above mentioned hypothesis.

@Dr.M Seems you have your answer, then.

@BryanKrause - well I personally think that said databases are susceptible to bias (e.g. like product reviews on Amazon) with people being more likely to report their negative experiences...

The only way to guarantee a fast peer review duration is to let quality consideration go out of the window and choose reviewers based on them promising something fast  (and getting rid of them if they don't deliver). High speed is bad for quality. Other than that, the variance of review times within any given journal is huge, with considerable probability to take much longer than the journal average, and choosing a journal based on expected time for the review process is affected by huge uncertainty.

Why speculate? The average review times are Google-able, e.g. here's a table with the data for the Nature portfolio. It's a long list, so only screenshotting the top portion of the table:

And here is the data for Scientific Reports:

Someone better at statistics than me could check if the hypothesis that Scientific Reports has longer peer review times is true. Me, I'd just say it doesn't look like there's special about it.

@ Allure : Thank you! I was unaware of this.


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Replacing tech reports: can we put good undergrad dissertations in arxiv?
My department requires dissertations from all honours students (being England, that's basically all of them).  Some of these are extremely good, even though they are written by undergraduates.  My department for some years created a tech report series, which included undergraduate dissertations with high enough marks and the agreement of the supervisor, but now this system has gotten lost in a morass of web redesigns etc.
Is there any new norm for archiving good undergraduate dissertations?  We were thinking of just putting it in arxiv.org, is that considered acceptable?  We are writing an article and want to cite the dissertation for the full implementation details.

So long as the material can be construed as "publishable" in its submitted form, and falls under one of the categories in arXiv, then it should be OK. However, I'd recommend making your question more general, by asking if there are external repositories for undergraduate and master's theses.

@aeismail I find this question nice "as it is". Moreover, it is not equivalent to "are there any external repositories for undergraduate and master's theses".

Unsurpisingly, I agree with Piotr.  Though I agree the general question could also be a question, average dissertations and tech-report-worthy dissertations are different things, at least at the undergraduate level.

My issue is that the question "reads" as too narrow, since it's basically asking a question that could be answered by looking at the arXiv.org FAQ's. That would mean it's not a good candidate for Academia.SE.

@aeismail I don't think that this question is too narrow. Also, arXiv FAQ (or rather - http://arxiv.org/help/moderation) is not very clear on that matter (nor it should be).

This question is perfect for this SE new site: undergraduates if you find it useful you can follow it and help us in spreading the word about it.

Yes.
Any research writing (paper, report, monograph, dissertation, preprint, etc.) approaching publishable quality is welcome on ArXiv, whether its'written by tenured faculty, postdocs, graduate students, undergraduates, high school students, or hamsters.
(I am the ArXiv moderator for cs.DM and cs.CG.  I have not, as far as I know, accepted a paper from a hamster.)

Thanks!  But a dissertation is not really a paper, but I am talking about dissertations that I think contain publishable material.  Is that close enough?  I'm sorry that we found the arxiv documentation a little vague on this matter.

The “whether it's written by …” clause lacks a “random paper generator” item

@F'x: well, it depends on how you interpret "approaching publishable quality" ;-)

@AnthonyLabarre Randomly generated papers have been published, so that should fit.

Seconding the main point of JeffE's answer, ArXiv is "only weakly moderated", and makes no demands about status, rank, university affiliation, etc.
However, there appear to be mild expectations about format. Beyond the lowest-level TeX/LaTeX requirements, it seems that papers should be in the format of a paper submittable for publication-in-a-refereed-journal. I can imagine the possibility that formats for undergrad dissertations might or might not be enforced, and/or might be substantially different (even if conforming to a formal requirement).
But/and I'd think that a rewritten version of a good thesis would easily be arXiv-able.

Even those formatting requirements are very mild.  All you really need is a title, an abstract, and a bibliography.

Thanks, @JeffE, for the authoritative comment. We'd hope that undergrad theses would be in the right ballpark, but I hesitated to presume! :)

Argh, this answer is the one that made JeffE's one into an Answer, so I wasn't sure how to allocate the points, but then with JeffE's edits he would have got it anyway... anyway, you have my thanks :-)

Can we send away for secret decoder rings when we have enough points? :)

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For LORs being drafted by the recommendee, do the contents need to be different?
I'm applying to a 24 week workshop (or short school), and I have two former attendees who are willing to write LORs for me. They are either nominated in the front page of the website, or still actively involves in the organization of the current season. They both tell me that I draft the LOR for them, and then they will edit it and sign it.
One of them say that this is just for using the personal reputation to recommend, so the content is not that much important. If so, then is it fine to have two LORs with similar contents? Logically the answer should be yes, but I'm not sure.
The workshop says that LOR is just optional, but it is required that the recommender is a member of the workshop network (e.g. lecturer, alumni, other members).
I haven't let them known that I also have another one to write a letter for me. Should I tell them about this?

It is hard to judge whether the advice you got (content doesn't matter much) is accurate or not. If they have a lot of experience with the workshop then it is likely accurate.
Make yourself an outline of what your assets are. From the outline either write two drafts stressing different things from the outline, or rearranging the ideas and paraphrasing differently.
And, yes, if the two know one another then it might be worth sending a mail to both of them pointing this out. While they seem to want to support you, they don't seem to want to put a lot of effort into it. Make it easy on them.


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Dealing with suspects of sabotaging experiments
In a group, postdoc A believes postdoc B sabotaged her experiments. A shares her frustration with the PI (without proof) in a "half-jokingly, half-serious" sense. Since then, strange things appear to be happening in the lab -- specifically, B's experiments are behaving strangely. There has been a serious decline in trust between A and B.
How should the two postdocs proceed? Should they meet? Should the PI mediate between the two? Should the PI talk to them separately? Or together?
Ultimately, how should the PI address the problem, knowing that an investigation is in practice impossible and with the goal of reestablishing a minimum level of mutual trust?
EDIT: Pushed by the PI, the 3 actors openly talked about these issues, agreeing that sabotage is extremely serious, but without pointing the finger to anyone. That seems to have released quite a lot of pressure and helped to normalized the situation. Hopefully it will last.

This seems to be a strange use of "boycotting" - do you mean something like sabotage, or intentionally interfering with experiments?

@BrianDHall sure, thanks. I changed it to "sabotaging"

So if I'm reading this correctly, postdoc A suspects postdoc B has sabotaged A's experiments. Now, postdoc B -- the alleged saboteur -- is behaving strangely. And A and B no longer trust each other. That sound about right?

To be honest, if I am the PI in this situation, I would strongly consider letting either, or both, A and B go. Sabotaging a co-worker's experiments sounds like a cardinal sin to me, and retaliating in kind is not exactly a sign of personal strength either.

@xLeitix Well, before doing that, I'd hope you'd consider that A sabotaging B's experiments means that A is untrustworthy, so their accusations that B sabotaged now carry much less weight. And that it could be C sabotaging both sets of experiments. Or that there's no sabotage at all and both experiments were upset by conditions in the lab (aka the cleaner).

Proof? Evidence? Really, be careful to accuse anyone without any of that. And countersabotage is a total no-no. Whoever sabotages, there are no excuses, and frankly, that deserves not only a firing from the group, but the termination of the academic career. I am sure there are job directions which can make good use of such imaginative destructive energy, but academia it is not.

I've edited the question to try to clear it up. If I misinterpreted or changed anything more substantially than I intended to, please edit appropriately!

That would be the time for the PI to call a meeting with A and B and have a conversation among adults. Topics to be discussed are: If A has a grief with B, she needs to be specific and put it on the table. If B suspects A, he needs to do the same. PI needs to say that this is unacceptable and that everyone needs to behave like adults or else.
If the PI does not call this meeting, then either A or B need to be the grown-up in the room and do so.
Ultimately, half-truths, allegations, conspiracy theories, "experiments not working well", etc, is a situation that is to nobody's benefit. The only way to address it is to talk about it.

Quite possibly. One of the outcomes of being confronted by your accuser may be that you are found guilty and thrown out of the research group.

Because there is no evidence, then everything radical is out of the question. PI cannot fire them. Sabotaging is really bad thing, and something must be done. Revenge sabotage is almost as bad as the first sabotage.
A has first accused B, but there is no proof, it could be that she just used B to went up frustration over her own failures. "half-jokingly, half-serious" sense sometimes is sign of conspiracy thinking and that there might not be any too good of a reason to believe in sabotage, but she has made the connection within her mind, so the perspective becomes biased and she sees more signs and so on... I do not know if you can see from the results of the experiment something, like if A had small failures, but B clearly has odd stuff happening. A's "revenge" could be B sabotaging own experiments to make A look bad. I do not know about prior relation between A and B, which might be the cause to the mess.
Building up a trust is almost impossible, especially if it is clear that someone has done something. Odd stuff happening around B might count as that something. They are already adults, so I do not think that an adult telling "kids" not to be such fools would work. Nice chat about promising future research in a different department that matches better the research interest of A or B might be in a place.

So what's your suggestion on how to proceed?

@WolfgangBangerth Having a chat with A or B or both about future possibilities elsewhere (implying that they had better take the change). Without evidence it is not feasible to destroy their careers. It can even backfire as a law suit. I do not know enough details or about the atmosphere to tell whether it is better to get rid off both or only one and which one. Rest of the department may have their own opinions.

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Publication of review's comments on scientific papers?
Personally I believe publication process is not optimized at all and is too wasteful. There are numerous problems associated with it, however, here I just point out one of those.
Due to formal presentation of papers, usually reading a scientific paper especially in field of science and engineering is time consuming. There are some points in the paper that only a specialist of that very field would notice. This is why the journal editors assign reviewers to judge the paper quality. Usually these expert reviewers would see insightful points on the paper, which would take a newbie months to notice.
Having said that

I wonder why the publication does not provide review comments alongside the paper? does it harm anything?
Would be OK if we ask the editor for the comments of an specific paper? if yes, how?

I think it would be a good idea for publishers to publish reviewer comments of papers as well, they can even make more money and reading and understanding papers would be easier.

Actually the idea in optimal conditions is that the comments are somehow incorporated (by mentioning or answering to them) in the article, so there is no need to provide them separately

After a while I find the website I was seeking! https://trialsjournal.biomedcentral.com

It would probably harm the reviewing process itself as it stands at the moment. Many reviewers only agree to review, because they can be anonymous and their comments are confidential. I therefore do not believe, that any editor of a traditional journal would give you access to the reviewer comments on a paper, however you ask.
Having said that, there are some recent developments in some journals, which I appreciate a lot, and which go in that direction:

Copernicus Publications is promoting an open review process. All manuscripts are published in a discussions version (pre-review), and reviewer comments are published and archived together with the article (and can always be referred to from the finally published paper).
Frontiers is promoting non-anaonymous reviews. The reviewers are mentioned by name on the title page of each article. In my opinion, this increases the quality and objectivity of reviews a lot.
There is always the possibility to publish additional reviews after publication on post-publication peer review sites, like PubPeer. Those can help you to find errors in already published articles, which may have evaded the original manuscript reviewers.

The peer review process, though not perfect, is one of the best ways to ensure high quality research. When one thinks of it, what are the true alternatives? Having an autonomous editor who approves everything or not based on his own experience is hardly objective.
As far as I understand it, you're proposing that publications publish imperfect papers with peer review comments alongside, or that the journals publish revised papers with peer review comments alongside. In the case of the former, it doesn't credit a journal or a discipline to publish knowingly imperfect papers and in the case of the latter, the reviewers' comments would already have been integrated into the text. Yes, it is time consuming reading papers, but peer reviewers only tend to highlight what they think needs improving. The academically sound material would not necessarily be addressed in comments.
If you are proposing that peer review comments make up a kind of 'summary' of the paper, that is not always the case. If a paper has minor amendments suggested the peer review comments could be just one or two lines for a paper which is thousands of words long. You'd still have to read the whole thing. If they request major revisions they will still only address what they think needs to be revised.
I'm sure many authors certainly wouldn't want a sub-par quality paper published with peer review comments alongside when they then know how the paper could be improved. It's much better to just get on and make the improvements. Yes, reading these papers takes time, but there's no short cut to hard work, and that's as true in academia as any profession.

Thank you for the great explanation. My question was not out of laziness :)   . I prefer Stackexchange review type,where you can find what and how is something changed.

I wonder why the publication does not provide review comments alongside the paper? does it harm anything?

Usually, the reviewer do just not include the information you want in their reports and if they do, the authors address this in their revision.
Reviewers are asked to review the paper based on correctness, quality, impact and similar things. They also provide a short summary of the paper in the beginning of the review, but this is often very short. If the reviewer think that the presentation of the paper can be improved, e.g. to make a contribution/problem/subtle point more visible, they would suggest this in the review and the authors are asked to improve the situation.
In most cases there would be no harm a-posteriori, but knowing this in advance would probably change the way, the reviewer writes their review. Also note that the comments of the reviewer would be for a previous version of the paper, and hence, you need to read more to understand what the review means. So, I don't think, that this would shorted the time to digest a paper.

Would be OK if we ask the editor for the comments of an specific paper? if yes, how?

In most cases this will not work, since the reviewer agree to write review under the promise that the information in confidential. So, the editors shall not release the reviews.
On a different note:

Due to formal presentation of papers, usually reading a scientific paper especially in field of science and engineering is time consuming.

I think you are wrong here: Reading paper is time consuming because science is hard, not always because the presentation is bad. Even reading textbooks is time consuming, and there are not too many "formal requirements" for textbooks (and a very different review process), so that authors of textbooks can write more or less freely as they want.

In general this is correct. But, there will always be cases when authors do not apply crucial changes requested by the reviewers, and some editors nevertheless publish the article. In such cases it can be of great value to see what was actually criticised, and what was changed in the end.

@Manuel Weinkauf, you can say it again!

@Dirk , I admit science is hard, however, sometimes people complicate what they've done in their paper , I don;t know, may be to hide their faults! Reviewer usually notices this, and provide a plaint English explain of what authors have done. By simplification, I meant this.


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How can I encourage students to ask questions in class
In my field (as in many others), students are assigned articles or textbook chapters to be read as preparation for classes (i.e. the whole class has to read the same set of texts). I encourage my students to write down any questions they might have while working through the text assigned for the next session. I feel this is a great way of trying to understand the content of a text because (a) it helps students to specify what exactly it is they do not understand, (b) they might then be able to answer the question themselves and if they can't (c) they can ask them in class.
Unfortunately, many students do not follow this advice to the extent that I think is required for university-level courses. I often get feedback from them saying that the text is too difficult and they don't know what to ask. Instead, they ask me to tell them in lecture-style fashion what the text is about. I do this occasionally, and sometimes it is indeed a good method. But it's clearly not something I can do all the time, as I can see that they tend to find this boring and don't retain as much information as if they had worked through the text themselves.
I also find that many students (except for high achievers and those who are very outgoing) do not want to ask questions in class because (a) they are afraid of asking a question that others might think is stupid or (b) they are afraid of seeming overly eager/like an overachiever.
Q: What can I do to encourage students to ask questions in class?

Here's what I've tried so far, with varying success:

Make it clear that reading academic writing is different from reading a newspaper, and that they need to actively work on how to deal with its complexity (and that learning this is indeed one of the great benefits of studying at a university). Then I make suggestions (using highlighter pens of different colours to mark different kinds of important information, underlining words or concepts they don't understand, using secondary sources to understand those concepts, making notes on the margins, summarising key ideas, making mindmaps, and asking questions in class). A minority of the students do indeed follow this approach.
Tell them that asking questions on the material helps them understand it better and helps me improve the class. (I can't always guess what's easy or difficult for you personally, so please help me make this class better by telling me what it is you don't understand).
Give examples of questions that are difficult to answer (I don't understand chapter 2, can you explain it to me?) and questions that are specific and useful for them and me (I understand that this theory involves concepts A and B, but I don't understand how concept C contributes to it.).
Ask each student to come with at least two questions on the text: Works well with a smaller group, with a larger group not everyone can ask their questions or it takes so long that everyone gets bored. Variation: Students write down their questions anonymously, I collect them and then go through them in class. This is a great method to avoid embarrassment, but takes very long.
Assigning students to small groups where they can discuss their questions. Then I go around and ask whether there are any questions they could not answer themselves. I find this works relatively well, but takes a lot of time. I also get many complaints that this method is pointless because the students can't answer each other's questions because they lack the necessary knowledge (although I find that in reality there are often questions that another student can answer). An advantage of this method is that students can admit to not having understood something in a small group instead of in front of the whole class.

Overall these strategies help, but I feel I'm not getting anywhere close to the optimal level of interaction. When I was a student, I often worked through a text (yes, not always, and I appreciate that not all students will always do this, and that's fine), marked the most important stuff and what I didn't understand, and asked question in class on what I didn't understand. I benefitted immensely from this, and I'd like my students to get these benefits, too.
Q: What can I do to encourage this learning style?
Note: The level of the texts is usually appropriate for the students, although I have in the past sometimes come to the conclusion that a given text was actually too difficult for them.

In which field are you? I think it can make a difference if it is math / arts / other.

Linguistics. Methodologically that's pretty close to sociology.

I don't understand why you have to either  1. get students to ask about what they don't understand (what you want), or   2. tell them in lecture-style fashion what the text is about (a method that I agree is usually not very effective).  Instead, if the students don't raise any questions of their own, why don't you ask them questions?

Am I the only one who sees the irony in not being able to get students of linguistics to effectively communicate? The instructors that I saw get the most class participation were, 1) somewhat self-deprecating, 2) Were really encouraging of the questions, even the obvious ones, 3) Had excruciatingly difficult exams. 4) Put questions that students asked in class that they answered directly on the exam. 3 can be incredibly effective, 4 can be iffy, because it could backfire and cause them to clam up even more, but if those are the easier questions....

@ff524 If a majority of the students hasn't understood the gist of the text, they won't be able to answer questions on it.

@Robert Yes, in which case asking them questions will help you tease out what they don't understand.

Your #4 is interesting -- you describe a method that works too well.  It seems that if everyone in the class were the ideal you have described, you'd have a hard time working within the time frame you have allotted to you.

I took a class where we were required to keep a journal, turn it in on Tuesday.  We got it back on Thursday.  I now wonder whether the professor got any sleep at all on Tuesday and Wednesday night.  He read each entry and responded to it.  In class, he lectured for about half of the time and moderated a group discussion for about half of the time.  That was before the internet -- it was a physical notebook that was handed in and gotten back.

Here are several ideas to consider. I'm not sure I necessarily recommend all of them but I've seen them being tried for better or worse results:

Make it a dialog by asking your students questions yourself. More specifically, pose questions which students are not very likely to just figure out; this will lead to almost no people raising their hands. Now pick someone you've decided in your infinite wisdom you should be hearing more from. Ask them to answer you. They may protest, or evade, but try to get them to explain what's preventing them from answering. Then "rhetorically reward" them for posing their problem in the form of the question. Repeat the question to the class, then answer it. Or rather - don't quite answer it completely, answer it partially so that you end up posing another question.
Teach slower. One of the reasons people don't ask questions is that they "lose" the teacher, who's going through things much faster for them to even formulate questions.
Don't hastily assume there are no questions. When you've finished a segment of your presentation, don't immediately rush to ask "any questions?" - make a pause first; then ask; then wait a while; like @Anonymous suggests, it should be a good number of seconds. It will seem like an eternity to you - but not to them, they're just catching their breath / trying to wrap their brains about what you just said.
Be more creative about how to ask for questions. Asking "any questions?" often comes off as you wanting to not hear any questions. A Professor at my alma mater is famous for using "so, are you 'buying' this? Yes or no?" and then saying "Well, ok, but if you're buying it, you're going to have to accept it as an assumption, and that's on you, not on me. So are you sure?"
Offer rewards for participating in class.  The final grade in the course can be improved over the 'dry' results of HW assignment and exam grades based on participating in class; and when students ask a meaningful question (but this is also for comments; you can't usually only reward questions), you write down their name.
Get someone to contradict you. This is obviously much easier when you're teaching history, social studies, political science etc., but with some work it's sort-of possible also in hard sciences and math. Either by having an opponent present cases in which your claim is difficult to apply; or by you intentionally glossing over a proof of some lemma; and so on. This of course requires the participation of a TA, another lecturer, or in some cases a student who's able enough to handle it (this can be a bit problematic in terms of his/her experience in your class, but in graduate school not terribly hard).
Plant student questions yourself (v1). Before class, find one or two willing students; give them a question on a piece of paper; ask them not to reveal it to their friends (but maybe make sure their friends will try to peek and read it); and ask them to raise their hands and ask the question at some point (perhaps say when it should be asked on the paper). Now, these can sometimes be questions you actually want to answer yourself; sometimes they can be "faux questions", the relevance of which you want to get other students to challenge; or they could be questions which you want to direct back either at the person who asked them, or at other in class - asking them for help in answering.
Plant student questions yourself (v2).  Add to the lecture notes several questions which are non-immediate conclusions, or lessons, which one can derive with some thought from what you're going to teach. Remind students at the beginning and the end of classes of these questions, and perhaps even state they may well appear on the exam, as stated or in variations. Perhaps have your TAs go over a part of them (not many) in their sessions, maybe once or twice at the beginning of the semester so that the students experience the nature of these questions. You are then likely to get either these questions themselves asked in class, or questions which students believe will help them resolve these questions.

Again, these different methods have pros and cons, and are rooted in different conceptions of the students-teachers relationship; take your pick according to your philosophy of teaching.

I frequently stop for questions. I find that it's helpful to stop for about seven seconds.
Seven seconds is longer than it sounds. It's nearly enough time for Usain Bolt to run 100 meters. Towards the end of it, you might start to feel a bit foolish standing in front of the class silently, smiling and looking around. I sometimes do.
But I often get a question around second five or six.

The power of a prolonged, intentionally awkward silence cannot be overstated. It doesn't work for everyone, but there are people who will talk simply to break the silence. For these scenarios, where you're trying to get people to talk, this is a fantastic approach.

I'm teaching a very large lecture class in linguistics at the moment; I use an anonymous live-polling system that accepts answers by text, Wi-Fi, etc.
Normally I open a lecture by quickly reviewing key concepts of the previous one and asking for votes on which concepts to go over. I wait a couple of minutes for results, then revisit the top five in more detail.
Then I stop halfway through the lecture, open the poll, stand there, and say, "Okay. Ask me questions."
Making a poll anonymous always brings the risk of abuse, but removes the fear-of-judgment factor whatever its cause (shyness/introversion/low self-esteem, doubt about worthiness of question, anti-'keener' sentiment, etc.). And I keep standing there expectantly even if there are no questions for the first couple of minutes, which usually acts as a further antidote to reluctance. They might as well if no one else is asking questions!
I usually get a mix of A) useful questions ("Why doesn't English have as much inflection as Old English did?" or "Can you explain the Great Vowel Shift again?"), B) silly questions ("How many roads must a man walk down?" or "I like your shirt; where did you get it?", and C) a few profane/nonsensical questions. I answer the A)s, playfully integrate a B) or two if there's time, and ignore the C)s entirely (or be facetiously dismissive of them if I feel like trying to make the rest of the class laugh).
I thought about doing this at the end of lecture, but when one student out of 317 in attendance decides to pack up and leave, they all do that. Halfway through seems to work better for waiting around for questions.

+1 for anonymous polling. I've seen that used to great effect, and in classrooms where almost everyone has a computer that can be a very good approach.

Have you tried using something like Piazza? In my NLP class, we use Piazza as a forum for questions in class, the assignments, and the textbook, but also to share current events and interesting tidbits about the field. Participation makes up 40% of our grade, and you're expected to have some sort of valuable input at least once a month, whether that means asking questions in class or facilitating useful discussions in the online forum.
What I was trying to get at is that an online forum is a useful place for people to ask questions that they may not thought would have been worth using class time to bring up.

I've used Piazza, and not to turn this into an advertisement, but that worked very well in a class I was in. It's a combination discussion forum/wiki/file repository created for classrooms.

While not against this altogether, I would actually want to avoid students investing times in writing and formatting long-form questions and focusing on their screen rather than on stage.

Extreme version:
One of my professors would always start his seminar asking for our questions. Once we stayed silent for some minutes, and the teacher broke off the session, asking us to return next week with better preparation.
In hindsight, one of the best teachers I have got to know.

You can start by asking them questions. The first step is often getting them just to start speaking. Once you set a conversational tone rather than a "lecturer" tone usually questions start to flow from everyone.
(1) Start with a simple true or false, or yes or no question and ask the class to give you a show of hands. Then you can say "Of those who said yes, can I have someone explain their reasoning?" Then afterward "Does anyone who said no want to pose a question to the people who said yes?" The key is the first question got everyone involved. Even if they don't understand the reading that well, they can still have an opinion. It's best to make both yes and no defensible positions. This can also work for tricky logic based questions where one answer appears quite reasonable (no one would think someone else is stupid for getting it wrong because half the class got it wrong).
(2) Piazza and other message boards are a fantastic way to generate discussion. Have students post a question to piazza and also actively encourage them to comment on each other's questions (you can even make this required). You can make question asking anonymous and you can also answer questions as a teacher. If you do this before class you can actually use the best questions posted by students in class. You can even say things like "Jenny had a fantastic question of Piazza about the reading yesterday, can someone other than Jenny share with us the main idea behind the question?" Note the "other than Jenny" signifies to the class, "I really should be reading these questions and thinking about them" Also if you are interested in gender equity, there are studies that suggest that women ask and answer more questions if they are able to do so anonymously.
(3) By asking them questions you are creating an environment of question asking. You are being a role model.
(4) Create an environment, where it is OK to be vulnerable. You can say something like "When I first read this passage, I was completely confused by concept X," Then say "How many people feel like they understand concept X really well." Then noting no hands go up "So most of us seem to have some difficulty with this concept, can anyone tell me what they found confusing?" You have just created an environment where people need not feel ashamed of not knowing because you have shown the whole class doesn't know and you have admitted that when you first studied this material you found it difficult.
(5) You can say there will be a quiz in class about the reading if people do not come with specific questions. As long as there are enough questions that showed an honest attempt at the reading, I will not give the quiz. This is similar to (4) but has some added teeth to it. I personally prefer method (4) as I don't like threats but I've seen this work for some teachers.
(6) Remember to positively reinforce the student's behavior that you want to encourage (not just the content they talk about). You can say "That is a good question John" but perhaps even more importantly, if you think it isn't a good question but you want to encourage the question-behavior "Thank you for asking for clarification on that, John, I'm really glad you stopped me". Thank people for asking questions.
(7) To maximize participation, use phrases like "can someone else tell me ...?" or "Can someone in the back tell me" or "show of hands" get everyone involved. Don't let one or two students dominate the class as this starts to discourage other students from asking questions.
(8) Actually wait for a long time for them to respond to your request You can start with "Any questions", but pause for 10 seconds (literally count to 10 in your head, most teachers wait way too little time between asking and starting to talk). You'd be surprised how long even just 2-3 seconds seems to you as the lecturer. Don't be afraid of awkward silence. Students need time to think about what they want to say.
(9) Indicate how you want them to ask. This may sound silly, but some students at least at first won't know what you want. Do you want them to raise a hand? Just shout it out? Different teachers want different things. Put your hand up when asking "Does anyone have a question, if you want them to raise their hand" or just say "Shout it out" if that's what you want them to do. Once you've established your dominant mode of response you no longer have to do this.

Some tried-and-true strategies:

Get down to earth. Go to the students. Stand next to the first rows of chairs when listening to the questions, as close by as you feel comfortable.
In a normal class, you'd talk to them standing at the podium or in front of the whiteboard. But when you look them in the eye and say "Any questions?," this elevated position makes you look like the Spanish Inquisition. If you go down to the audience instead, you turn into their ally. It's also easier for students to ask you something when you are within a hearing distance and they don't need to shout. Once you get a question - repeat it loudly for the whole audience, thank the student who asked it with a nod or a smile, return to the podium to show slides or write on the whiteboard. Repeat for the next question.
It's easier to raise a hand than a voice. If you know which parts of your lecture may be most difficult to comprehend, offer them a small topic to discuss. For example, "From the mid-terms, it seemed to me that we are not fully clear on the topic of rainbows. How many of you would like to hear more about the green color? Or discussing orange would be better?"
Never ask "Who doesn't understand green?" - that's the inquisition role again; save it for the exam. Ask "How many...," let them raise hands and see for themselves that they are not alone who'd "simply like to hear more." Warning: don't do this for more than a couple of quick questions, otherwise they'll never learn to actually formulate their questions for themselves.
Plural is braver than singular. Meaning, students are more likely to speak up as a group than alone (not only students, actually - it's crowd psychology). Use it. Once you get one question, turn to the students sitting nearby for more. For example, you get a vague question about the blue-ish part of a rainbow. Show thumbs up to that student, now make eye contact with their friends and lead them to clarify or to narrow it down "Should we discuss how blue merges with indigo or how blue merges with green?"
Don't fall for the "Everything!" trap. There's always one aspect of a question that they need more than the other. Students may not see a continuous spectrum of their studies, but you do. Help them to see these connections and make these choices. Also, say explicitly how your answer to one question may connect to other questions.
If possible, have a plant in the audience. Get a fellow TA, a graduate assistant, or a student in that very group to be a magician's help. When I was a PhD student, we played these roles with another TA for each other's classes. It usually went like this:
TA: Any questions on the topic of rainbows?
(Long dead silence)
Me (shyly): What about white?
TA (encouraging, patient): What about it?
Me (mumbling, lacking words, turning to other students): Well, you know... how do you call that thing... that...
Someone (saving me from this idiotic mumbling): Dispersion.
TA (turning to that someone): Ah, so we wanna talk about the amount by which light is refracted?
...And it went from there. We got out a very specific detail that students want to discuss: my mumbling was intentionally vague, so that the helping student could ask something important to them by offering a word for me. How did we know it was important? It's always easier to say out load the word that's on the tip of your tongue. If they quickly said "dispersion" - that was because they were thinking about dispersion.
By doing this, we were taping into several things: compassion for a "fellow student" (here it was important to actually turn to the people around, showing that I needed their intervention); a chance to feel smarter by helping out someone who "forgot" a word; breaking the dead silence; demonstrating that the TA is kind and patient even if the question is dumb. It required a good deal of humor, but we saved each other quite a few times over the years.
In my classes nowadays, there's always a bright creature who studies hard, comes to the office hours, and by the time when we get to questions, knows almost everything. I usually say in advance something like this: "Listen, it's a great question you had for the office hours - I'm sure some of your classmates would like to hear the answer, too. If there will be a pause during the class, do you mind asking this question again, on behalf of everybody?" The bright student is usually happy to help and feels comfortable asking the question knowing already the answer.
Be kind, relaxed, and patient. It's important to show that you don't rush or dismiss a half-baked question, you understand that their adrenaline levels are already high, and you don't see their questions as a waste of your time. Be patient, kind, and comfortable even with the dead silence: "Any questions? (everyone is quiet) Wow, that's a lot. Please, don't speak all at once! (nervous laughter) Take your turns at the mic! (louder laughter) So, who goes first and who goes next?..."

In my experience (on both sides of the desk), students not asking questions isn't as much out of reluctance as it is out of not knowing where to start.
It may help to walk them through how to identify questions.  For example, you could read through an article together in class and break down the meaning of every statement, noting on the board every question or potential question that comes up in the process.  (Is that a technical term?  What does it mean in this context?  How does it apply in this case? etc...).  You could do this early with an easy article, and later with a harder one, and come back to it when anyone seems stuck.  (Or do a similar demonstration of some other method.)
Your #3 is to give them examples of questions, but I think providing examples of the process for coming up with questions is more important.
It may also help to ask them to send you questions before class as they do the reading.  Asking for questions in class puts all of them on the spot, which can make them forget the questions they thought of earlier.  This may be especially helpful when students feel compelled not to re-read the article on the spot (weather due to the vibe in your class or out of general habit).

I think there are a couple of things going on in your question.  It might be helpful to look at them together and separately:
(a) How to get students to do the reading
(b) How to get students to take more responsibility for getting their money's worth from the class
(c) How to make the class more interactive
(d) How to help students to look at the material critically and learn how to ask good questions.
For (a), it might help to take the cognitive approach (I'm drawing an analogy with cognitive therapy, where the therapist explains how something about the human body and psyche work): present some study results that show that the most efficient way of teaching something is for students to read the carefully selected background reading before coming to class, so the professor can help by underlining some points, providing helpful context, going further, etc. etc.
I heard a radio program that explained how it was that physics professors started to use the clicker.  Apparently, it wasn't originally used or intended to be a way for students to prove that they were present and paying attention (as I have seen it used now).  The way its use was described in the program was this:  The professor would pose a question that required some thought, but no messy calculations.  The students would respond with the clickers, and if a large number of students responded with an incorrect answer, he would ask them to take a couple of minutes to discuss the question with one or two neighbors.  Then he would ask the question again.  He noticed that the proportion of correct answers was dramatically higher the second time.
I once took a database design and programming class online, where students naturally found themselves asking questions in order to do the assignments.  The questions had to be sent by email because of the online format.  The remarkable thing was that the teacher responded to the questions quite quickly.  If she hadn't, we would have learned not to send our questions to her, and learned instead to stoically stay up all night struggling, or to pose our questions elsewhere.
What I'm getting at here is that if you respond in a positive and prompt way both in class and out of class, that has to be helpful.
She gave us weekly online quizzes based on the reading.  That ensured that people read the required chapters in the text book.
For (d), perhaps you could give them a take-home test where they have to invent some test questions for the unit you've just finished.

Do they trust you and your general judgement? If yes, you can try this: tell them there will be exam/test/other assessment based on texts 1-3 they will soon read. And the questions will be their questions if they will be reasonable enough. That's why it's important for them to trust you - so they know you will fairly judge the "reasonableness" of questions. And they will clearly see how they can benefit from reading texts and asking questions.

Prerequisite: The university policy should allow the instructor to ask some bonus questions in the exam.
One of my professors had a really good way to deal with groups that do not ask questions. He put a bonus question in the exam from one of our in-class questions. I also have adopted this method and it worked really well for me.
If a students asks a good question, then I wait for the class to answer. If there is no answer from the students, or it is answered but is still a really good question, then it is listed as a possible bonus question.
The motivating idea is,

If the bonus question is yours, then you get the bonus points. You
  don't need to answer the question.

In addition, I sometimes make a conceptual mistake while solving a question on the board. In your case, maybe it might be a wrong reasoning while explaining something. Students who point out the mistake and correct it would also get some participation points.
One last thing I realized is, people usually tend to remain silent because they cannot guess how the class will react. But usually, the questions they are afraid to ask are not only theirs.
To break this ice, I try to ask the stupidest questions myself.

OK, this part of the text assumes that people need social interaction.
  But how can this be even a scientific fact? How can we even measure this?

This might be a totally absurd example, but I hope the idea behind it is clear.

I often get feedback from them saying that the text is too difficult and they don't know what to ask.

Focus
For the questions: focus on one specific part of the text. May it be because it is very controversial, polarizing, prejudiced or interesting in any other dimension.
Still encourage the students to read and try to understand the entire text but just limit the in-class discussion to a subset of the text. Most likely this approach results in overlapping questions and a more vibrant discussion since students just focus on that particular part of the text.
Size
Start with a small paragraph, vary the size, find out which size leads to the best results.

This site provides a number of techniques that can be applied to your field:

instructor provides an answer, and students brainstorm questions. This can be a great way to review, or as an introduction to a unit to find out how much students know. Once students learn some of the strategies for developing “great” questions that are described below, displays like these are good for practice and formative assessments.
It’s a big start to get students in the habit of asking questions, but it’s even more important to help them to identify the types of questions they are asking.  A simple distinction to use with younger students is, “Thin and Thick” questions.  In this day and age, a “thin” question might also be labelled as “Google-able.”  If you can easily find an answer in a book or the internet, or it’s just a matter of saying, “yes” or “no,” then it’s a “thin” question.  “Thick” questions require more thought and often don’t have one right answer.  They are great for discussion and research projects.
Teachers are often encouraged to raise the level of their own questioning by using question stems related to the higher levels of Bloom’s Taxonomy.  But this doesn’t mean that students can’t use it as well. this reference gives some examples ways that students can use the above question stems to write their own tests or quizzes or as focus points for research.
Dr. Sandra Kaplan developed the Depth and Complexity icons in order to help students go beyond basic understanding of topics, and the icons have become well-known to teachers who are expected to include “rigor” in their curriculum.  In classrooms where the Depth and Complexity icons are woven throughout the day, students become familiar with the meaning of the symbols and how they can be applied in different subjects.  It is not unusual for them to discuss the multiple perspectives of the Civil War or the ethics of Little Red Riding Hood.  One of the icons is, “Unanswered Questions.”
Promote “What if?” Questions
  A teacher named Carla Federman actually assigns her students to do research projects based on what if’s.  What if “The Army-McCarthy hearings had never been televised?” asks one student in her research.  Another student poses, “What if Albert Einstein’s letter to Franklin D. Roosevelt was intercepted by the Soviet Union in 1939?”  Students must consider the short and long-term consequences of their what if’s, while demonstrating their understanding of the historical contexts they cite.  This is an outstanding example of how student questions can be used create engaging and empowering learning activities.  For more information about “What if?” projects,  see reference
Conduct Socratic Seminars The Socratic seminar is a formal discussion, based on a text, in which the leader asks open-ended questions.  Within the context of the discussion, students listen closely to the comments of others, thinking critically for themselves, and articulate their own thoughts and their responses to the thoughts of others.  They learn to work cooperatively and to question intelligently and civilly.”
Give Plenty of Opportunities for Reflection, It isn’t only important to ask questions of others, but also to get into the practice of questioning our own actions and work.  Most teachers are familiar with the students who are quick to finish, yet have many errors.  Telling them to check over their work may buy the teacher some time, but is rarely productive if students haven’t been taught actual processes for evaluating their own products.  By giving students time and the tools for reflection, educators are teaching the valuable skill of self-assessment.  It is also important that teachers are careful to show that, although they do want assignments completed in a timely manner, it is more important to do quality work than to speed through it without any thought.

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