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Selecting journal reviewers through cover letter
I was planning to use mdpi.com to submit a paper to "Entropy" journal. The journal perfectly matches the area that my paper covers. However, they require a cover letter to five reviewers selected by myself:
http://www.mdpi.com/journal/entropy/instructions

Coverletter: Check in your cover letter whether you supplied at least 5 referees. Check if the English corrections are done before submission.

Is this the standard procedure? Can you propose other similar journal? I am getting afraid that receiving feedback is not an easy task, and I can wander with the paper for a year or so.

I agree. It is done.

I would advise suggesting reviewers, or offering to do so, even when you are not required to. I've been in situations where the editor left my manuscript aside for a few months, only to ask me for suggestions when I contacted him or her wondering about the state of my paper.

I wouldn't say that a journal asking for reviewers is "standard" practice, but it is by no means rare. For instance, nearly all ACS journals require that the paper submitter provide the names of between three and six potential referees. Other journals that I've submitted to, including J. Chem. Phys. and the Physical Review series do not require referee lists of any kind.
It should be noted that the choice of referees is entirely discretionary on the part of the editor. The editor is free to pick from any or all of the names on your list—or none of them, if it's an area the editor knows well enough to assign referees independently.

Typically journals with broader scope, or those for interdisciplinary subjects, will be more likely to ask for referee suggestions. In all likelihood this will speed up the refereeing process, as otherwise the editors may send your manuscript out to whom they thought to be good fit to review your paper, only to get a letter back 3 weeks later saying that your paper is outside of his or her expertise. For field specific journals this is much less of a worry.

I've encountered this before - as aeismail has said, it might not be "standard" practice (implying most journals do it) but its certainly at the very least common.
This is often intended to provide focus and speed for journal editors to get papers out. Finding appropriate reviewers is a long and tedious task, and if editor's come to rely too much on "their" expert reviewers, they're likely to burn them out. The approach of recommending peer-reviewers gives you, the author - and presumably an expert in your field - an opportunity to weight in on who is qualified to review your paper, while avoiding people who would have to abstain due to a conflict of interest, or who you feel might not judge your paper fairly.
Essentially, you should be considering people in your specific field who aren't your direct collaborators, but who might be disposed to look on you and your work in a positive or at least neutral light - avoiding people who don't like you, or who think "Paper Topic is a waste of time and research dollars, and should never be published".


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Sources of information about postdoctoral/PhD grants and funding
We are a research group in Spain. For first year postdocs and PhDs from other european countries that want to come to our lab, there is no support for spanish ministry of science. Therefore we wonder where can we find information about such funding from any other country in the world.

This is a good idea, but I fear that the directory would be quite large and quickly go out of date. We have a department that produces an online directory of all the funding opportunities available at all levels, across all departments. It covers everything from travel grants to multi-million euro EU projects. There are many many opportunities. Maintaining such a list across countries would be difficult.

could we acccess your online directory?

Unfortunately, it is only accessible to staff and only in Dutch.

it is to our advantage to avoid encouraging competition — [citation needed]

As a PhD student trying to find a good postdoc position it's in my interest to help you find funding for places. These links may help as they all currently have open calls for projects/fellowship funding:

Google Awards http://research.google.com/university/relations/research_awards.html
Marie-Curie Actions http://ec.europa.eu/research/mariecurieactions/
ERCIM https://fellowship.ercim.eu/

Please let me know if you manage to get some funding ;)

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What to do when you get a grant and move to another institution
My general question is; let's say that you are PI and apply individually or jointly with other research groups to a grant, and you get it. After some months, you move to another institution; can you generally "move" all the money and resources you were awarded with or should you abandon them?
The question goes for H2020 projects or any other national or international funding schemes (NIH, NSF, UK, etc)

And in particular this goes for H2020 projects.

This happened to a colleague of mine for FP7, I assume H2020 will be pretty much the same. Essentially, you have two options:
(1) Find a proxy to formally finish the project on your behalf. That is, find somebody at your current institution with a high enough status that he is allowed to take over the project without much administrative quabbles (e.g., a senior professor), and formally hand over the project to him when you leave. You will of course still do the actual work - the handover is just a formality. Of course this requires a significant amount of trust and goodwill (on both sides), so you better be good friends with the person that proxies for you. As long as you both are at the same institution, the administrative effort of this solution is not too high.
(2) Officially transfer the project to your new institution. This requires an amendment of your DOW (description of work), and the sanctus of your new institution, all partners of the project, and the european commission (i.e., of the PO and the responsible lawyers on EC side). This will take long - expect the entire process to take possibly a year or so. Additionally, there is a chance that some negotiations between you, your old institution, and your new institution are required (e.g., to answer the question to what percentage the overheads should be transferred to the new institution). H2020 proposals are good money for universities, and you should not expect your old institution to let go of such a project easily.
Edit: Clearly, option 2 is only available if your new institution is also eligible for H2020 funding.

What is allowed depends on a number of factors. For example the funding agency may not allow you to move the grant. This is especially true if it is an international move or if the grant requires a resource that is not available at the new institution. It also depends on your current institution. They may not allow you to take equipment that was previously purchased on the grant with you. You new institution may also not allow you to bring the grant over if it does not provide sufficient overhead. If the time remaining on the grant is short, the two institutions may decide to not formally transfer the grant and work off of a sub contract instead. That said, generally for non-international moves you will be allowed to bring over the unspent money.

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Optimal configuration of a research group
In most of the European Universities I know, research groups are created from the equivalent of Assistant Professors and the Principal Investigator is voted in some sort of election, where there are elections every 2/4 years. In groups with such profile I have usually seen that scientific output is low and that most of these members are not really motivated to do research and are only affiliated to these groups for CV and promotion purposes. But this is of course my personal experience, I do not state this is always like this. From the other side I know other groups that are created from scratch from somebody with a very good CV, who has a vision and ambition, and who gets all research group members not from Department colleagues but from funding he/she attracts.  All group research lines are derived from her/his experience and CV and scientific output in this case and according to my experience, tends to be high. Based on your personal experience or factual evidences, what is the most optimal configuration for a new research group, the former or the latter or do you think there are other different configurations?

If you figure out all combinations for research groups then there are examples of all of them being successful - can’t see there being any one solution for this.

I think that what the research group for promotion purposes is not optimal and than the group around a PI with track is one of the best ones

I've worked at several European universities, and I've never seen or heard of the first type of system you describe. Could you specify where this is used?

@silvado I think such systems are used when you need a research group for grant reasons. So everyone wants to do their own (albeit slightly related) thing, but you only get the grant if you have a "research group"; might be split between different institutes or even different universities and people only meet once or twice a year.

@Dirk what do you mean “for grand reasons”?

Sorry, I mean for a grant, that was a typo.^^ So someone gives you money to do research, and you want to have it look good to them, so you form a research group, at least on paper (and CVs).

Ok now, yes that is what I wanted to say

Given the way you framed the question, the answer is obvious. In other words, you have set up a straw man for us to knock down. That is not a good question. So can you tell us why you are asking this question? What is the real underlying question you want to ask us, or is this just a rant?

sorry if the question was not clear. These are the two schemes I know for research groups. For me the latter is the optimal one. But I want to know if someone knows other more optimal configurations for research groups. If that is not clear just tell me and I will rewrite the question.

[citations needed]

@lux about what ?

Pretty much every claim you make (scientific output is usually low, members are not motivated to do research etc. Based on what evidence?)

I have rewritten the question in order to explain that the two groups are based on what I have seen and not scientific bibliography (although such might exist)

What is a "research group" in your perception? And why wouldn't the individual teams in the first model (assistant professor + staff") be functionally equivalent to the groups in the second model?

My impression is that staff, which is overbooked with teaching, will have in most of the cases no time at all for research, or they will be very limited. But this is my impression and I might be wrong at all. My main question is if apart from these two kind of groups you think there are other better configurations

If you want to maximize the output, impact and success of a research group you have to increase the synergetic potential of the staff, set up good research questions, acquire funding etc.
The PI can be a genius, but if he is unable to identify good researchers for his team, researchers with complementary abilities and lead a team, then he will underperform. Extreme cases of such PI's are savants/prodigies (e.g. autism syndrome) with limited social skills.
There are nowadays companies who "rent" savants or people with special abilities in math/informatics to other companies to solve distinct problems, but taking care of the social integration and well-being of them by setting the right boundary conditions for such jobs. This is not very different in research groups, you often have persons with very special personality, interests and social/cognitive abilities.
The optimal configuration of your group will always depend on what the research group is investigating and what the existing team is looking like. You don't want to have only alpha-males on ship if you set up a team to fly to mars.
There are even studies what kind of staff number is ideal in distinct scientific fields, a particle physics group has from theoreticians to experimentalists up to technical employees a very different structure in comparison to english literature.
The question is rather how do you develop from the current group structure to a better one, going from zero directly to the best one is only possible in a hypothetical perfect world with unlimited funding :-)

Thanks @user847982 for your very insightful answer. I agree with your view and like your sentence "You don't want to have only alpha-males on ship if you set up a team to fly to mars.", which explains perfectly your point. Regarding "There are even studies what kind of staff number is ideal  ..." can you add some references?

@Opentheway see here for example https://psychology.stackexchange.com/q/10/9423

I assume you are basing this on European model, so in my experience the groups based around some common interests are the strongest one because they have a vision that can lead group. Usually these are friends or couples, that succeed to attract funding making multidisciplinary team. In such a team everyone knows each roles and they keep each other back by making sure people are represented in publications in terms of authorship equally. I would suggest you to take a look on Research Gate lab profiles where you can see how members of particular lab are connected and what grants or projects they menage. In my opinion it is the best way to discover dynamic of a group and internal structure. Second things are Center of Excellences, they are now because of HORISONT2020 becoming more popular and are highly hierarchical. However primordial idea for their creation was done trough application of group or consortium of reaserchers and scientist, in there you can observe same things as in your question, however structure is maintained highly hierarchical. In my opinion best way to organise research group is around "friends and family" because you need to trust people in order to follow through with your agenda. I'm not saying that groups that are based around one person are bad, but due to increasing emphasis in academia on teaching, management and bureaucracy, alone PI in current European funding scheme structure can not survive.

Thanks for your answer @SSimon. Regarding your answer, the two group types I described are based on what I have seen with my own eyes in different European countries, and what I have read or understood from non-EU countries. Of course for the latter my opinion might be very biased or invalid. The "family and friends" group is a very interesting configuration that I will add to the list and which I have never seen (unfortunately for me). I think that when it works it can be very strong. But from the other side and according to my experience sometimes working with friends can be problematic ..

.. I mean problematic because when they do not follow deadlines and do not want to work, you do not want to remember them about that since you do not want fo lose your friendship. What do you think about this?

@open the way Actually, academic power couples are quite famous in Europe. Well when you get grant everyone is doing on their own part,it doesn't mean you actually work together. That is why you have students and hire reaserchers:^), being part of some group so called academic clik. Most effective workers are your students and postdocs. Others on possition will tend not to work so much.

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How to get information about new citations in Google Scholar without making profile public
Once per week I check my Google Scholar profile and I can see my citations count is increased. I would like to know, to which papers/works my increase in the number of citations is related to. How can I know this without making my profile public?

Help about a specific product/service isn't considered OT?

Out of curiosity, why do you not want to make your Scholar profile public?  You don't need to provide a picture, a web address, or a public email address, and your name is already on your papers.

I created a Google Scholar account so that my research is visible. I wonder why someone would need to hide that.

A not-so-portable-and-possibly-glitchy-idea might be to create a little program that scans your Google Scholar page every so often and checks for which citation counts have gone up.  You can then search for papers that cite those papers in particular (rather than having to search for all of your papers).

yes, that is the best option, how would one do that?

You can set an alert on "New citations to my articles" and receive this information by email.

Yes. But I do not want to make my profile public. Is it there any other way?


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How to use more than 8 boolean operators in ScienceDirect advanced search?
The advanced search in the ScienceDirect database seems to be limited to 8 boolean operators at max. This number of operators might not be sufficient, especially when applying a search string within a systematic literature review that is valid for other databases, e.g., ACM DL or IEEE Xplore DL which are capable of accepting search strings holding more boolean operators.
What are strategies to apply a search string with more than 8 boolean operators to the ScienceDirect database?

Please post the exact error message you received so that people might be able to help you.

@Tripartio "Use fewer boolean connectors (max 8 per field)"

Split it into two (or more) separate queries and combine the results.

Talk to a research librarian at your institution.

If the error message explicitly says that the system only supports max 8 per field, then you should follow the advice of @Louic.

@Louic is there any tool to find the distinct results from the search results obtained from multiple queries?

A reference manager?

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What research has examined the cost in time and money of conference attendance?
I am looking for surveys/studies that quantify the time and money academics spent on conferences/symposia/workshops/etc by both organizers and attendees. Specifically, I'm interested in both academic and institutional costs related to conference, travelling, and administrative tasks related to travel. (In my experience the overwhelming majority of expenses are covered by employer/grant/etc anyways.)
I am most interested in the field of computer science, and academics affiliated to US institutions.

Please clarify who spent the time and money? Organizers or attendees? And also the field?

@scaaahu I am interested in both.

@scaaahu I am also interested in comparing different fields but I specified one in the question. Basically my interest is in assessing time and money spent on conferences in academia, but circumventing to one field and one country is already a good start.

You might want to search around for the budgets for particular conferences which sometimes give you a breakdown of number of attendees, country, and other information you might find useful from past years.

What counts as time spent on a conference?  Presumably you include time spent attending the conference or travelling.  What about reviewing papers?  Preparing slides?  Writing the papers?

@AnonymousMathematician Conference, travelling, and administrative tasks related to travel.

By "money academics spent on conferences", do you mean money those academics spent personally, or money that was spent by their employer, or both?

@O.R.Mapper Both but I have mostly interested by money that was spent by their employer. In my experience most (> 90%) expenses are covered by employer/grant/etc.

@FranckDernoncourt I've added your clarifications to the body of the question.

I published a paper:
 Anderson, L., & Anderson, T. (2009). Online professional development conferences: An effective, economical and eco-friendly option  Canadian Journal of Learning  Technology, 35(2).
in which we calculated the costs (transportation, hotels, meals etc.) in dollars and in Carbon costs using a medium sized conference in the UK.
We were interested in showing the HUGE cost and carbon savings if the conference was held online and used this data in our book on Virtual Conferences.


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I'm in a religious country, and my religious supervisor is praying. What should I do?
My supervisor and all his other doctoral students are practicing religious, while I am not, I am "non-religious".
We never discuss religion together, but sometimes they all leave to pray together, and leave me alone, which makes me uncomfortable.
Surely, if they knew I'm "non-religious," it would annoy them.

How do I react to a situation in which they all go to pray except me?
Do you think I have to open this debate with them, and close it once and for all?
Should I pretend to be like them, pray with them?
EDIT: I am in a predominantly Muslim country, MENA (Middle East and North Africa), and not being Muslim is not very welcomed in general. For example, eating during the month of Ramadan is not legal, and can be a source of physical or mental violence in the street. So even if my supervisor is kind enough as well as his other doctoral students, they will be disappointed if they know my situation.

If you don't go pray with them, how did they not figure out yet that you are not religious? Do they think you pray alone at a different time?

Comments are not for extended discussion; this conversation has been moved to chat.

There are situations in which you need to be sensitive to others and they should extend the same courtesy to you. However, there are some places in which religious feeling is so strong as to overcome such sentiment. It can be dangerous in many ways (academic, physical,...) to disagree with religious "consensus" in such places. There are some colleges in the US, in fact, in which this is a problem.
However, to "fake" being a member of a religion is equally dangerous, so you need to be careful. I don't know what people's assumptions about you are. But if they are aware that you aren't a member/adherent of the dominant faith you are probably best advised not to participate. If they are not aware and are making assumptions that you are just an apostate then it can be very dangerous.
If your professor has an open enough attitude you can speak with him/her for advice. But the first rule is to be safe. If you are in a place in which you are required to be a "believer" and you are not, you should work to find a more compatible place. Religious sentiment is often other-than-rational.

Comments are not for extended discussion; this conversation has been moved to chat.

I grew up in a Muslim-majority country. Do's and don'ts:

Do show respect for the religion. That means avoid doing things like comment on how inconvenient it must be to pray five times a day, don't offer non-halal food, don't invite people to lunch during Ramadan, etc.
Do do as they do, if possible and not inconvenient. For example if you take lunch together, order/pack something halal. Unless you have special dietary requirements that require you to eat pork, don't eat pork when with others.
Do dress conservatively. If your institution has a dress code, follow that. If you're female, you can usually refuse to wear the hijab if it makes you uncomfortable (depends on country however), but still dress conservatively - e.g. don't wear something sleeveless, and wear hemlines that go below the knee (this rules out wearing shorts in public).
Don't pretend to be Muslim. You can't fake it. Learning how to pray in the religion takes time; the chant is nontrivial as well.
Don't pretend to be Muslim #2: just as important, once you identify as Muslim you could be bound to obey a different set of laws. Sharia criminalizes things which are fine in contemporary Western culture, such as homosexuality. If you're homosexual but identify as Muslim, you could bring the religious police on your head.
Don't pretend to be Muslim #3: in some countries, if people believe you are Muslim, it can cause you a lot of inconvenience. It doesn't take much to become associated with the religion (extreme historical example, less extreme modern example), and once you become associated, it can be really hard to leave the religion. Potential problems you could face go up to death. In the meantime it's not just you that's affected: in many countries, there are restrictions on Muslim persons marrying a non-Muslim; plus any child born to a Muslim is automatically a Muslim.

Exception: if you were originally a Muslim but no longer believe in the religion, you don't have good options. The above advice will still bring the religious police onto you, because you're now an apostate. You would either have to pretend to be Muslim (at least you should know how to pray) or leave the country and work elsewhere.
tl; dr: Leave religious people to practice their religion and don't criticize them for it. They should do the same to you.

"any child born to a Muslim is automatically a Muslim" that's very broken. The newborn isn't any religion yet (except perhaps deist which appears to be the natural state of man). Even the LDS has a very good idea of what age of majority means.

@Joshua you sure? https://en.wikipedia.org/wiki/Wong_Ah_Kiu this implies that the Malaysian authorities considered her to be Muslim simply because she was born to Muslim parents.

The Malaysian authorities are simply wrong, and the fact they intend to behave as though it is true is why it's broken.

@Joshua for practical purposes, "any child born to a Muslim is automatically a Muslim" is true enough. Right or wrong, child can be treated as a muslim with all the risks that goes with it, and warning about it is OK.

@Joshua: Theologically, they may be wrong, but legally, they get to define what’s right.  To be irreproachably clear, one could say “any child born to people legally considered a Muslim, is legally considered a Muslim”.

100% agree on the not faking part, which is a terrible idea for many reasons, but on the point of law, doesn't one have to sincerely recite the shahada before two Muslim witnesses for a valid conversion to occur?

In all honesty, the first two of these are excellent advice regardless of the religious tension in the room.

Your answer is useful because it helps to ensure OP's safety. Still, it boils down to "be tolerant towards religious intolerance". :-/

@aidanh010 sorry for not responding earlier. I'm not an expert on Islamic regulations, but I added a link to Sol Hacheul about being accused of having converted.

I also spent a few years in a MENA country in an academic environment. As you say, eating food/drinking water in public during Ramadan was illegal, as were certain standards of dress, however my experience over the years was that this did not in any way mean that the individuals I lived and worked with (including those who were practicing Muslims) were by default unaccepting of my non-religiousness. I am curious why you say

Surely, if they know I'm "non religious" it will annoy them.

and

So even if my supervisor is kind enough as well as his other doctoral student, but they will be disappointed if he know my situation.

Perhaps you have more reason for believing these than you have included in your question, however, in my personal experience, none of my Muslim friends/co-workers ever expected me to conform to their religion. I certainly never pretended to be Muslim, and like other answers, suggest that you do not do this as this is likely to make the situation more awkward ('I converted to fit in' is probably not the best answer to give to an observant member of any religion).
My advice is that perhaps this does not need to a bigger issue than any other lifestyle difference that you might have with your co-workers, and not to read too deeply into it (as in assuming they have some kind of expectation of you), unless they give you reason for it. Government polices do not necessarily reflect individual expectations. By all means, if you feel unhealthy pressure or feel unsafe, don't stay. Otherwise, similar situations where there is a difference in lifestyle/culture between members of the group occur all the time.
Perhaps another group you join might go out regularly for coffee/alcohol when you are unable to join for dietary/religious reasons, or in another group everyone else has kids, so leaves early, or do play-dates on the weekend. But in such situations, the activity you have to miss out on is surely not the only way to build rapport/respect within your group and strengthen your relationship with your supervisor. So if there is no actual pressure for you to have the same religious beliefs, try to decide if you're bothered by their religious belief. If not, then focus your energy on finding some other topic/hobby that you have in common. If both you and they are respectful of differences, there may be no debate to 'open'.

I totally agree with you, if you are a foreigner and you work with them, even if you are not religious it will not create any problem, it will be okay.. Here for example the tourists can eat during Ramadan, and the restorants are open for them .. but not to the citizen of the country

It depends on which country you are talking about in the middle east. I'm from Iran and I would say not participating in religious practices is really common among young people and if somebody attends those religious practices will be mocked heavily. For the rest of my answer, I assume you are living somewhere maybe in the Arabic countries of the middle east. Also, my answer is not really depends on your relationship with the ones that have strict religious beliefs (it means you can replace your supervisor or his students with anybody else like your friends, family, etc.). Also, I assume you are a Muslim by birth (it means you are Muslim cause your mother and father are Muslims) and then you changed your mind based on your personal thoughts.
You mentioned that all of them will pray at the pray time but you don't join them, and some people here suggested that it may implicitly implies that you are not a believer and if they didn't tell you something until now, it's quite OK in their opinion. Unfortunately: It's not true!. It means at the best they just think you may have a good religious reason (e.g. had sex last night and didn't wash your body) and because of that good religious reason you can't join them. Or, for whatever reason you prefer to pray privately.
The main key point is: Did ever your supervisor or his students tell you why you don't participate in their religious practices?
It is a really serious problem if you are Muslim by birth and when you grew up you changed your mind to not to be a religious person. In fact, in Islam beliefs, it's not like you can change your mind after sometime and they welcome you and wish you good luck with your personal thoughts and ideas! It could cost you your life (seriously!). But as far as I know, their rule is that if somebody don't believe in Islam or for whatever reason changed his/her mind to not follow Islam's rules, you would be safe as long as you don't express your ideas in any way to the public and your society. This means if your supervisor or his students asked you about why you don't participate in their religious practices? You need to have a really unimportant or common reason for it and not saying I don't believe in your beliefs! I mean you should say I'm a practitioner certainly but for some reason like being sick at the moment, I could not attend those practices with you. Otherwise, if you want to express your true beliefs that you don't believe in Islam, it will lead to a lengthy discussion with them about why you don't do it and they will try to convince you and if you don't accept their ideas it makes the problem bigger and bigger. So, for every time just bring a fake reason and move on, or better idea is: to not to be there when they are practicing their religion. Also, Buffy suggested you to change your location. Honestly, it is not really easy to relocate to somewhere else when you are from middle east and it may be your long-term goal rather than a short-time answer to your question and your situation that you are trying to deal with it.

Great answer, from someone who know "exactly" how religion is a in our countries ..you said everything! Thank you @Alone Programmer

Exactly! it happens with me many times.

They already know you are not an observant Muslim. If they thought you were one, they would have invited you to go with them. If you actually were one, you would have asked where to go for prayers at the first prayer time on your first day there.
They seem to have accepted you do not pray at the Muslim prayer times, and have no problem leaving you without putting any pressure on you to join them, which is what you would be trying to get in any conversation about the matter. On the other hand, they feel a deep obligation to pray at certain times, and I assume you do not want to try to stop that.
This seems like an "If it ain't broke, don't fix it." situation. You already have everything you could possibly gain from a conversation about the matter. On the other hand, discussing religion at work is always high risk.

~Note: I am an American, and while I studied at a largely international college with large populations of all major religions, my answer may not accurately reflect cultural expectations in other countries.~
First of all, I do not think that you should pretend to be religious if you are not. It sounds like it would be quite uncomfortable for you, and could lead to many negative feelings if they found out that you had been lying.
Instead, it sounds like you should have a conversation with your professor. It is not reasonable to ask him or other students to refrain from praying. However, it seems like your biggest concern is that it feels awkward and you do not want them to judge you for being non-religious. The easiest way to deal with this is to tell your professor about your concerns and ask honestly if he is bothered by it.
Tell him that you have noticed that he and the other students go pray together and that you have felt uncomfortable by being the only one who does not because you worry that he could be annoyed or feel disrespected by your lack of participation. He will likely say that it does not bother him that you are not religious, although he may be curious as to why you are not if that is the norm.
At the end of the day, if he is uncomfortable having a non-religious student, he may not be a good fit for you. Knowing that will allow you to decide what to do next. It may be possible to change advisors or it may not, but you won't lose anything by having a polite and honest conversation.

Thank you for your answer, as you said, the main thing is to be honest with yourself and with others, but I think It's not to me to   open a this discussion, but if they want to discuss someday I will be honest.

I am in the U.S., obviously a very different culture.
The way I think things OUGHT to work is this: If these people you work with have different religious beliefs than you and so periodically go off and pray or do whatever related to their religion, they should not pressure you to participate or penalize you in any way for not participating, and likewise you should not pressure them to not do this. They have the right to practice their religion, and you have the right to practice yours or not practice any.
I don't see why this should be any different than any other difference of interests. Suppose I worked with a group of people who, say, all loved to eat Italian food, and I don't like Italian food, and periodically they all go to lunch together at an Italian restaurant. It would be rude for them to pressure me to eat Italian food just because they like it. But it would be even more rude for me to say they shouldn't eat Italian food because I don't like it, or to complain that I am left out because I don't share their taste in food.
I think you should just accept that you don't share this particular interest with your co-workers and that this inevitably means that you will not share certain activities with them. I'd say, so what?

Although I agree with the sentiment expressed in this answer, I don't think it's very helpful to the OP to express the wish that everybody in the world should just get along with everybody regardless of personal beliefs, which is essentially what you're saying, but not the reality everywhere.  In particular, the impact of religion on life is vastly greater than the impact of food preferences.

I'm sorry if I was unclear. My relevant point is not that EVERYONE should be tolerant of other's religious beliefs. I'd say that's true but as you say, the OP can't make that happen. What I'm trying to say is that HE should be tolerant of other's religious beliefs. If others want to practice a religion that he does not share, he can politely not participate. There is no reason for him to complain or turn it into a battle. Just politely say "have a good time" or whatever is appropriate when they leave.

Belated afterthought: Yes, obviously religion is more important than food preference. I was trying to make an analogy comparing something important to something trivial, maybe that didn't come off clearly. And the flip side to my comment is how tolerant they are of him. If knowing that he is not a devout Muslim leads them to actively hate him, that's another issue from what I was trying to address.

how do I react to a situation in which they all go to pray except me?
  Do you think I have to open this debate with them, and close it once
  and for all? Should I to pretend to be like them, pray with them?

It is up to you. If you feel encouraged to accompany them, then you can tell them to inform you, and tell them that you want to accompany them. Otherwise you should not go even if they invite you, you should tell them not to invite you as you do not prefer to.
Religion is something personal. Even in Muslim countries, no one can force you to pray.
In my opinion you should not open debate about this unless if you are interested about knowing more about what they are doing.
Your supervisor has certain rules and regulations to evaluate you. None of them can be praying. Even in the most religious countries. So you should not worry.
And no, you should not pretend to be like them and pray like them. If you do this, you are wasting your time. Your prayers should have meaning to you, and should make you feel better. If this is not the case, no one need it from you.

"Even in Muslim countries, no one can force you to pray." Are you sure?!

Yes I'm pretty sure and I'm talking from my own experience. No one will drag people from their offices to pray. It is true that in some countries shops are obliged to close in prayers times. But even with this, workers are totally free not to pray and stay inside the shops if they like and they consider it an official break. This is in shops and public places that deal with customers. But closed offices like corporates or universities are different and they are not required to close. It is totally one's own will to pray or not.

You are Muslim by birth or you are talking about your experience as a non-Muslim foreigner which resided in a Muslim country for a while? It really makes a difference.


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What is IRDAM Journal?
I was reading Clinical Chemistry Guide to Scientific Writing Series. One of the articles is titled: “If an IRDAM Journal Is What You Choose, Then Sequential Results Are What You Use”.
I have encountered this term in this site also. Can anybody explain this term?
A Google search asks ”Did you mean: IRDA Journal”
In the article I linked, it is explained as "Introduction, Results, Discussion, and Methods".  I understand its meaning as this readily. What I would like to know following points.

Which type of journal articles are suitable for this style?
Which branches of academic endorse its usage?
Are there any other such styles exists?
Are there any other abbreviations exists?
finally but not least, why should I follow this type of sequence?

If you look at this article, you can see that IRDAM is an acronym for Introduction, Results, Discussion, and Methods. IRDAM is a style/format of presenting results in publications.
Quote from the article:

The IRDAM format requires a substantial change in how the Results
  section is organized. Because the methods are listed at the end of the
  paper, or online, the reader is not exposed to details of the
  experimental protocols and methods before the results are presented.

See also,

The format used by many high-impact basic research journals, such as
  Nature, Proceedings of the National Academy of Sciences, Journal of
  Clinical Investigation, and Journal of Cell Biology, is arranged so
  that the Results section immediately follows the Introduction. The
  Methods section is placed at the end, or it may even be published as a
  supplemental data file.

I’ll just comment to say that I love this IRDAM format (but I didn't know of the acronym)… It makes papers so much more readable to the non-expert, while retaining all the information needed.


text:
Do people actually buy research articles?
Research articles are often priced at 20-40 USD. I know that typically a researcher's institution subscribes to myriads of journals, and that some research articles are accessible online for free either legally or illegally, but I am curious to know some numbers that would help quantify how many / often individuals buy research articles, and how much money journals make from this source of income.
I am not looking for guesses or opinions, but actual numbers.

Companies that perform research usually do not subscribe but purchase individual articles. this is of course not individuals doing private purchases but will in some fields make up a large portion of the single article sales.

I bought a research article when I was a postdoc.  I was collaborating (via email) with a Spanish mathematician, and we found a paper that from its title sounded like it might overlap with our work.  I was sufficiently worried that at the time, $25 was worth some peace of mind.  This is a sad story: not about the article itself (there was little content in it of any kind) but that I could be that young and desperate.  Nowadays I would on principle spend more than $25 of my time getting the article freely.  But what you do even once probably happens a non-negligible percentage of the time...

I bought one obscure paper. When refereeing a paper for a conference that had a very tight and strict deadline, that obscure paper turned out to be absolutely necessary, and I didn't have enough time left and couldn't wait until my university's library could loan it from another library.

I would like to add to this a request for the results to be broken down by discipline,  if possible.  I'm sure the data would be dramatically different between, for example, mathematics and medicine.

@YuichiroFujiwara: Why didn’t you ask the publisher (or conference organiser) for giving you access to that article? Whenever I reviewed something so far, the publisher offered me access to journal articles for purposes of the review and I would also consider it the publisher’s responsibility to organise access to articles not included in this.

@Wrzlprmft I wish I could. But I really didn't have time. The authors claimed a "theorem" which I didn't think could be true. But they gave a sketch of a proof, so I tried to reconstruct the complete proof from it, prove it in my own way, etc., all to no avail. I asked my friends, and search the literature if there is something useful, too. And about 12 hours or so before the deadline, I finally stumbled on this obscure paper whose abstract claims to contain the key result I needed to mathematically disprove the authors' claim.

I work in an R&D department as an engineer. I have a personal IEEE digital library account (US$40/month, 25 articles) which serves most of my needs.  However, I still find that I buy about 2-3 articles per month.   Note that when you shell out real physical cash for a article, you are far more selective about what you read.  That's an enormous change from when I was in academia.

I am student and I recently bought my first article. It cost $20 and is about a subject related to my thesis.

I happened to buy a few articles in the past. I bought a special issue of the Journal of the Audio Engineering Society I've wanted to keep because the topic was of particular interest to me and at the time there was no internet access to the content. I also bought an article once when I was in hurry and didn't have the time to wait for the interlibrary loan.

I once bought a thesis.

I tried digging through the 2013 annual report of Elsevier. Under "Revenue" (page 111) they list both "subscriptions" and "transactional" - but the latter include not only reprints, but also books etc.

As you can see, even if we lump books and reprints together, it is still less than subscriptions.
To get a more complete answer you may have to ask them directly.

This is great (+1). However, to allow for speculation, does Elsevier have a large book segment (a la Springer) or do they fully concentrate on research material?

@xLeitix from http://www.elsevier.com/about/at-a-glance "almost 2200 journals and over 25,000 book titles". I would call that a large book segment.

While I can't give actual firm numbers, I know that two (non-academic) consumers of academic articles are law firms and pharmaceutical/life science companies. One of my former classmates worked as a research assistant for a law firm that handles biotech and patent cases, and I recall having a conversation with him where he said they easily spend $20-30,000/year on articles, with the exact amount depending on the cases they see and how much background information they need. These costs are wrapped up in the general legal fees charged. From my own experience, I worked briefly for a life science startup, and we would purchase around $600-1,000 in articles a year (although we tried obtaining articles through academic collaborations as much as possible).

Some University Libraries will also buy/rent individual articles for their faculty and students when they do not think a subscription is worth the money.

Speaking as a librarian, very rarely - only if it's urgent and can't be obtained in a useful way through ILL. The cost of journal article purchase is usually three or four times an ILL fee.
More generally...
I ran some numbers on this for JSTOR in 2011, based on their public filings - it's hard to be sure, but the answers were "very little". In 2008, 0.35% of their income came from pay-per-view, and based on the quoted average, this came to something like seven or eight thousand articles/year.
It later transpired that themselves suggested around twenty thousand a year, but the numbers for this didn't quite add up, as the per-view price would be substantially lower than expected, so either a lot of material was somehow discounted or only the cheapest articles were being purchased. However we sliced the numbers, the easy answer was "not enough to really be significant". JSTOR have, to their credit, substantially widened public access since then, so these numbers will probably have dropped further.

An order of magnitude estimate for the revenue a publisher might get from these direct purchases is "several thousand dollars per month". For a publisher as large as Elsevier it might reach the low six figures per month. Given that Elsevier's revenue is in the billions, this is literally a rounding error.
Source: I used to work in academic publishing.

This begs the question of "Why do they bother?".
Presumably it must still be worth the costs of offering the service.

@Flyto I didn't work in the e-publishing department but I suppose that once you put the articles online (which you have to do anyway), it's very easy to offer it for sale as well. Unlike print copies, selling an electronic copy of the article barely costs anything, so why not.


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Reference on the time it takes for a source code used for a research article to be released
Is there any research/study/survey/... that looked at how much time it takes for the authors of a research article to release the source code? Ideally I'm looking for an approximation distribution.
This question is a follow-up of Reference on availability of source code used in computer science research articles?

Are you asking about how much time the authors typically invest in preparing the code, or about how much time passes between when the article is ready and when the research code is ready?  Either way, there is a lot of potential ambiguity here.

@DavidKetcheson   I'm asking how much time passes between when the article is ready and when the research code is ready. What else should I clarify?

What do you mean by "ready"?  When a preprint is posted to arXiv?  When the manuscript is submitted?  Accepted?  Electronically published?  Print published?  And what do you mean by releasing the code -- especially in the case that it is developed in a publicly accessible repository?

@DavidKetcheson Ready = made available online. I'm fine with other definitions too (since there haven't been that many answers so far…). Releasing the code = make the code that was used for the paper publicly available.


text:
Do tenured professors work less or more than non-trenured professors?
Is there any research/study/survey/... that looked at how much time tenured professors work in comparison with non-trenured professors?
I am especially interested in the field of computer science (machine learning) in the US.
So far I have only found a small-scale study (survey of 30 professors from the same university):

I'm looking for some more exhaustive surveys.

It's also going to be interesting to see if this is broken down between hard and soft money positions.

The National Center for Education Statistics in the United States surveys faculty of post-secondary institutions (see the National Study of Postsecondary Faculty page for information on methodology). The most recently available data is from their 2004 survey, with 26,110 respondents across the United States.
According to this survey, tenured faculty worked 53.3 hours a week on average, and tenure-track untenured faculty worked 53.7 hours a week:

The NCES allows you to create custom tables from this dataset using the PowerStats tool on their website. (You have to create an account to use the tool.) This is a valuable tool if you're interested in exploring these and other statistics.
For example, here's the same data broken down by rank, with the percentiles for average hours worked per week:


text:
How can I create a DOI for a paper that was uploaded to arXiv but not published somewhere else?
I wonder whether there is any way to create a DOI for a paper that was uploaded to arXiv but not published somewhere else, and have the DOI points to the arXiv URL (e.g., not pointing to some researchgate page). While there are reasons that arXiv does not provide DOIs (Why does arxiv.org not assign DOIs?), I prefer to use the same identifiers for all my research papers.

The faq page is https://www.doi.org/faq.html and it is the first question there.

@Dirk Thanks, is there a RA that does what the question is asking?

Something being in an FAQ somewhere doesn't mean it's off-topic. For one, the FAQ does not open for me at the moment, so it's not even a universal source. Voted to reopen.

@Dirk: I would consider the answer from the FAQ incomplete - using RAs is not the only way of generating and using DOIs. Some open science repositories, such as Zenodo and figshare, provide these services for free and directly (that is, without need to interact with the RAs).

@AleksandrBlekh - no, the FAQ is correct. Ultimately, figshare etc issue dois via a RA - though as this is back-end infrastructure, it's pretty invisible to the end user. They're not operating outside that system.

@Andrew note the difference between "incomplete" and "incorrect". The FAQ is correct, but if you say A (only RAs issue dois from IDF's point of view), you have to say B (there are third parties that do this for you).

@yo': Thank you for expanding on exactly my point (+1).

@Andrew: As yo' emphasized the issue, I hope you agree with my statement now.

arXiv now provides DOIs: https://blog.arxiv.org/2022/02/17/new-arxiv-articles-are-now-automatically-assigned-dois/

@GoodDeeds thanks, you are welcome to post your comment as an answer

Ultimately, no, you can't. There's no infrastructure to say "I want to get a single DOI for XYZ arbitrary url".
DOIs for most scholarly publications are issued through CrossRef. CrossRef do not assign DOIs directly, but delegate this to members or their agents. Members, who are usually publishers, pay a fee to the central consortium, and agree to issue DOIs based on a fixed set of rules.
As you can see from these rules, the general sense of membership is "organisations issuing DOIs for stuff they control". While there isn't an explicit prohibition against assigning DOIs to third-party material (which surprised me!), point 4 comes pretty close:

Members have an obligation to maintain the metadata and URLs associated with all registered DOIs.

There is also a general prohibition of 'duplicative' works including preprints:

Crossref only registers DOIs for Definitive Works (or Versions of Record, if not formally published) but not for Duplicative Works, as defined in the Crossref Glossary. This means that only original scholarly material, for which there is no actual DOI at the time of submission, and no expected duplication in future, is admissible for Crossref DOI registration. Crossref does not permit multiple DOIs to be assigned to certain closely related versions of a work, and hence does not support assignment of DOIs to Pre-prints or Post-prints of Definitive Works or to the Personal Version or a Self-archived Copy of a Definitive Work. For the same reasons, materials for which DOI duplication can be reasonably anticipated, such as an Authors Original Draft of a work being prepared for publication, are not admissible for Crossref DOI registration.

Putting those together, it seems likely that CrossRef's terms would prevent a member agreeing to issue a DOI for a (potentially duplicative) work hosted somewhere out of their control.
So, could you get a DOI from someone else, outside of CrossRef? Probably not. DOIs are only issued through a number of central registration authorities (eg CrossRef, DataCite). These have fairly well-defined areas of activity (eg DataCite won't issue DOIs for publications) and, to the best of my knowledge, none offer a "DOI for an arbitrary URL" service.

Thanks! List of DOI Registration Agencies: https://www.doi.org/registration_agencies.html ; Explanation of the roles of Registration Agencies vs Registrants: https://www.doi.org/doi_handbook/8_Registration_Agencies.html . I also haven't run across any registrant offering some "DOI for an arbitrary URL" service yet. Out of curiosity, where did you see that DOIs for most scholarly publications are issued through CrossRef? I don't know how to know which Registration Agency was used to issue a given DOI.

(I found the answer to my question: the RA is in the DOI metadata, e.g. https://api.crossref.org/v1/works/http://dx.doi.org/10.1002/(sici)1099-1573(200003)14:2%3C118::aid-ptr493%3E3.3.co;2-g is CrossRef)


text:
What is a typical retirement pension plan for professors in the United States?
I have read some posts regarding academic salaries such as
In which countries are academic salaries published? but none about retirement pension plans.
What is a typical retirement pension plan for professors in the United States?
I assume there might be some significant differences between public and private universities. Research/study/survey that tried to quantify it on a larger sample is welcome.

I've never heard of an actual academic pension plan in the US. A private retirement investment savings account (401K or similar) seems to be the status quo.

Background info on 401(k) and similar retirement plans: https://en.wikipedia.org/wiki/Retirement_plans_in_the_United_States#Defined_contribution_plans

@David Really?  They are standard around where I am, generally all the state universities are in the same program (and often with other state workers).

Many use 403(b) plans

@guifa Ah, OK. I do know of some pension plans when professors at public universities are incorporated into a larger public employee pension plan, such as State of Illinois and State of California.

This varies widely from state to state, and dependent on many other factors. Certainly there is no uniform national structure, standard, etc. As in some comments/answers, in some cases pensions are state-controlled, and thus can be bait-and-switch operated and modified after-the-fact. In some cases, which may seem better or worse depending on the political climate, pensions are essentially equivalent to private pensions, with varying contributions from "the employer"... but/and the state cannot so easily manipulate that money.

AFAIK, all pensions are calculated basically the same, and I'll use Alabama, Tennessee, and Georgia as examples since I'm familiar with them.  In the public system, these are often pooled between all universities and colleges and often with the K-12 system or all public employees.
You have three variables: the eligible salary, the number of years worked, and the multiplier.
The eligible salary is calculated through a variety of methods, but tends to be the average of the highest X years of work over the last Y years.  For example, in Alabama, it's the average of the highest 3 years of the last 10 years.  In Tennessee, it's the average of the highest consecutive 5 years.  In Georgia, it's the average of the two highest consecutive years.
The multiplier is probably the single most important variable, though.  My father, for instance, worked in Alabama, with a 2.0125 multiple.  Let's say for instance his eligible salary was 100k to make the math easy.  If he retired with 10 years of service, he would receive ~20k per year.  With 20 years of service, ~40k, etc.  For me in Tennessee, my multiplier is only 1.5.  If when I retire I have an eligible salary of 100k, with 10 years of service, I'll only make 15k.  With 40 years, I'll make 50k.  (Yeah, my dad got a much better deal, and that's before we talk about the DROP program).  Georgia, for reference, has a 2.0 multiplier.
A minor difference thing to consider are time to vesting (Tennessee is only 5, but Alabama and Georgia are 10), but over an entire career, those don't make much of a difference for overall payout.
Because the ways to calculate the eligible salaries (highest two years really helps folks in departments with rotating chairs), I'm not sure how well one can generalize about the pensions.  One thing for sure is that they tend to be quite decent since you also collect social security benefits.  Anecdotally, for instance, between his pension with 30 years worked, social security and differing retirement tax rules, my dad takes home more now than when he worked.  Plus in academia we tend to be able to work well into old age which really boosts our pension income.
Based on what I've read, private pension funds work the same way, just with ever so slightly different variables.

In some states, there are public retirement/pension plans that the university will contribute to on your behalf as a state employee, but there are differences across states. For instance, I used to work at a university in FL and selecting the teacher's retirement fund in Florida was optional. In Alabama, where I am now, it is mandatory.
If a university is a non-profit, they will often offer a 403b or 457b plan, but contributions from the university vary. These work similar to a 401k plan at corporations.
Just remember that state governments control a lot of the retirement plan options in many states and can change after you take a job. When I took my job in FL, the university contributed 13% of my salary to my 403b without a match requirement. The state government changed a year after I started the job and reduced the employer contribution AND required a mandatory match (talk about bait and switch!).  I'm in Alabama now and participate in the mandatory state retirement plan (which I must contribute to), but also take the option of an additional 403b. So, it's all different, but you often have multiple options at a single university.

As mentioned in some of the other answers, this depends on the state you're in. In Texas, when I started as a postdoc in 2002, I had the once-in-a-lifetime option of either going with the state Teacher's Retirement System, which is defined benefit plan similar to the ones discussed by @guifa in one of the other answers; or going with a 401(k) into which I would pay 6.75% of my salary and the state matches that with 6.5% (now 6.65%). Given that the terms of the state-run system are subject to what the state legislature feel like doing, I went with the latter. It also has the great advantage that you do not lose your benefits if you later switch to a university in a different state.
Colorado has a similar system, except that that there was no choice for university professors to join a state-run system -- only the 401(k). In Colorado, you contribute 8% and the state 11%, which sounds more generous than TX, but the situation is in fact more complicated because, for difficult historical reasons, Colorado does not participate in the Social Security System for its state employees, and so I will not get Social Security benefits for my time here.
In both cases, my universities offered the option of contributing to a 403(b) in addition to the 401(k), but the university did not match anything there.

My public university in Colorado actually offers the obscure 401(a) instead of 401(k), not sure if yours is the same.  The main difference is that a 401(a) is mandatory - you don't get to choose how much to contribute.

Interesting. I have to say that I didn't look too carefully -- everyone who doesn't max out the match is not paying attention, so the question of how much to contribute has only a single, useful answer. (Also, hi neighbor!)

In the U.S., preparing for retirement is often quite different now from how it was 30 or more years ago.
Now, many workplaces, including a lot of universities, have pushed the responsibility to the employee.
I will describe my spouse's plan, in a large university, where my spouse started working in 2000.
The university contributes 10% of my spouse's salary to a retirement investment.  A nonprofit financial service called TIAA (Teachers Insurance and Annuity Association) receives the funds every pay period and invests the money.  But it is up to the employee to instruct TIAA how to invest it.  TIAA has a bunch of different options to choose from, which are kind of like mutual funds -- different mixes of types of investments.  The basic ingredients are stocks, bonds and real estate funds.
My spouse can put additional money into the retirement investment if desired.  Up to 10% of the annual salary can be invested per year, as pre-tax dollars (i.e. not subject to income tax).  That's the thing called "501 K."
If you want to learn more about how it works, you can look at the TIAA website, and you can also call them up.


text:
Contacting promotor and assistant/supervisor in regards to master's thesis after weeks of radio silence
I am a master student and currently finishing my master's thesis.
Ever since the beginning of COVID I have been experiencing depression and anxiety. This resulted in not being able to work as hard as needed on my thesis and led to a few delays of intermediary (but not compulsary) deadlines during this year. At the beginning of summer, my promotor, assistant and me made a raw time schedule to make sure I would be able to finish and hand in my thesis before the deadline.
About three weeks ago, I was supposed to send them a mail with my progress but due to the lack thereof and a multitude of anxiety attacks, I convinced myself it would be better to wait to send an email until I have something to show for. This anxiety related situation dragged out and now, with two weeks to go until the final deadline, I have most of my thesis written, except for the discussion of some results of my experiments (which I partly still have to create), and which is the most important chapter of my thesis.
My intent is to send an email on Monday, but I have no idea on how to address the situation. In my mind, they, my promotor and assistant, probably think I have given up on making the deadline of my thesis. I basically went radio silent for a couple of weeks and the guilt is eating me up. In addition, I don't even know if it is still possible to do the amount of work that is still needed to complete my experiments as I have not started my last one yet.
Could anyone give me some insight on how to handle my situation? Thank you.

Related, not duplicate: https://academia.stackexchange.com/q/151426/68109

In my experience, this situation is pretty common, so even if the advisor/promoter aren't happy about it, they likely have dealt with this situation before. I think you can let your guilt go for now. The best course of action is simply to acknowledge the lateness without dwelling on it, and try and resume normal communications going forward. I think you know your mistake here, but it is always better to send an e-mail with an update when you hit a deadline, even if you don't have "enough" progress to show. Your advisor likely wants to help, but they might feel like they don't know where to start if they haven't heard from you.
A simple statement such as: "I apologize for the tardiness of this e-mail, I know we had originally discussed a deadline nearly a month ago. Due to the pandemic situation, I have not been able to make progress on my thesis as quickly as expected. Here is my current progress. [description]. My plan for the next few weeks is as follows...." If you have concrete suggestions for how they can help, I would put them in your e-mail. Otherwise, let them take the ball from there on how to support you going forward.
In the meantime, if your situation allows you to access mental health support services, I think they would be useful in helping you find more healthy coping strategies in the future.

"this situation is pretty common", and I imagine that unlike Freddy, many students probably don't care enough to apologize for their tardiness.


text:
Good source for pre PhD level papers/dissertations in Mathematics
I am looking for a good source to get my hands on some pre PhD level maths papers/dissertations, because I want to get a better feeling what is expected. (i.e. BSc and MSc Dissertations)
My department is unfortunately not at liberty to make MSc Dissertations available for copyright reasons, so I am stuck with asking individual people. In order to get a good overview I'd really like to get my hands on a much bigger selection of papers though, so I'm looking for a good online sources.

Your best source of such information would be to look for electronic repositories that are at least partially "open." The openThesis repository offers one such source, and you might find some information on sites like academia.edu.
An alternate source would be to look at individual school's repositories. For instance, MIT's DSpace offers copies of many recent MIT thesis and dissertations, which can be previewed by anyone, although you need to be a member of the MIT community in order to be able to download and print documents from the site.

A quick Google search for "partial fulfillment master science mathematics" finds hundreds of MS theses in several branches of mathematics.

I'm now a PhD candidate mathematician, working towards understanding what really constitutes a paper as well. If you are considering going after a math PhD, I recommend finding an area you're interested in, finding papers in that field, and backtracking enough until you understand what's going on. I think math is very-well suited to this style of behavior.
For example, I'm interested in number theory, and I've recently been hearing a lot about automorphic forms and multiple Dirichlet Series. So I find this paper by Dr. Hoffstein. Some of it is understandable, some of it isn't. Going through it, I isolate 3 potential sources that might help me understand - the first references are frequently on background material, and here he references Selberg's work. Conveniently, my institution has access to electronic archives of his work, so that's great. It also references an Analytic Number Theory textbook by Iwaniec. Finally, I realize that this is largely built on this previous paper, with Dr. Hoffstein as one of the authors, from years before.
And then I can rinse, wash, and repeat. In this way, I both get an idea of what papers are like, how far removed they are from current material, and how advanced the math that goes into them are. A key aspect of this idea is that it's easier to go after particular research papers, theses, and dissertations than it is to find whole repositories that you can go through. So perhaps you should try a similar approach, suited to your interests.
As always, a good place to start is the arxiv.
On the other hand, it sounds like you're preparing to write a bachelors thesis, and that's of a different calibre. I suspect that your school has its own standards, and the best way to prepare for that is to simply do your best and ask your advisor lots of questions along the way. Ultimately, your school can't demand from an undergrad much more than it prepares you for (a vast difference from the life of overgrads, in my opinion).
As a last note, Harvey Mudd has a large archive of their undergrad math senior's theses here, and they might be what you're looking for if you don't like my previous idea.


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Benefit of Putnam exam
I am generally interested what are the benefits of Putnam (from both students and Professors' point of view), apart from the fact it is fun (for some) to solve difficult maths problem. I recently read a post on here that a good Putnam score would aid PhD application. If someone would elaborate on this a little, it'd be great.

Maybe the reason the Putnam is in the US has to do with our capitalist values, or some difference in our college cultures?  The Olympiad is international, there is some national pride involved, whereas the Putnam is not.  (When I was in high school in the US, I never heard anything about the IMO.)  Also, at least in some East Asian countries, exam competitions probably viewed differently because of the entrance exam culture.

@VahidShirbisheh this is at University level? interesting.

@Kimball: in the days of Communism, there were many more similar mathematical competitions in Communist countries. As far as I can tell, it has nothing to do with capitalism.

@PeterShor: That's interesting, though it makes sense.  I was thinking our "capitalist values" might have something to do with motivating competition among individuals.  However I suppose in any country competitions were a good way for governments to identity talented individuals.  I wonder if some of these competitions were related to the Cold War and the like.

The genuine benefits I think all fall in the category of "distinguishing oneself" ... from other applicants to grad school, for example... much as with the IMO (Int'l Math Olympiad).
That is, an otherwise merely-very-good record (out of 100s?!?) can distinguish itself from others by a pretty-darn-good Putnam score. What does it "really" mean? Well, maybe not so much about higher-level mathematics, but the "exclusivity" of "having pretty darn good Putnam score" is undeniable. It's a thing that can be capsulized and "explained" to the public in PR, whereas it's harder to popularly explain progress or work in genuine mathematics (without severe distortions...)
Even at beginning-undergrad levels, kids who do at-all-well on the Putnam get substantial recognition within their math dept, often are treated more forgivingly of other quirks or inconsistent performances in routine coursework. (Given the stodginess of much of the routine undergrad curriculum, this is a good thing, since it is completely reasonable to not quite be able to consistently comply with the apparent requirements...)
The flip side is that there's a hazard here, as in all contest-math, that the quick gratification (if one receives it...) may make long-term study and research look less rewarding in comparison. In happy cases, one can "warm" to more prolonged projects, and more-delayed gratification. But quick contest-things like Putnam can be encouraging, and are noticeable pluses on a CV or grad school application. Just should not be over-interpreted.


text:
How to describe the relation between a course instructor to his teaching assistant?
How do you describe the relation between a course instructor to his teaching assistant? Is he the "teaching supervisor" to his TA? This is encountered during PhD application. Thanks!

I think the answer is between supervisor and mentor.

I agree that "mentor" is a terrible choice (never use "mentor" like it's a job title).  I would usually write something like "TA for course MATH XYZ, taught by A. Nobody."  If the professor actually provided some kind of training or something, you can discuss that, but otherwise phrase things in terms of your relationship to the course, not the professor.

@user14449: I wouldn't be so quick to say that a professor wouldn't mentor his teaching assistants with respect to honing their teaching skills. Also, the question is asking for another word to describe "the professor for whom I served as a teaching assistant." While scaaahu's answer isn't 100% correct, it's not completely wrong, either.

It sounds like the question is that you need to fill in the "In what context have you known the applicant" box on a PhD recommendation letter.
If this is the case, then, for this particular point, I would not list "research supervisor," since this is clearly a teaching situation. However, "student" also doesn't make any sense. So, if there's no specific option which clearly satisfies this, I would check off the "other" box, fill in "teaching supervisor," and then explain the relationship clearly in the text of the recommendation letter itself.

"I was her teaching assistant" also works.


text:
What would you call the temporary advisor assigned after enrolment?
What would you call the temporary advisor assigned to a PhD student upon enrolment, who is in charge of the student until the student finds his/her research advisor? "temporary advisor", or "course advisor", or ...? Thanks!

Their first name.

@JeffE: In application to other PhD programs.

In the program where I currently work, we call such advisors "academic advisors," which makes the distinction with the "research advisor" or "thesis advisor" fairly obvious.

I'd imagine the particular terminology varies from one department to another.  I've heard that called a "provisional" advisor.  In my department you start with a "provisional committee" of two people.  The provisional advisor is assigned based on the student's research interests, so often they wind up being the "real" advisor too, later on.


text:
Where to advertise PhD positions without paying a fee?
We have several opening in our group working in the field of computer science and electrical engineering (more specifically digital system design). We put an advertisement in our webpage and also another in the university portal. But we don't have applicants yet. I was looking for some websites to advertise the positions. I found that most of these websites (e.g. researchgate) ask for money. Do you know any website for advertising phd positions for free?

There are some field-specific websites, but they often charge a listing fee. If some money can be found to pay for the listing fee(s), and the site gets a wide exposure, it is absolutely worth advertising. You'll get more high quality applicants to choose from, and the cost of the advert is usually trivial in comparison to the cost of supporting a PhD student for 3+ years. If your positions are unpaid, it might be inappropriate or forbidden to advertise on job websites.

I frequently get announcements from different mailing lists of projects and departments. Send it to your colleagues and ask them to forward it to interested parties.

@Ronald I modified the question according to your suggestion.

If you add the exact fields of electrical engineering you might get more specific answers. For example, if it involves power systems / smart grids, then I would suggest to post on PowerGlobe mailing list.

@electrique I added the exact field

Euraxess may be an option. Its openings are quite heterogeneous (sciences and humanities). Despite the name, it is not restricted to European countries.
There are other free scholarship aggregators like scholarship-positions.com. If you search academia.stackexchange you may be able to find others.
Also, you may be able to find reddit channels associated to your area. At least in computer science it is not uncommon to see such openings posted there.
Another option is trying to locate a google group where other labs in your field post their openings.

@ncasas has given a good answer. Two additional options are

Mailing lists - some disciplines/areas of expertise use these to advertise. For instance, I have frequently seen PhD and research positions advertised on the AIS mailing list, a mailing list used amongst information systems research, and on the an SEM mailing list, a mailing list used by researcher who use structural equation modelling in their research. If you can find either type of mailing list (i.e., related to your discipline, or your areas of expertise) then those would be good places to advertise.
Internal mailing lists. I occasionally hear about positions from my supervisor or others in the school who receive emails from others who ask them to advertise positions within the school. If you have contacts in good universities who may have graduating students who might be interested in your positions, then you could probably pursue this option.

You could also use:

Social media - like twitter or specific groups on facebook
Blogs - if there are some scientific blogs about your discipline/area you could write an email to an author and ask him/her if he/she could post this advertisement


text:
Are reviewers required to check for originality?
Suppose a person writes a research paper without doing a complete literature survey, and sends it to a peer-reviewed journal. Assume that the results in question have been obtained before by someone else.  Is it mandatory for journal editors to check the novelty? If not and if the editors also don't know about the pre-existence of this research, then who is liable for the aftermath?

Depends on whether the authors deliberately stole someone else's ideas.  In mathematics, concepts are rediscovered many years later.  This doesn't mean the authors stole the ideas.  They just didn't know that another author had the same ideas before.  For example, it's written in a different language.  You can also ask a similar question: if the ideas existed in a different language, and you didn't know about it because you can't read said language, who is liable if you publish the ideas?

There are examples of people in application fields "discovering" and publishing (in highly-regarded journals) well-known mathematical techniques, decades or centuries after the original mathematical publication.  As far as I know there is no real "aftermath" to these publications.

It happens in engineering as well. Nobody reads 50-year-old books on engineering for insight, and of course they don't include any computer-based methods (and they probably aren't on the internet either). So people write papers about this wonderful "new" insight they just discovered...

Bear in mind that almost no literature survey is "complete" in the sense of having read all previously published works which might have introduced a concept or idea. While access has been increasing for the past few centuries, so has the number of papers which would need to be read.

Who is liable for the aftermath?  The author, and only the author.

As I see it, the reviewers and editors don't have an obligation to redo the literature search.  However, the reviewer should be someone who is sufficiently familiar with the topic that they would be reasonably likely to know about relevant prior work, and should be able to identify serious omissions in the literature search. A reviewer who doesn't have that level of expertise should not be assigned, and if assigned should probably decline to review the paper.
Of course, if the reviewer does know about prior work that duplicates the paper under review, then they should require the authors to cite it, and evaluate the paper based on its novel contributions only, if any (or as an independent simultaneous discovery, if the timing makes that a possibility).
Final responsibility for the content of the paper always rests with the authors alone.  However, if the paper is accepted and later found to be a rediscovery, a common course of action is to print an "acknowledgement of priority", a short note citing the previous paper and acknowledging that it was first.  Typically it wouldn't be retracted.  (Of course this only applies if the editors believe the paper is really an honest independent rediscovery; if it is plagiarism then it should be retracted.)

+1, with emphasis on the fact that "duplicate" work can imply parallel work and not necessarily plagiarism. The works need not actually "seem" to be alike to duplicate results. Good reviewers know the field, but aren't infallible.

There are around 20,000 papers added to Pubmed each week. Even my narrow field adds 230 a week. Being able to know all the relevant literature for a paper is impossible. Thus it is not a question of whether the current work missed anything from the literature review, but how important are the things that are almost certainly missing.
Part of the job of a reviewer is to be familier with a field and to know whether there are any glaring omissions in the review. Anything in any of the interdisciplinary journals or the fields top in-house journals. They might do a quick search to see if anything blindingly obvious jumps out that the happened not to know about. But no one can be certain that something important hasn't been missed.


text:
How can I migrate a library from Calibre to Zotero?
I've got a well organized Calibre library, but due to full text PDF search, web clipping and basic bibliography management, I decided to move to Zotero.
I can import .bib records easily, but is there a way to have them linked with corresponding PDFs?

You could possibly ask this at http://tex.stackexchange.com if it is on-topic for them

I thought about that first, but was afraid of the very same beurocracy: strictly speaking, this isn't more tex than academia :) Will try nextdoor anyway.

@gman I really don't think this would be on topic at TeX. I don't see any reason it should be off topic here, given that software questions are not inherently off topic

@JustinasDūdėnas note that cross posting is not allowed on SE, so if you want to post this on TeX (though I wouldn't recommend it), delete it here first.

Are you asking about migrating PDFs from Calibre specifically, or just adding PDF files to Zotero records? If the latter, there's this

I think this is on topic -- it is about software that is used by many academics.

Is there any way you can get a link to the PDFs exported from Calibre? If so, it's almost certainly possible to import it into Zotero

Discussion here suggests that you can export a Calibre catalog as BibTeX

click the arrow next to convert books and create a catalog in bibtex format.
  ...
  (you have to select at least 3 [books])

You can then import the BibTeX into Zotero. Whether that transfers PDFs, comments, and tags depends on the ability of Calibre to export that metadata (all of it is supported by BibTeX).
A thread on Zotero forums indicates that Calibre may sometimes assign "silly dates", so you may want to look over your library after import.

I have identified the origin of these silly publication dates (Jan. 1st, year 101): that's the metadata I have in my calibre database for some e-books, probably a default value assigned by calibre when a specific date isn't available in the imported document and designed to stand out when sorted in ascending or descending order.

Alternatively, if you want Zotero to try and find the metadata for your books, you can just drag and drop the PDFs into Zotero and use the Retrieve Metadata function to look up metadata. May even want to combine both approaches and merge duplicates at the end (by selecting the best metadata from both software).


text:
Why should I write a good undergraduate thesis?
I am nearing the end of a semester-long bachelor thesis in computer science. My supervisor suggested I set aside the last month (around 20 working days) for actually writing the thesis document. As such, I have begun this period now.
Why is a thesis important?
Given limited time, I am confused as to why I need to write a good thesis. I am not against writing it, I just want to understand why a good thesis is important so that I can optimize my time accordingly and focus on the important sections.
For instance, if I were writing a paper for a conference, my goal would be to convince potential reviewers (as well as the research community in general) about the merit of my proposed ideas and their novel contributions. As such, I know the intended audience and the intended message for such a paper. Along these lines, who is the intended audience and what is the intended message for a bachelor thesis? Firstly, I doubt many would be interested in reading a bachelor thesis, so this confuses me when I think about who I am writing this thesis for. Secondly, should I consider the intended message as convincing the reader of my ideas, in which case the thesis essentially becomes a long research paper?
I am dealing with these questions because I've found that I can write better and more persuasive matter when I think from the reader's point of view with a clear message to convey to him/her. But currently, I am neither clear about the audience nor about the point to make with my thesis.
I spoke to my supervisor about this. He said the thesis document is a report of all the research activities I did during the time allotted for it, which includes all experiments irrespective of their results. In contrast, a research paper focuses on one method which worked very well. With this in mind, one could say that the intent of my thesis is to inform, so that all experiments (with positive or negative results) serve as some kind of knowledge contribution to the research community. However, this still leaves the question of who the reader is, what should I assume about them, etc.
Which sections are the most important in my thesis?
Part of the reason for asking the former question is to obtain an answer for this question. Which sections are the most important in a thesis and why? From my understanding, the sections which stand out (like the abstract, introduction and conclusion) are the most important as they're the most likely to be read by potential thesis examiners, peers, etc.
Is there any other section that I should especially focus on?

Welcome to Academia.SE. I'm afraid questions about undergraduate matters are considered off-topic here, so your question is not well-suited to this site.

@JessicaB I had read the scope mentioned here, where only questions about undergraduate admissions and undergraduate life (examples indicated extra-curricular life) were considered off-topic. Moreover, I found the bachelor tag, which is why it never occurred to me that my question could be off-topic. Please correct me if I'm misinformed :)

@JessicaB: Please also remember this. (And even with the old convoluted rules, this question would have been on-topic, since it does translate to master’s theses.)

The real problem is that this is ten questions, not one.

Somehow lost in all the comments and answers (but maybe I've missed it) is anything about what I would have thought was the most important reason for doing this, namely learning how to effectively write technical/scientific exposition. Whether you go directly into industry or continue in academics, you're going to have to write about what you and others have done (e.g. grant applications, a summary of your company's team's work on some recent project, papers for publication, performance reviews of people under you in which you have to describe their work, etc.).

Just came across this quote: '“Whatever your life’s work is, do it well. ... As one college president said, ‘A man should do his job so well that the living, the dead, and the unborn could do it no better.’ If it falls to your lot to be a street sweeper, sweep streets like Michelangelo painted pictures, like Shakespeare wrote poetry, like Beethoven composed music; sweep streets so well that all the host of Heaven and earth will have to pause and say, ‘Here lived a great street sweeper, who swept his job well.'” Martin Luther King Jr.

The audience
The correct, but somewhat cynical answer is that the main audience for a thesis or dissertation is the examiners. They'll have to grade it (or at least sign off on it), so you want to convince them to give you the grade you want. The next audience you'll want to target is actually yourself.
Some years from now you'll have forgotten some of the details. You can try to track them down again, but if you've written stuff down in a format that's helpful to you it's going to be a lot quicker and less painful. Basically, if you write the document well it can be a great reference. (I admittedly haven't opened my bachelor thesis many times, but I looked something up in my Masters thesis just yesterday.) Sometimes the thesis can also be useful for students doing their projects on the same topic, in the same research group, etc.
The other big point is that writing the thesis is supposed to be practice for future writing of e.g. dissertations or papers.
What sections are most important?
From the practice angle, all of them. To convince your examiners, probably introduction, results and conclusions - but different people will have different priorities. However, it's a case where you have a few people who are supposed to read your thesis, so an excellent abstract is less important than in a research paper. Basically, you want to show that you understand the field, and have done good work.

I recently finished a Bachelor's thesis in physics, and the faculty I asked for advice generally agreed with what has been said: that your target audience is the examiners and yourself. While correct, I know that I found that a bit demoralizing--this was a project I'd been working on four years and cared a lot about, and writing about it for a group of professors who just wanted to get through it as quickly as possible seemed like a let down--so I took some advice for my adviser and wrote it for a future incoming student in the lab (whether such a student is ever likely to read my thesis or not didn't really matter). Basically, I wrote for myself four years ago, before I joined the lab, discussing everything I'd learned about the project and how the lab worked and explaining all of the nuances of our research that I'd learned the hard way, as well as of course discussing the results of my research project, suggestions for future work, etc. Imagining an actually interested audience who could learn something from my work made the process a lot less painful, and I think it also made my thesis significantly better, because it forced me to actually take the time to explain why I did each step of the project and the theoretical backing behind the experiment, rather than assuming that my audience had prior knowledge of these topics. (I worried a lot that I included too many "intro-level" details about my project, but all of my evaluators actually gave positive feedback on that.)
So, the point I wanted to make here is, yes, your adviser/evaluators are your "actual" audience, but if that seems intimidating or unhelpful to you, you can always imagine a different audience to give your work more of a purpose. As others have said, the main purpose is to show that you have done significant work, learned scientific thinking, and can explain it all clearly, and that should come through regardless of who you have in your head as your audience.

You don't say what program you are enrolled in, but I am going to answer this from a sciences point of view. Undoubtedly much of this will also apply to other subjects.
The final year research project is often the culmination of the entire degree program. Within such a module you are expected to demonstrate that you can behave, think, write and perform like a scientist. In contrast to other modules, where the aim is to demonstrate that you can learn, understand and apply the knowledge that others have accumulated, here you must demonstrate that you can generate your own knowledge and approach the world with a "scientific" frame of mind.
In the ideal world, all undergraduates would have exciting, well-designed thesis topics, which, if correctly executed at a level that can be expected from an undergraduate, would produce interesting conclusions irrespective of which way the results turn out.  We do not live in this world. Thus, in an undergraduate project, you must be able to demonstrate the required attributes, even if not everything you did (or anything you did) produced exciting results.
I do not think it is cynical to suggest that the target audience for  your thesis is the person marking it (be that your supervisor or some other examiner). The purpose is to convince said person that you can use your assigned topic to show your ability to think, act and write like a professional scientist. Convince them that you can set your topic and your results in the relevant existing knowledge, that you understand the design of the experiments, that you understand the limitations of the data collected, if things didn't work that you either understand why they didn't, OR have strong ideas for how you might investigate the causes of the failures and that you understand what your results say about your original topic.
The way you do this is by writing a document that looks like the sort of document a professional scientist might write (or more accurately, the platonic ideal of a professional scientist might write).

Let me suggest that the audience consists of two people. Your advisor and yourself. Your advisor is an important part of the audience since he will grade it and (hopefully) give you feedback on both the content and the writing.
You are part of the audience since at the point you are in academia, you simply need the practice of technical writing and carefully organizing your thoughts and arguments.
However, some things you say imply that this is more of an "experience report" than a true thesis, and that may be the core of your dilemma.
Research is a plunge into the unknown. Sometimes we find that what we thought was true turns out to be false. That is knowledge, just the same as learning that it was true. Of course, you need to provide the evidence that leads you to your final conclusion in either case. But no research is a "failure" unless it is carried out improperly or carelessly.
But the advice to lay out what you have learned in a coherent way is good advice. Write for your advisor. Write for yourself. Maybe more will come of it, but that is all that is needed at this level.

The convincing part should be done by the research, the text should only be a clear representation of that. If you have a result, then I may find that convincing because you told my how you got there and I found that approach convincing. I should not find that result convincing because you said that in a certain way. The text is important because it should be clear, but the convincing is not done by the text. For example, be sparing with adjectives: you give the evidence, the reader decides for her or himself whether that is strong evidence (or not).
When I grade a bachelor thesis I don't value the abstract. The introduction and conclusion play very specific roles. The introduction poses the research question, the conclusion answers the research question. I do grade those parts, but I pretty much ignore the rest. Most of the grading happens in between. I need to see a clear line, which typically helped a lot if you follow the standard format in your discipline. Maybe you are allowed to deviate from that, but experience tells us that that almost always ends in a disaster. If some part is weaker, then that will cost you.

As an undergraduate in a science field, it is unlikely that you've produced anything publishable, but you can always look into undergraduate or other smaller journals/conferences as a venue. If you think you have a publishable core (and I'm guessing this is likely why you're here), consider taking the time to write it in a way that you think might be publishable, but communicate your intention to do this with your professor upfront. Ideally, if your goal was to produce something publishable, your advisor should have known this from the start, but hey, we all are where we all are. I will never advise against trying to publish your undergraduate thesis (it's what I did in a history field), but just know it will take many hours of editing, adding, and improving to make it happen.
If you have no interest in publishing it, then write it up the way that will be most useful to you in the future or the way that will make it the most fun to write. Either way will let you highlight the things you are proud of/enjoyed doing and get through the boring stuff quickly. If you go this route, have fun with it. Create a unique acrostic with section headings, try out a unique way of organizing everything, add in a running joke, or do whatever you want to make the paper a fun reference to look back on.
It's 50/50 that this is your only undergraduate paper you'll ever read again, so whatever you decide just do something that will make the memory of writing it happy and not just a thing you did begrudgingly.