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Assessing bias in experiments on immortalized cell lines?
I'm writing a systematic review on endothelial cell cultures undergoing a certain treatment. In all studies included, the cultures come from an immortalized cell line. I'm assessing bias in the studies, following the Cochrane tool for critical appraisal, and noticed that many of the protocols do not describe random allocation of treatments. Furthermore, the Cochrane tool is specifically developed for RCTs, and a few of the questions feel only loosely applicable to the specific conditions of in vitro studies. As far as I know, there's no critical appraisal tool specifically developed for in vitro studies of cells, only human or animal studies.
I'm probably getting caught in the weeds here, but I have a few questions. Would random allocation of treatment vs no treatment potentially harm validity, if all the cells come from the same cell line and are essentially identical? If we deem random allocation non-applicable to the specific context of in vitro cell culture experiments, is it kosher to modify the Cochrane tool and omit random allocation as a criterion?
Hope this makes sense. Thanks for your help.

This question might be more viable in a different site, but, even if people here do deem it too technical, it seems to me a very good question... :)

Welcome to Academia SE! This is a great question, but it is outside the scope of this particular site. Note in the desccription of appropriate topics at https://academia.stackexchange.com/help/on-topic: "Please do not ask … about the content of research and coursework rather than the processes of researching, teaching, and learning. Most likely, there is a Stack Exchange site dedicated to your field, where such questions are a good fit. If not, you may help creating a new site on Area 51."

I think you should be able to get an appropriate answer on the Medical Sciences SE instead: https://medicalsciences.stackexchange.com/

Thank you all so much! English is a second language for me and I didn't immediately understand the difference between content and process of research. I see now, and I'll repost.

I’m voting to close this question because it has now been cross-posted at https://medicalsciences.stackexchange.com/questions/32528/assessing-bias-for-in-vitro-cell-culture-studies


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How helpful is a github portfolio of everything learnt in engineering school for higher academics?
I'm an engineering graduate from Nepal and I'm currently re-studying various concepts that were taught in college in good depth. I'm putting them in my github. Not because they'll help me for something in future, but because I regret not keeping my notes that I made safely and I want to put them safely now. I'm printing them out as well as putting them in github, double backup.
I was brainstorming if showing this portfolio to prospective colleges would be of any help? It's like having a blog but I don't intend to generate any money. My main motive is one I already said above, other is to have others collaborate and point out flaws in my understanding.
Currently, I am working as systems administrator.
I'm asking this if this is worth showing for or not. For graduate admissions? I've really low gpa (70%, A good gpa in engineering is 80%), and I'm looking for ways to overcompensate it. I've not found anything yet.

You need to be careful about copyright.

Can you elaborate? I didn't get it. Copyright from whose pov?

You can put your own notes, since you own copyright, but putting up the professor's notes and handouts and such can be a problem. You can't republish the work of others, especially if doing so reduces the value of it, such as can be the case with exercise solutions and such.

No, I'm putting my own notes.

If you want them usable by others, it would be good to state an explicit license.

While the exercise of placing your notes on Github might help you keep things organized, I would not hold out much hope of either anyone else reviewing your notes and pointing out flaws, or of any grad school admissions folks going through it to evaluate it.

"It's like having a blog but I don't intend to generate any money" Do people write blogs intending to generate money?

@AzorAhai-him- There are blog sites that facilitate contributors making money, like Medium.

Generally, the organized form of knowledge that people learn from are books. Textbooks in particular are typically written by experts in a given field and a good textbook writer puts a lot of effort and knowledge into one, often over years or decades of teaching related courses where they encounter the specific difficulties that students face.
So, I guess I'd question a bit the value others would get out of your notes. Wouldn't they be better off starting from a textbook? You may have gotten benefit from making the notes as this activity tends to help solidify knowledge and force you to confront gaps in understanding, but someone else doesn't get the same benefit from just being handed your notes.
I don't think there's really a harm in making them public as long as you're not including copyrighted material and aren't doing things that instructors might find dodgy like posting solutions to problems found in textbooks. I'm not really seeing how your notes will compensate for a low GPA at all, though: they're mostly just evidence you've taken some courses, your grades in those courses seem like better evidence to me. And, I can't imagine people taking the time to edit your notes for you and act as volunteer tutors.
Stack Exchange is probably a better format to ask questions to improve your understanding; it still won't be a way to substitute for a poor GPA but learning to formulate your questions in a useful way for Stack Exchange will help create a library of knowledge here, just make sure you're posting on the right site and following the guidelines on that site for asking good questions.

What can really compensate a low gpa except research experience?

btw, I extensively use stackexchange to solidify my understanding already. I am talking about the pov of proving myself that I'm a dedicated student to prospective college w/o a great gpa.

@knamerakhau For graduate admissions? Research experience is probably more important than GPA (varies by field and country), but GPA may be necessary to get through the initial "filter". The best way to show you're a dedicated student would have been to be successful as a student as demonstrated by your grades. If you put all that effort in and still didn't understand, I don't think there's really a way around that: if there are limited places in graduate school, they may go to people who performed better in their classes. There isn't really a magic button or formula to skip ahead.

Due to some reaons, I could not put effort while in college. Why do you assume so negative of me. SMH

@knamerakhau I'm not assuming anything negative about you, I'm just trying to be realistic. If you're involved in a competitive admissions process, you'll be competing with people who performed better and could put in effort while in college. That's not really fair to you, of course, but it also wouldn't be fair to them otherwise.

source: Stack Exchange

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

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How long to get permission from publishers before reusing your works in the dissertation?
I have a few works published in the ASME and Elsevier. Those works will be my parts of the dissertation. I was wondering if anyone has experience in requesting permissions before reusing those in your dissertation. How long it will take to get permission from the publishers?

Have you checked whether the publishers already have a policy that lets you reproduce your own work in a dissertation/thesis without separate permission?

@BryanKrause I just checked the copyright and it shows "Authors may reproduce and distribute the Paper for non-commercial purposes only. Non-commercial applies only to the sale of the paper per se." Does the dissertation belong to the non-commercial category?

Thanks, @BryanKrause. Good idea to check the copyright.

Elsevier at least has an explicit policy that names dissertations and theses specifically. Are you planning to sell your dissertation? Are you planning to publish your dissertation with someone who will sell it?

@BryanKrause Those are good questions. Definitely not for any profits and interest! I just want to finish my dissertation and get my degree.

The usage of your own published work in your dissertation is so bog-standard that I would simply assume that you can and leave it at that. But good that you are thinking about this, most PhD students (and people posting here) seem to not even be aware that copyright / copyright transfer is a thing.

When you give copyright to a publisher you normally get back a license for certain uses. Use in a dissertation is included in all but very strange situations. The rise of "stapled theses" depends on this. Somewhere there is "small print" that explains the details, possibly on a web site and possibly it was given to you directly when you signed over copyright.
Yes, a dissertation is non-commercial. It doesn't compete with the publisher's interest, and, in fact, enhances the value of the work since it raises the profile of the author.
You can ask your previous editor, of course, but I expect th answer to be "you can use it immediately in a dissertation".
Imagine the opposite case in which publishing implies you can't get your degree because your work can't appear in your dissertation. That would destroy both academia and the publishing industry. Publishers have a vested interest in supporting their authors as long as they don't compete directly with their financial interests.
Caveat: IANAL. There are exceptions to everything.

Thanks, Buffy. I sent an email about the permission to the publisher a few days ago. I still don't get any reply... I don't know how long it will take... Hopefully, they can reply to me soon.

@Simon potentially a long time.

Each conference venue, journal, etc, should have a locatable statement about conditions of re-use.  Most will make allowances for you to use in your dissertation; some will have weird hoops to jump through; some won't give a blanket permission statement; some won't actually have any statement at all.
For those that have generous and easily findable policies, great, just archive that information for later use. But do make sure that you fully understand the terms.
For those that have hoops, or are unclear, or don't grant permission:  You'll have to e-mail someone.  Sometimes that will be obvious.  If not, default to the editor or the conference organizers.  Important note:  Some venues that require you to ask permission will tell you flat out, "Allow so many weeks for us to answer."
Pay attention to that amount of time.  Then add 50%.  If they don't specify a time limit, assume at least a month.

You do not need to wait for permission
The Elsevier copyright agreement states explicitly that an author's rights include the right to

Re-use their own material in new works without permission or
payment (with full acknowledgement of the original article)
[emphasis added] :

Extend an article to book length
Include an article in a subsequent compilation of their own work
Re-use portions, excerpts, and their own figures or tables in other works.

Clearly this would cover your intended use in a thesis.
The ASME pages are not as well organized. Nonetheless, you will find that there is an ACME Rights and Permissions page which includes the following statement about the retained rights of authors ... which I have reproduced in full.

Retained Rights of Authors
Authors retain all proprietary rights in any idea, process, procedure,
or articles of manufacture described in the Paper, including the right
to seek patent protection for them. Authors may perform, lecture,
teach, conduct related research, display all or part of the Paper, and
create derivative works in print or electronic format. Authors may
reproduce and distribute the Paper for non-commercial purposes only.
Non-commercial applies only to the sale of the paper per se. For all
copies of the Paper made by Authors, Authors must acknowledge ASME as
original publisher and include the names of all author(s), the
publication title, and an appropriate copyright notice that identifies
ASME as the copyright holder.

Again, you are on safe ground. Your question does, however, prompt two further thoughts. First, remember that it is wise to store (indefinitely) a copy of the copyright agreement that you (or your corresponding author) signed. Second, there's the question of how I found the pages from which I have quoted. Answer: I used Google and searched for
Elsevier copyright agreement which immediately brought up the page from which I have quoted. I also searched for ACME copyright agreement but that led me into a quagmire. Instead, noting the terms used in the Elsevier agreement, I tried site:acme.org author rights and that produced the relevant page.

I had to do this for my PhD thesis, and there's a very simple answer to this question: go to your article/chapter/whatever on the Elsevier/ASME website and click the link for requesting permissions or rights to the content (as shown in the screenshots below for random Elsevier and ASME journal articles):

These types of links (most publishers have them, nowadays) will usually take you to a 'copyright marketplace'. From here, you make a free account and fill out the electronic form, detailing specifically what you want to use and how you want to use it (could be a figure, table, full article or chapter, etc.).

You will then be told how much the rights for the content will cost and be given a license to use it. None of the content I asked for had any cost attached to it, so you shouldn't worry about that, particularly if you say you created the content (one of the options for the 'Who Will Republish the Content' question is 'Author of requested content').
You will get an answer almost immediately—the only time I did not get an answer immediately (the system works out the cost and permissions automatically–the form isn't reviewed by a human, generally), I received an email within 24 hours with the permissions.
Going through the process means that you are given a little certificate formally giving you permission to use content from a journal or book, which is important to keep, in case someone asks you to prove you were allowed to use the content.
You can use this method to get rights to use other people's content as well; I used several figures from books published by other authors in my thesis after getting permission this way.

The answer is in your copyright agreement with the journal. However, I have never seen an agreement that prevents an article from being used in a dissertation.

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


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Is it normal to partially cover fees to attend the conference by PI for postdoc?
If you are working as a postdoc, would you expect your PI to cover all fees for your conference attendance?
I heard some labs cover all, but I am not sure what is the culture and conditions in here. Thanks.

In my field (biomedical science) it is expected that grant funds cover reasonable travel. Most often those grants are to the PI of a lab, but sometimes post docs have their own grants to cover travel.
In any event, though, this is absolutely a conversation that needs to specifically occur with every conference attended, it is not something to be assumed. The conversation can be started as simply as "Will you/the lab be able to cover my travel to X?" and should occur before plans to attend are made.
Similarly, if someone is "sent" or otherwise compelled to go to a conference, it should absolutely be funded; students, post docs, etc should never be pressured to spend their own funds to attend a conference.
If you are in a field where conference presentations are considered the primary publication mechanism (CS, for example), I would suggest asking explicitly about travel funding before taking a job as a post doc and make sure that your expectations and the PI's expectations about travel (frequency, distance, etc) are compatible.

Likewise, PIs should not expect anyone to travel to a conference they aren't funding them to.

@AzorAhai-him- Absolutely. Added to the answer to cover that.

First of all, if your advisor/supervisor requires you to be at the conference, I would expect that they should also have no problem covering the full travel and lodging costs at the bare minimum. In the vast majority of cases, I would expect they also will cover the conference fees (in case there are any). The main nebulous part, if any, would be the food costs. The convention for how this would be handled depends largely on the home department and the specific conference.
If it's a conference of your choosing, then of course you can't expect to always be funded for that. You will need to work that out with your supervisor (beforehand).

The convention on food costs (and to a lesser extent also e.g. hotel costs) also depends on local tax law.

How would food costs depend on the conference?

@AzorAhai-him- some conferences include full meals, so the registration cost may possibly include the meal cost. But I've also seen conferences with no fees, that also have free meals.

@taw I’ve never seen a free conference or one with full meals ♀

Research budgets should cover people's expenses - and that's also what's normal. The question of whether it's:

The lab/group budget/grant
The PI's research budget/grant
The post-doc's personal budget/grant
The department/university budget/grant

should depend on who got grants or a budget and for what purpose. If you, as a post-doc, have a specific allowance for attending conferences (and it's not too small), then it is normal for you to be expected to actually use it. But if post-docs in your field or your group don't typically have such budgets or allowances, then it is normal for whoever does have them to spend them on researchers attending conferences.
The exception is when there is so little money that funding conference attendance is at the expense of core research activity. I have not been in that situation myself, and at any rate I would expect there is no one universal "normal" in these cases.

PS 1 - Often, in order to normalize there being a personal conference attendance budget - a struggle is required by the organized academic staff, e.g. a union. Sometimes, senior academic staff members might push for this at the department/faculty level or the university level, without require harsher confrontation. Or, contrarily, university management may impose "taxes" on other sources of finance to ensure such budgets or allowances for post-docs and/or graduate students.
PS 2 - It also relatively common, but not as common, to cover conference attendance expenses for conferences you are not presenting anything in. Again, if it's your budget, you can obviously do it.

In some cases (every physics group I've known in the UK) the expectation that a conference fee and travel will be covered by grants so strong that it can be assumed that if you go, you won't be paying for the necessities.  That partly comes from employment law, but PhD students aren't employees and the same expectation holds.
But there would be a discussion about the merits of attending (e.g. internationally, only if presenting) that would include the financial position, as well as the suitability of the conference.  This would include potential co-authors, quite likely including the PI; if the PI/grant holder wasn't a co-author a separate discussion would be a good idea.
In a well-functioning group such a discussion with the PI would be expected even if the attendee had access to their own travel funding.  This is because for a few reasons: you're representing the group so the PI should know in advance; they may know more about the conference and likely attendees, to optimise your attendance - or ask you to meet someone while you're there; it affects the time you have available for other priorities in the lab.

It is commonly expected for funding to be available - as part of any lab - to attend and/or present at relevant conferences. That said, the actual amount available, of course, is specific to each lab’s funding allocation/distribution. While that is completely variable, you - at minimum - should not have to cover your own travel or lodging. At best, your food and transportation should also be covered. At the end of the day, be sure to have this conversation (along with all required documents) with your supervisor/PI.

Discuss and agree first and check your lab policies and the project budget. In our group your are paid to attend a reasonable number of reasonable priced conferences (travel and lodging included in the price) but generally under the condition you have a first authored paper accepted for oral presentation in one of the main conference sessions (I.e. not doctoral consortium preprogram). Whether you get the cost back for a poster depends ( we sometimes allow junior PhD candidates to attend a conference on poster alone). But such rules differ substantially between groups even within a university.


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Marie Curie fellowship - is it possible to defer the start?
I haven't won any MSCA fellowship yet, but in case I were to win at the next round, would it be possible to defer the beginning of the fellowship? (I have an assistant professorship and am involved in a project as PI, it would be better to wait for the end of the probation period for me and for the end of the project, so a deferral of 6-8 months)
Thanks a lot

Why don't you ask the program manager?

Why do you want to apply for a MSC as an assistant professor?

There's not a clear answer from the European Commission, but this guide is a good place to start. I'd suggest following the section called "In case of problems."
Generally, academic fellowship programs let you postpone (or probably more accurately, "revise your start state") for a number of reasons. I'd recommend, when you ask for a revised start date, to cite that you want to ensure the integrity of your current project and would benefit from additional time. Best of luck!


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How to handle Supplementary Instruction of Subject-Deficient Students with language difficulties
I work as a supplemental instructor for students that come out of high school with subject deficiencies. They are admitted as conditional students, and they are required to meet certain benchmarks in order to proceed. These subject deficient students are required to take supplemental courses alongside their first lecture in whatever subject they might be deficient in. The instructors for these supplemental courses, or enhanced labs, are all undergraduate students. We work alongside the professor of the lecture to develop lesson plans that coincide with one another. For example, in a Statistics lecture, the professor will only teach statistics, but in the lab, I work to teach algebra components they missed (or forgot in the case of non-traditional students) alongside reviewing the statistics covered before tests.
Typically, the number one problem is that these conditionally admitted students are on completely different levels from one another. This has its own solution that has always worked well.
That being said, another problem has arisen. I have a student in my lab that speaks very little English. Due to this, he has been struggling severely but hasn't dropped the course due to an incredible perseverance. The issue at hand is that I have absolutely no idea how to support him as an instructor and the professor I'm working with is also at a loss. When consulting with the Academic Support team, they're also at a loss, because we don't have a lot of support for languages from his region.
How should I go about handling this student? At this rate, he will assuredly fail, and I don't want to just leave him to drown. Collegiate statistics can be hard enough for students as it is.

assuming that this student met the English proficiency requirements of your school it is still common for esl students to fail courses due to language issues. this is due to the fact that they have to acquire the language of the course in addition to everyday English.
if you are willing you can try to accommodate this student through providing additional teaching and or additional time for assignments and assessments.
from personal experience for a hard working esl student the second time through id always a charm. as their language skills improve the chances of repeating are drastically reduced.

Do I need to accept that him repeating the course is likely? He is going to additional instruction with the tutoring center, but it doesn't seem to do the trick.

@ryan language acquisition takes varying amounts of time for people. If he has the work ethic he should pull through. It's never impossible to pass but the scenario you described paints a bleak picture

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


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Where should I put a plot that summarizes my entire thesis?
My thesis is structured as:

Introduction
Methods
Study A
Study B
Conclusion
Appendix
Bibliography.

I have a plot that summarizes both study A and study B. The logical place to put it would be the conclusion chapter, but my guide told me to make it text based. I think it's just his preference rather than a formatting rule. But I would put it in the conclusion chapter only if no other way is present.
I was thinking of making it a chapter 5: Results and Discussion, but there isn't enough content for an entire chapter.

If the plot serves as a visual summary of the main contributions and conclusions of your thesis, it can be included in either the conclusion chapter or the introduction. Placing it in the conclusion chapter allows you to provide a concise overview of the key results and highlight the main contributions of your research. On the other hand, including it in the introduction can be helpful in helping readers better understand the importance and contribution of your thesis from the very beginning.
If the plot requires more detailed analysis or discussion, it may be more appropriate to include it in the results/discussion chapter. Here, you can present the plot and provide a comprehensive interpretation of the results, explaining how they align with your research objectives and contribute to the broader field of study.
You could also have multiple versions of such an important plot in different chapters of your thesis. Having a plot that summarizes the findings of your thesis in the introduction can be useful in providing an initial understanding of its importance and contribution. Additionally, you can include a different version of the plot in the conclusion chapter to reinforce the main findings. For a more detailed analysis, consider including a comprehensive version of the plot in the results/discussion chapter. The specific placement of the plot and whether to have a single or multiple versions of that plot will depend on the structure and guidelines of your thesis, so it is advisable to consult with your advisor for their input.

It is hard to say without knowledge of your thesis or figure. I suggest you ask yourself how much background and details are needed to understand the plot?  If it is a conceptual figure illustrating the main results, it might fit well in the introduction. There it can serve as a motivation and guide for the reader what to expect. However, if the figure only makes sense after reading both studies then that constrains the figure placement. If your advisor wants the conclusion chapter to be purely text-based, and you want to avoid a very short discussion chapter, you could consider putting the plot in a discussion section at the end of the Study B chapter.

Just an addon to the above. I have seen work where the final conclusion (in your case the comparison figure) is in the Introduction where the authors state that this is the finding of this work and will be explained how we arrived to this by the end of the thesis...
But in general, listen to your advisor, he must have a reason for a text only based conclusion.


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Should I ask the professor, whether he can give funding for masters instead of phd
I recently had an interview with a professor regarding a PhD opening in their research group, for which I applied and successfully interviewed. The professor has offered me the opportunity to pursue a PhD at their university, which is located in the USA. While the university is excellent, I have always had a personal goal to attend a university ranked in the top 100, and eventually progress to a top 20 or even higher-ranking institution. However, since a PhD will be the final degree in my academic career, I am keen to have an affiliation with a prestigious university such as Caltech, MIT, Stanford, and others.
My question is how I can approach the professor to inquire about the possibility of funding for a master's degree only. I want to clarify that my interest in pursuing a master's degree elsewhere is not due to any concerns about the research quality or the professor's group. In fact, I greatly admire their work. My main concern is fulfilling my aspiration of being affiliated with a highly ranked university.

It could help you achieve you goal. It could also (and I find this much more likely) be a way of sabotaging your academic career in the pursuit of an essentially narcissistic goal. The goal of having a successful academic or professional career is a fine one and it might -- or might not -- be that aiming for a top 20 institution is the best way to achieve this in your particular situation. The desire to be "affiliated with a highly ranked university" for its own sake, however, strikes me as a clearly narcissistic one.

To be clear, I don't mean this as an insult -- it's normal to have narcissistic desires of various kinds. I simply mean that it would probably do you well, in terms of both professional success and just general life happiness, to re-examine your deeply held self-image as "someone-who-will-have-gone-to-Stanford".

Preliminary comment: Thinking in terms of ranking is usually not a good idea. You should think of the best place you can be for your specific area of interest. That may be the best groups in a field and yes, they may be at a top-ranked university, but then again, they may be further down that ranking list. Just generically aiming for high-ranked places is not going to advance your career unless you can be motivated by prestige only and you do not care what you do.
Now to your main question: can you ask for MSc studentship only? You can ask, but it is not a good move. If you get offered a PhD and downgrade your acceptance to a MSc, it shows limited committment and interest on your side (and correctly so, given your thinking in terms of ranking), and it's a waste of time by the prof to educate you in a field, only to see you leave.
In fact, many profs would like to upgrade some of their MSc students to PhDs when they are good. The opposite direction is not attractive unless the student is weak.

I don't think that this would be received well (but I also don't think anyone will take it personally). Just be prepared to either have the professor say no or even rescind the offer altogether. Masters are usually not funded, at least not fully. Why would a PI waste funding on someone who will only be around for 1-2 years and will never really do work on the level of a PhD candidate? On top of that, PhD funding is often specifically earmarked - it isn't a free pool of money. I guess if you really don't want to be at a particular university it doesn't hurt to ask since you don't lose anything (other than a guaranteed funded PhD).
So on some level, you have to do whatever you want. If your goal is "go to a top 100 (or top 20) university", shoot your shot. I personally think that rankings are crap and almost always very biased, but that's not really relevant here.
I would caution you about chasing names and prestige in general though. By all means try to go to the best, "highest ranked" university you can. But be aware that many "mid-tier" university are, practically, just as good as the best. There are obviously advantages to having a brand-name degree, but if the program you are considering is solid and fits well then it will probably allow you to get where you want to go. I doubt you will advance that far on degree name alone - you still need to do good work.
That being said, I think the most important consideration is your situation. Do you have any offers from better universities? Do you think you have a realistic shot at a "top tier" university? Why bother to do a master's at this university at all? Why do you feel that you need to go to a highly ranked school?
Your answer to those questions might help you make a decision. You have an offer from a university you describe as excellent with an advisor you "greatly admire". In my experience it is very easy to get greedy when you have a "safe" option in hand. Basically just be realistic.

One correction: we can put MS students on grants like a PhD student. There are no additional restrictions. It's more the matter of your other points. Why invest in someone who will never become as productive as you require?  The most expensive and least productive years for students in research are the first two. I have found two PIs who paid for MS students in 13 years, and it was because they were already admitted and were deemed "special".

You seem to have hit all of the important points. I also doubt that it could happen or that it would be advantageous if it did.

@yourfriendlyresearchadmin I was actually supported by grant money during my masters! But at the time, I was really the only master's level student who received any money and, as you say, I was already admitted (I don't know that I was special though haha). I was referring to university funded spots. I least at my last institution, the department was able to provide funding for some PhD students. This was straight from the school's coffers and did have some restrictions i.e., you couldn't just decide to use it for a master's student. I realize this might be institution specific.

@sErISaNo -- it's not only institution specific, it's school, and department specific.  It really is up to whoever controls the purse strings.  Where I work, that is the PI, who may have discretionary funds or grant funding.  If they don't want to use it, that's the end of the conversation; there are no larger dept funds for this.  At my previous institution, PIs had very little discretionary funding, and it was more likely that students were admitted as PhDs and just left with the MS because it wasn't working out (I worked in Chemistry) -- however, it wasn't planned to be an MS upfront.


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What happens if one of your committee members die after your initial submission?
There is one of the members of my committee that is extremely old (like 80+) and smokes like a chimney. I was already wary of my supervisor pretty much forcing me to include him in my jury committee. Right now he is, supposedly, the only member that has to submit his comments after my initial submission, and every day that goes by I am more and more concerned that he might fall ill or die. What would normally happen if he dies or some debilitating illness doesn't permit him to evaluate me? Would I have to submit to another member of the jury and wait again for my evaluation?

This question is being discussed on Meta.

I'm voting to close, because only but people in this student's program aware of their own rules and procedures can correctly answer this question.

The straight answer to your question, as posted, is: check the rules of your program.
However, I'll answer a related question: How should you prepare in case a committee member dies?
You should get an extra committee member, and ask them to read your thesis. Explain that the old committee member has not evaluated your thesis and that you are concerned. With this strategy, you get the ball rolling. In case your old committee member dies, the extra member is already up to speed and ready to take over without having to restart the process.
However, don't count on it! If he's 80 and smoking, chances are he will live to be 200, and bury YOU :)

That last statement :D ... It's kind of true... I also wondered why professors with such a great career never retire at old age!

Your university will require a certain number of committee members.  If you fall below the minimum, then a new one must be added.
It is too late for you now, but in general I suggest having an extra committee member.

Who knows? It depends on the specific rules in your institution, which may or may not cover this particular situation. If there is no rule in your institution for that case, than someone in power will make a decision when necessary. Usually, the institution tries to be reasonable when something like this happens.


text:
How do I publish my book free as a free to read website with webpages?
I saw a website where authors have published their entire book as a website. How can I also do it? Which website gives such tools?
http://www.feat.engineering/

How about a Gitlab or Github repo?

The source says the page was generated using bookdown 0.11.1 and GitBook 2.6.7. Bookdown itself is described here and seems like a reasonable option if you like R Markdown:

The bookdown package is built on top of R Markdown (http://rmarkdown.rstudio.com), and inherits the simplicity of the Markdown syntax (you can learn the basics in five minutes; see Section 2.1), as well as the possibility of multiple types of output formats (PDF/HTML/Word/…). It has also added features like multi-page HTML output, numbering and cross-referencing figures/tables/sections/equations, inserting parts/appendices, and imported the GitBook style (https://www.gitbook.com) to create elegant and appealing HTML book pages. This book itself is an example of how you can produce a book from a series of R Markdown documents, and both the printed version and the online version can look professional. You can find more examples at https://bookdown.org.

There are also other options, like BookML that's built on LaTeXML.

Thank you! This is very helpful.

There are various way to publish online your book source.
Furthermore to GitBook, you can choose PreTeXt, or if you familiar to programming Sphinx would be a good choice.
One benefit of Sphinx is you can use a free online hosting service.
ReadThedocs.
See some examples.

Abstract Algebra and Its applications : PreTeXt
GNU Scientific Library Manual : Sphinx


text:
Pages: Cite an article from a journal
I want to cite an article from a journal, e.g. AMS.
So in the journal, there are several articles from different authors.
Actually I thought that in my bibliography I have to print "pages 56-67", when these are the pages where you can find the article.
But now I read several times, that I use "652 pages" to show, that the whole journal has this amount of pages.
What is correct?

The number of pages in a journal issue or volume has no bearing on how to find a specific article (which is what the citation is all about providing).

I am curious where you saw that you should use the total journal page count in a citation.

Use the page numbers for the article you cite along with the date and issue number of the journal. I doubt that the "several places" that say otherwise really refer to this situation.

It is not uncommon for bibliographic information about a book to include a statement of the total number of pages it contains. It's particularly common when you look at the bibliographic information from a publisher, rather than in a reference list of cited publications, but it does sometimes occur in bibliographies as well.
In the case of journals, which are indexed by year and issue (among other things), the total number of pages in any particular issue is not of great relevance and most referencing styles do not make allowance for that information to be included. As @ethan-bolker says, it is sufficient (and usual) to state the page or pages where the relevant article can be found.
Note: As a matter of style, rather than substance, some journals give only number of the first page of an article (e.g. 626); others give a page range and full state the relevant pages (e.g. 626-639); and others give a shortened version, where possible, of the page range, omitting redundant digits (e.g. 626-39).


text:
Convention: Comma and period in an enumeration
I am writing a master thesis in maths and I use lots of enumerations in theorems. I am not sure, how I use a comma and period correctly. As I was told, there has to be a comma after an item, except the last, which has to be ended by a period. Like in the following example:

But now I have a more difficult enumeration:

The items itself contain a period at the end. So I would

not end the first item with a comma

and

not end the second item with a period.

But then I have the impression, that I do not use a certain style continuous.
What do you say?

Actually, the structure and meaning are clear without any "end" punctuation at all. Seems pretty inconsequential.

Keep in mind that most people here will be used to producing academic texts in English, and their answers will reflect that. I'm not sure you can safely assume the same conventions apply across languages. I suspect you'd be better off asking your supervisor.

For what it's worth, I generally used sentence punctuation in my PhD thesis (submitted in English at a German institution), but did not use punctuation after conditions like those in your second example (for example). I don't remember if I was following any particular style guide or just doing what felt right to me, but there certainly wasn't any criticism of the formatting.

I've read a lot of math, and I'd say that the commas after the 1 and -1 do not usually appear there.  As for the others, I might change the first period to a semicolon, but wouldn't worry too much about it.

@Mike I would recommend making this an answer

No mathematician here, but just to suggest another solution I would usually add a colon after "gelten" and would use no other punctuation in/between the equations.

Note that the rules for punctuation are different between English and German. I'm not sure whether that affects the answer in the maths case, but in the question, "not sure, how" and "impression, that" the commas are incorrect in English and should be removed (though I believe they are good in German).

Isn't it usual to put the reference to an equation to the right of the equation? Example.

@AndrewMorton in this case, this is acting like an itemized list (like bullet points), so it should be on the left

The problem with punctuation marks in mathematical formulae is that they can appear to be parts of the notation. I personally would not use them.
The way you decide this for yourself is to look at a copy of a classic mathematical text in your field and then copy their style.
If your thesis supervisor has told you to use a certain style, use that style.

(+1) Your first sentence is something that, over the years, I've felt more and more strongly about, at least in my personal writing when I don't have to conform to styles in place by others (e.g. in my day-job writing and editing work).

To me, it's really irritating when someone adds punctuation after a URL, and in copying it, the URL doesn't work.  A similar paradigm would be part of math.  Also, separately, different regions of the world would interpret ',' and '.' differently.

Worse is when a mathematician is so enthusiastic about their result that they add an exclamation mark at the end of the sentence and now you have to guess whether that factorial is part of the formula or not!

@Stef while I don't support the use of exclamation marks in this context, one way to do it is to put it in parentheses "we see that x=0 (!)."

"The problem with punctuation marks in mathematical formulae is that they can appear to be parts of the notation" would you mind providing an example? (And not the exclamation mark/factorial example, as it is pretty rare for an exclamation mark to appear in mathematics.)

@Stef This seems like a really artificial example, as formal mathematical writing should not have exclamation points in it.  Of course, in informal mathematical writing, you can do whatever you want, but then the question is kind of moot, since no one cares what you do on your own time.

Besides the factorial symbol, the question mark symbol is (now) standard for this function. Also, a colon : (sometimes a semicolon ; is used) and a vertical bar | are often used for "such that" in describing a set, and =: is often used for "equality by definition". There is even a double factorial symbol! Although I've never had to deal with a factorial symbol followed by an exclamation symbol, I often deal (my day job) with factorial symbols followed by a question mark.

@XanderHenderson Let's disagree on this. I have no idea where you draw the line between "formal" and "informal" or why you think mathematicians "should" write the way you like rather than another way. As for your last sentence, I don't know what it is that you call "your own time", but given how much work goes into writing a book, I find the contempt of your comment that "no one cares" extremely distasteful.

@Stef It is not contempt nor disdain.  What you write on your own time (i.e. for yourself, not for publication or dissemination) is entirely your own business.  When you are writing for no one but yourself, you can write however you like.  No one else should care what you do with your own notes.  With respect to drawing a line between formal and informal, this is how all writing is done---when you are writing in a formal voice, you are following a narrow set of rules (e.g. as set out by a style guide)---that is what it means to write in a formal style.

An informal writing style can be a lot looser, and most people won't care if it follows some particular set of conventions or rules.  But you generally aren't going to be publishing informal writing anywhere but, for example, a personal blog.

I have to disagree with Thomas Schwart's advice (particularly the first sentence—as a matter of opinion, I don't think that properly punctuated mathematics is ambiguous).  Mathematical sentences, including sentences which contain notation, should be punctuated in accordance with the normal writing standards of the language being written in.
For further details, I would recommend having a style guide handy.  The standard guide for writing mathematics in English is the AMS [American Mathematical Society] Style Guide.  The relevant material for punctuation is in Section 12.7.  Quoting directly from the introduction to that section:

Mathematical expressions, including displayed equations, are treated as phrases or sentences and are punctuated accordingly (see section 13.4).

There is quite a lot of discussion on lists in Chapter 6, and Section 13.11 is relevant with respect to the punctuation of things in the cases environment.
(Of course, if you are writing for a particular advisor or journal or organization or whatever, and that advisor, journal, organization, or whatever tells you to do something different, then do what they ask you to do.)

Regarding Satz 3.1.8(a), I would already dispute the assertion that the item itself contains a period at the end. In my view, the first three commas are dictated by the case-structure of the specific mathematical expression*; but the period is in a slot for a global punctuation mark that treats the entire mathematical expression as a black box. So the rule for what punctuation to put there is the same as in Lemma 3.1.6—that is, the period should be replaced by a comma.**
*People have different conventions for punctuation in case-structures, but my main point doesn't depend on whether those internal commas are used (personally I prefer using them as given).
**It is always a valid optinon (at least in English) to replace a comma by a semicolon if the comma is separating phrases that themselves contain enough commas that the semicolon would add clarity.

Unless you've been given some guidance from the people writing down rules for theses at your university, just pick a style you like for enumeration from a respectable journal in your field, and use it.


text:
What is "educ times"? A journal?
I am looking for the original article about the Cullen numbers. But all I can find is the reference to "Question 15897" in "Educ. times 534, 1905". But I cannot find the "educ times" and I can't find any information, what it is at all. Is it a journal? Can you help me with that?
I found some other articles about Cullen numbers, but they all just refer to the "educ times".

This kind of research is something your local friendly librarian can usually help you with.

see also: https://academia.stackexchange.com/questions/134634/how-can-i-find-an-old-obscure-or-otherwise-inaccessible-paper-when-the-usual-m

This link should take you to an image of the relevant page
https://archive.org/details/educationaltimes58educ/page/534/mode/2up

The Educational Times was a British journal published in the nineteenth century that addressed a wide variety of topics including a section in which readers can propose mathematical questions and submit answers to the questions that have been submitted.

See here under Info > About.
Searching for "Cullen" and going to the second results page (where we find a single entry for December 1905) gives you an entry that is probably what you are looking for:

15897 James S.J. Cullen   58  1905-12-01  James S.J. Cullen   N/A N/A 85  Number Theory

(Some general information about the periodical to supplement Stephan Kolassa's answer)
Some useful information about the Educational Times can be found in Grattan-Guinness's 1992 paper A note on The Educational Times and Mathematical Questions, and in Janet Delve's 2003 paper The College of Preceptors and the Educational Times: Changes for British mathematics education in the mid-nineteenth century, and in Delve's 1999 Ph.D. thesis at Middlesex University [1]. See also the Mathematical Association of America's web page The Educational Times Database: History of the Educational Times and Mathematical Questions, 1847–1918.
The mathematics questions, sometimes with supplementary comments and additional answers (and perhaps even additional questions), were republished in Mathematical Questions and Solutions from the Educational Times.
Many of these periodical volumes can be found at the Internet Archive (Example) and at Google-Books (Example). About a year ago I spent several hours each day for a couple of weeks downloading all the volumes I could find (various google-search strategies were used; 5.6 GB of files total). In case anyone is interested, for Educational Times I was able to get 13 volumes among volumes 14-44 [2] and all of volumes 46-75. For Mathematical Questions and Solutions I managed to get every one of the volumes (75 volumes in 1st series, 29 volumes in 2nd series, 6 volumes in 3rd series).
[1] Incidentally, only the first 197 pages (and Appendix B) of Delve's thesis is online, and thus MISSING are Chapters 5, 6, 7, 8, 9 and the Bibliography -- a total of at least 168 pages. In September 2022 I informed the Middlesex library staff about this, and they eventually told me (February 2023) that apparently a mistake was made during the original digitization, and although after my inquiry they made extensive enquiries to find an original hard copy, they have been unable to locate one or to contact the author.
[2] Specifically, volumes 14, 17, 22, 23, 26, 30, 31, 33, 35, 37, 39, 42, 44.

The Educational Times.
Specifically, Volume LVIII, Dec. 1 1905, p. 534:
enter image description here


text:
Cite an article from an old journal
I want to cite the article on pages 29 - 30 from this journal:
https://www.biodiversitylibrary.org/item/86583#page/7/mode/1up
The cover of the journal is:

So I created a bib-entry and have this:

But if I download the citation from the website https://www.biodiversitylibrary.org/bibliography/39008, I get:

So actually I would say that I can rely on these notes, but the author "Niels Bohr" is not named in the journal.
Is my attempt wrong?

Generally, trust your eyes over an automated citation generator. They're a convenience, not a truthtelling oracle.

@Anyon Thank you, this is very helpful! I always thought that these files are supervised, so that there is no mistake in it.

Lose the biodiversity site.  Why would you use anything other that the original publ8cation?

@ScottSeidman Because the original publication is from 1879, so it's not in stores anymore

@lereu - that has nothing to do with how yu cite it.

@ScottSeidman You asked why i use biodiversity. I suppose it's not a bad source and it's the same journal as I find elsewhere. Tell me if I'm wrong.

You don't need to cite where you got the article.  You need to  cite the article.  Proceedings articles are articles, not books.

Proper citation in MLA, from Google scholar: Pocklington, Henry C. "The determination of the prime or composite nature of large numbers by Fermat's theorem." Proc. Cambridge Philosophical Society, 1914 18 (1914): 29-30.

This paper is indexed in ZBmath, including a bibtex entry: https://zbmath.org/bibtex/02619247.bib

The proper citation in MLA format is

Pocklington, Henry C. "The determination of the prime or composite
nature of large numbers by Fermat's theorem." Proc. Cambridge
Philosophical Society, 1914 18 (1): 29-30.

Proc. Cambridge Philosophical Society is a journal, not a book, so the style you've chosen is incorrect.

I used @article in my bib-file.

@lereu.  Sorry.  The style bibtex or biber chose is incorrect, as "In:" suggests a book.

Which should I use then?

The one in this answer is correct.

Hm, this site tells me that the use of @article is correct (see the box in point 4): https://www.overleaf.com/learn/latex/Bibliography_management_with_bibtex#Enter_(\mathrm{Bib\TeX})

@Lereu It's probably the bibliographic style (bst file) you're using and not the @article that causes the "In" to render.

My guess is that the OP uses biblatex. For some reason, its default style uses 'In:" for journal articles as well.

There's nothing wrong with in, at least not semantically. You are citing a specific article which appeared in this issue of this journal. Sure, a book chapter is in a book, but an article is also in an issue. Yes, the in can be elided, but I don't see why it would be wrong, as such. Not in accordance with MLA, possibly.

"In:", for journal articles, is not in MLA, APA, Chicago, Harvard, or Vancouver styles.

The point of a citation is to make it possible for the reader to find the cited reference. The first one does just that.
Your paper is about mathematics. I wonder why your citation has a biodiversity URL. I would search for a better one. Wikipedia offers https://archive.org/details/proceedingsofcam1718191316camb/page/28/mode/2up with the full text.
My guess would be that the physicist Neils Bohr appears in the second citation because he was one of the editors of these Proceedings, which cover many sciences.

I worry that my surveyor say "citation wrong".
And thank you for the hint, but does it matter from where the journal comes? The journal in your link is the same (and I try to avoid archive links).

The text of the citation tells the reader everything: Author, title, journal, pages. The URL is a bonus feature. Why not offer a link to the full text? You cold avoid the archive by finding the actual page at https://www.biodiversitylibrary.org/item/108208#page/12/mode/1up . I might provide both URLs. I don't know who or what your "surveyor" is.

Surveyors are two profs in univerity that will review my thesis

Your surveyors will be just fine with the first citation, with any URL(s).

The second bib-entry is clearly borked in several ways. Ignore it.

Strongly borked. It seems to be about a different paper: different year of publication, different page numbers, and different author(s).

This isn't really an answer. If you point out how it's "borked", perhaps, but as it stands it is a comment. And not a very informative one, really. I mean, you're not wrong, but you don't tell anyone why you're right.

If @terdon's comment makes you want to include more details, you're welcome to use those in my first comment.


text:
Professor want to discuss my grades
Is good or bad sign that my professor want to discuss my grades on my previous midterm right before class? I’m scared. I believe he’s going to kick me out of class.

Why the plagiarism tag? Is your professor discussing the grade with you because of plagiarism?

Is good or bad sign that my professor want to discuss my grades — depends, are your grades good or bad?

Look at it from the position of the professor. He/she/they see a class full of students. They have done their midterm, and you see some are exceptionally good, and some struggle. You want to speak with both groups. The ones that have done very well, may benefit from some extra material or a more challenging exercise. You want to talk to the ones that did not do well in order to figure out what is going wrong. Is there something you (the professor) can do to help them.


text:
What Types of Publications Are Common in Student Research Competitions at Academic Conferences?
I am interested in understanding the specific types of publications that are typical for student research competitions at academic conferences.
What are the common formats (like extended abstracts, posters, etc.)? How do these differ from other tracks, such as full paper submissions? Also, what criteria are used to evaluate these student submissions?

Why does it matter what's typical? If you want to participate, what matters is how the specific conference you're considering does it.

The only 'student research competition' I'm familiar with is Best Poster awards which clearly are all about your poster (and your presentation of it to the various members of the selection jury).


text:
Why should a publication present results in a way that significantly differs from the discovery of said results?
In the various projects I've worked on, professors have insisted that a writeup for a journal submission should state and prove only the final results (rather than describe the process of arriving at those results). I see how this makes things concise, but it seems to obscure the process of discovery.
Here's an example of this situation from a mathematics paper I've worked on.
What I did:

I have a direct proof for "X".
After looking at my direct proof for "X", I see that I could generalize "X" if I prove "Y" (it was not immediately clear that proving "Y" was useful for proving "X").
I prove "Y", then prove "Generalized X" (duplicating some work from the proof of "X").

What the paper does:

Prove "Y".
Use "Y" to prove "Generalized X".
Refine the proof of "Generalized X" ever so slightly to get "X".

My frustration:
I feel like the paper is good reference material, but it's not educational. I think a reader would stand to benefit much more from a direct proof of "X", since it shows why I would try to show "Y" in the first place.

Folks have expectations of what a paper should look like. You can put the educational stuff on your blog.

Would the direct proof of X be worthy of a paper by itself? Can it stand on its own? In that case, the problem resolves itself - the second paper can refer back to the earlier work in its introduction. But if it's not the case, if it's fairly trivial, then it makes perfect sense to cover trivial-X as an afterthought to Generalized-X.

What will be most useful to readers, for understanding the final result?
The primary purpose of a research paper is communicating its original results.  Educating the reader about how research works in general is great, but should generally be considered a secondary priority in a research article; if you want to focus on that, you can write it up separately in a different venue.
On the other hand, sometimes the final result — if simply given on its own — may seem unmotivated, or overly abstract, and will be difficult for readers to understand.  In that case, it can be very helpful to lead up to it by presenting some edited highlights of the process of discovery.  (Or by giving a worked example, or a high-level overview, or various other things.)
So if your co-authors are really saying “You should always give just the final result!” then they’re being shortsighted and unreasonable.  But if — and I guess this is more likely — they’re suggesting it because they think it’s clearer for readers, then it’s a judgement call about exposition and pedagogy, and you need to discuss it as such.
There’s not much value in recording the process of discovery for its own sake.  There is great value in describing the process of discovery if it will give readers a path to understanding results which otherwise might seem abstract and impenetrable.

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


text:
Courses to take for a statistics PhD
I'm wondering in general how courses from outside statistics/math are viewed in general PhD admissions.
In particular, are courses in graduate economic courses like macroeconomics valued at all or is it just econometrics and nothing else.

It certainly depends on what the school you're applying to and the career you'd like to have. If the school is heavily interested in pharmaceutical statistics for drug development in clinical trials, macroeconomics probably won't be the most important course for you to take. In general though, if you're heading for a PhD, it can't hurt to have a very broad background knowledge on the different application areas in which statistics is used.
I'll also mention that if a course is important to you, you should detail (in your admissions essay or other medium) why and how it helps you to be a better student in statistics. Macroeconomics isn't the same as probability theory, but if you make a convincing argument that your knowledge of macroeconomics has helped you to better understand the field of statistics, then the admissions committee will probably take that into consideration.


text:
Challenges and Considerations in Unfunded Remote Research for Researchers from Restricted Countries
I am interested in understanding the nuances and core objectives of pursuing remote research studies, particularly in scenarios where funding is not available and the researcher's nationality (e.g., Iranian) poses additional challenges.
What are the main goals or benefits for an individual engaging in unfunded remote research, especially when facing restrictions due to their nationality?
I am eager to hear from individuals who have navigated similar challenges or have insights into how researchers can maximize their learning and contribution under such circumstances.

Afaik a lot of similar blocks are topic-related. Probably you can expect more problems in a nuclear chemistry topic as in population genetics. Another option if the project runs in the name of a neutral country, like Saudi Arabia.


text:
How to Professionally Conclude a Collaboration with a Professor to Pursue New Academic Opportunities?
I've had a fruitful period of collaboration with my current professor, but I'm now looking to explore new academic opportunities and challenges. What is the best approach to professionally conclude my existing working relationship with my professor while maintaining a positive rapport?
I would appreciate advice on navigating this transition, ensuring a respectful and appreciative closure, and potentially seeking guidance for my future endeavors.

Depending on the academic area, this frequently seems to be easier when one is changing institution than when when is trying to change one's group of collaborators within the same university. Distance frequently disrupts even the best intentions as far as continuing collaboration go; when the intention is to loosen one's collaboration ties, the move provides a natural break.

what do you mean by conclude? You no longer want to work with the current professor even if there are suitable topic? If not, I don't think you need to conclude.


text:
Handling Research Data from Iran: Ethical Considerations in the Absence of an IRB
Ethical oversight is crucial in academic research, especially when dealing with human subjects. In many countries, Institutional Review Boards (IRBs) provide this oversight. However, in some regions like Iran, no formal IRB system exists. I am interested in understanding this question:
What ethical considerations should be considered when using data collected from human subjects in Iran, where there is no IRB?

That is a great question! It does not only affect Iran but several other countries. We have an epidemiological database that was built in the late 1990s. We still use it today sometimes for certain epidemiological questions / papers. Yes, we still publish with it after 30 years. Opportunities, however, have grown thin. The reason is that many journals require an IRB number. If you cannot provide one, you cannot publish. It is that simple. We had that multiple times now. Imagine the situation: one did nothing wrong but is punished for a lack of standards in a certain country. Of course things changed over the years, however, it is very costly and sometimes impossible to get retrospective approval. To summarize things, please consider the following points:

although an IRB might not exist at this stage in your part of the world, you likely have access to online resources and may still be able to draft your protocol in the best way possible (e.g. with regard to participant rights, data protection, etc.)
although an IRB might not exist, you should still obtain written and oral consent from every single study participant (!)
always (always!) contact the respective journal before submitting your paper and ask the editor whether he would still consider your manuscript despite the circumstances. Else you will experience a lot of frustration.

Finally, I see tons of papers from Iran in my field - many of them have an IRB number. Could you contact researchers from other universities?


text:
Why are Applicants Often Asked to Draft Their Own Recommendation Letters in Academia
As I know, it's not uncommon for professors to ask students to draft their own recommendation letters in academic settings.
Firstly, I want to know how this impacts the authenticity of the recommendation. Writing one's own letter can be challenging, as it's essential to balance highlighting strengths and achievements without sounding boastful. Moreover, ethical concerns arise when students write their letters, which professors sign off.
What are the reasons behind this practice, and how do institutions view it? Also, how can students and professors collaborate to ensure that these letters are ethical and practical?

I don't write LORs for graduate admissions, but have for job applications broadly (academic, national lab, industry jobs). At the very least I want to know how the applicant thinks my letter fits into their application, that is, what I should be focusing my comments on compared with other references. If the applicant does not know, well, that is a good starting point for a discussion. Any outlines or drafts I've gotten serve as a reference to make sure I've covered the appropriate points. I've never signed a LOR the applicant drafted.


text:
Inclusion of a Personal Photo in Academic CVs: Appropriate or Not?
I'm in the process of refining my curriculum vitae (CV) for academic purposes, and I'm contemplating whether to include a personal photograph. This decision seems to vary greatly across different cultures and industries, and I am unsure about the norm within academic circles.
Is including a personal photo in an academic CV generally considered appropriate or advantageous? I am concerned about potential positive or negative biases that might arise from including my picture. Additionally, I'm interested in understanding if the inclusion of a photo is perceived differently in various academic fields or geographical locations.

related: https://academia.stackexchange.com/questions/98364/photo-requirement-on-cv


text:
Feasibility and Legality of Simultaneously Being a TA and RA During a PhD Program in Different Countries
I am currently exploring the possibility of undertaking a PhD and have a query regarding the roles of Teaching Assistant (TA) and Research Assistant (RA). I am particularly interested in understanding the feasibility and legality of holding both positions simultaneously during a PhD program. My questions are as follows:
Is it common or acceptable for PhD students to be both a TA and an RA at the same time?
Are there specific countries or universities where this practice is more prevalent or officially permitted?

It's common to combine partial roles to add up to a full position.
It's not common to have separate full jobs especially at multiple universities. It's possible one or both would consider this fraud. A PhD is a full time position, it's plenty of work by itself. It's not reasonable to expect to do two at once.

Giving Ph.D. students jobs is considered giving them support. These academic jobs are limited in number and therefore, pretty much any university regulates them, with a maximum number of hours and maybe a maximum of pay. Since Ph.D. students are often foreign nationals lacking the right to work in the country of their studies, there is usually another limit, that typically is also enforced by the university.
Thus, you can be a half-time TA, a half-time RA, or a quarter-time TA and a quarter-time RA simultaneously.
If you have the legal right to work outside of the university and do so, then you will be considered a part-time student and usually are not eligible for either.
I am describing this from a US-perspective. Customs in other countries might differ.


text:
Switching Fields in Grad School
Is it Possible to switch to Theoretical Physics from Chemical Engineering ? If so,  how can i do it ?

It would help to know how far along you are in physics, and what courses, if any, you have taken in chem eng.

Possible duplicate of Graduate school admission with a degree in a different field

I am a fresher in Chemical Engineering dept.  our classes will start from 25 th of February . I am currently doing Classical mechanics from  Taylor  and Linear algebra from Strang's book .  Also i covered  some topics from  Griffits's Electrodynamics .

it would be good to add whether you are just switching departments at your same institution, or needing to change schools as well.  Also, indicate your background i theoretical physics.

i am not only switching departments but also schools.

You will need to speak to the different departments on this. You may lose credit for the classes you have already taken in Chem. Engineering since the two fields are different. It is not "impossible", however, these two department might have different requirements for admissions, so you may not be admitted to the Theoretical Physics program. Again, best to speak to your adviser and the departments.


text:
Are rebuttal papers too narrow in scope to get published, and is there an alternative?
When reading a recent philosophy paper I spotted what I believe to be a subtle error in one of the assumptions their main argument relies on. I am not exactly an active participant in academia, so I seek some perspective.
What is the customary way to bring up this kind of observation? Is it a paper submitted to the same journal the original paper was published in?
It seems to me that this kind of rebuttal paper would naturally be quite narrow and possibly quite short, too. Do journals go for that kind of papers? I'd quite like to participate in the discussion the paper in question is part of, and I definitely wouldn't mind submitting a paper of my own, but the narrowness of the scope for the rebuttal paper makes me wonder if it is overreaching.

The nice thing to do would be to write to the authors first. You can also / subsequently / instead post your comments on pubpeer.

As a sidenote, when criticising published work in a formal paper you should be a lot more sure than "I believe". The first step would be to validate that this is indeed an error, including communicating with the author and other experts in the field to ensure that you aren't just misunderstanding.

You could look into whether the journal publishes a suitable content type. Might be titled comment, reply, or something similar.

It is important to note that there is a distinction between an error and a legitimate difference in opinion. This is fairly clear in hard sciences, but in fields like philosophy, you need to understand the norms of the field, and for that you need to work with somebody with experience in academia.

I published something like a rebuttal, or rather a correction, of somebody's paper once. On another occasion, I prepared a technical report with a critique of somebody's results that wasn't published, although I'm considering making a very subtle published version of it. In my case, I don't see a necessity for something like that to be published in a peer-reviewed journal. I could as well publish a report or submit a paper to arXiv. I realise that your preferences and circumstances may be different.

Rebuttals, critiques, commentaries, letters, reply get published. They are handled differently across journals.

What is the customary way to bring up this kind of observation?

Approach varies across fields and policies of each journal

correspondence
letter to editor
discourse
rebuttal, critique, commentary

An approach is to engage the author(s) as professional colleagues. This can be by politely and scientifically pointing out the 'error' and how to rectify.
Another is to write to the editor in similitude to the type one would have written to the author(s).
There are platforms that enables engagement on articles such as PubPeer. When using PubPeer, one might want to take note of

Barbour and Stell (2020)
Ortega (2022)

Talking of platforms, journals and research communities are providing platforms for readers to engage on articles. See for instance this on critical realism and AIS elibrary which allows commenting across many of its published articles.

Is it a paper submitted to the same journal the original paper was published in?

As alluded to, some journals are welcoming of critiques while some ain't. The wordings use and the categories varies. Rebuttal was used in Green and Krasno (1990). Mingers used critique in his rebuttal of Demetis while Demetis and Lee used commentary in their reply.
It is not unusual for commentary having different meaning across journals, hence journals tends to define and/or provided guidelines. A case in point International journal of qualitative studies on health and well-being
[Reference]
Green, D. P., & Krasno, J. S. (1990). Rebuttal to Jacobson's" New evidence for old arguments". American Journal of Political Science, 34(2), 363-372
Demetis, D. S., & Lee, A. S. (2017). Taking the first step with systems theorizing in information systems: A response. Information and Organization, 27(3), 163-170
Berterö, C. (2016). Guidelines for writing a commentary. International journal of qualitative studies on health and well-being, 11(1), 31390

Barbour, B., & Stell, B. M. (2020). PubPeer: Scientific assessment without metrics. Gaming the metrics: Misconduct and manipulation in academic research, 149-155
Ortega, J. L. (2022). Classification and analysis of PubPeer comments: How a web journal club is used. Journal of the Association for Information Science and Technology, 73(5), 655-670


text:
How do I find out if I want to switch to experimental physics for PhD with little experience?
I finished my master in physics and now want to pursue a PhD (or its equivalent), both in Germany. I did my master thesis (1 year) in the field of quantum computing at a research institute, where I continued working and now could do the PhD. This work is at the intersect of computer science and theoretical physics. I like the work and I feel like I get a lot of opportunities there. But I also feel like I lack the excitement about the work that it takes to do a PhD. I always get very excited when hearing about experimental physics. But I am not sure if I had that excitement when working there or if it is rather in the context of listing to other people only. And I feel like I risk a good job that I have for sure now. Also, I have almost no training in experimental matters. I touched maybe twice an oscilloscope. Although, I have read about a number of examples where it worked out despite a lack of experience.
On top of that, I don't want my current boss to know about my doubts about continue working in his group. I feel like it could affect our relationship very badly and maybe I want to continue working with him. He is very well connected in the community and I am afraid that if I contact someone he will hear about that.
So, there are basically two questions: 1) How do I find out if I really want to switch to experimental physics, while working a full-time job? 2) How do I do it without my boss noticing?

If you do not trust your boss, leave as soon as you can.

@AnonymousPhysicist It is not directly about trust. He gives a lot of opportunities (like taking a master student to an international conference), but tends to become quite resentful if he feels like this is not valued the way it should be. I did not consider this to be such a red flag, but I have little experience. What makes you react this way?

"I don't want my current boss to know about my doubts about continue working in his group."  That means you do not trust him.

If your goal is "excitement," do not get a PhD.  "Exciting" research results require a lot of background work that is not exciting.  Maybe try a career in sales. Sales is an example of a field of work where projects reach rapid conclusions.
If you are considering switching from theoretical physics to tabletop experimental physics, ask yourself:

Do I like working with my hands?
Do I like broken stuff?
Can I tolerate relying on other people?  Even if they are weird people?
Can I tolerate continuing to do my existing tasks like calculating and writing? (Yes, experimentalists have to do those too.)

I would not recommend getting a PhD in tabletop experimental physics unless the answer to all the questions is yes.

Thank you. I think these are the type of questions I searched for.           I don't see excitement as the goal but as a prerequisite for good work or at least get somehow through a Phd. If I don't believe that the outcome of my work will be something cool some day in the future, what is the motivation to stand up in the morning?

What exactly do you mean with relying on weird people? How is that specific to experimental physics?

@GreenPhi There are plenty of weird people in other fields.  In tabletop labs, you have to physically share equipment with them - they are unavoidable.  In theoretical and computational research, if you don't like somebody you can stop working with them and they can't take away your essential equipment.

I see. If there are people who dislike each other, does this need to work together rather lead to active rivalry or passive silent tolerating each other, in your experience?

It depends on the individual.

Here's an example of what it's like to work in experimental physics. If you pump atoms into a vacuum with a specific magnetic field & laser beams, you should end up with a magneto-optical trap. So you set up your atom source, your vacuum chamber, your electromagnets, etc., yet when you look at your detector there are no atoms. Something's clearly wrong, but what? Some possibilities could be:

Maybe the atom source has run out and there are no more atoms left.
Maybe there's a leak in the vacuum chamber.
Maybe the laser beams are of slightly incorrect frequency.
Maybe the laser beams aren't aligned properly.

Maybe you check all these things and find that there are still no atoms detected. Time to start thinking about what other things could've gone wrong:

Maybe the vacuum isn't vacuum enough (i.e., the pressure is too high). But the vacuum pump can't bring the pressure any lower. Does the department have a better vacuum pump?
Maybe the lab temperature is too high and this is affecting the trap (does this actually affect the trap? Better check the theory and see if there is an impact).
Maybe the detector is broken. (Buying a new detector could cost a significant amount of money, not to mention paperwork, so are you sure it is broken?)

In the last case you could easily end up with this related problem:

Ok, so the detector is broken and we've ordered a new one, but it will take a couple of weeks to arrive. What do I do in the meantime?

These are the kinds of problems that you'll be solving in an experimental physics PhD. If you enjoy these - as oppose to enjoy reading about the results - then you can consider switching to experimental physics.

Thank you, this is helpful.    I enjoy debugging code (most of the times). I imagine this to be somewhat similar. But there I know what to do and to check. Do you usually spend more time testing things or figuring out what to test?


text:
I'm applying to get a Masters with Transfer and Transient undergraduate semesters during undergrad
After graduating high school, I went to a private out-of-state University for one semester, and it wasn't a good fit (it was a very strict religious institution), and so after the first semester, I became a transient student at a local community college, where I took courses for three semesters.
After getting the required hours I needed to transfer, I enrolled into the flagship University in my state, and graduated from there after three more years with two bachelors degrees- one BA in a modern language, one in BBA in International Business.
During one summer semester, I enrolled in a joint program between the flagship University I was attending, and the University to which I am now applying, for a foreign language program.
There's no academic dishonesty or anything to hide from those earlier schools, but I wasn't sure what is relevant or necessary to include as a part of my academic history.
The application I'm using offers the following guidance: "List each institution after secondary school, Including [University Name], that you have attended or are currently attending."
Additionally, there is no description, or note field where I could offer further explanation.
So, with that as background, here are my questions:
1) Generally, should transfer students put their old institutions on their history, even if they seem to be irrelevant (courses transferred, and graduation from the new University)?
2) Should I put the first religious University as one semester, or three semesters, or not at all? (Technically, I took classes there only one semester, but I was technically enrolled for three.)
3) How should I represent the community college where I was a transient student?
Or, since all credits transferred, do I need to list this institution at all?
4) How should I represent the joint foreign language program I attended between the University I graduated from for both degrees, and the school to which I am now applying? There was no degree for the program, but did offer course credit.
Any and all thought or feedback is appreciated.

In the U.S., for example, your should list all enrollments, and send all transcripts.

So, Transient and Transfer-from school to be included, does that also include the foreign language joint program? I tend to think that if they at least see an attempt to represent that program, that they won't look down on me for their online form not being conducive for showing certain enrollment types.

Admissions committees in the U.S. are well aware that their on-line application set-ups, usually designed by people who have little to do with the actual process, and scant knowledge of it (!!!???), are clumsy and inaccurate. Sure, it's not good to completely mess up the on-line forms, but no one is surprised when there are awkwardnesses.

The irony here is that I'm a software developer by trade. :) Thanks for your advice.


text:
What do camera ready figures mean nowadays?
A journal I am submitting to requires camera-ready figures. What does this term mean nowadays? Does it imply high resolution? My figures are in png format and have 96 dpi. Enlarging it can produce some jagged edges. Should I update them to eps or pdf format?

The journal most likely has DPI requirements for images; you should try to find these out. In any case, 96 DPI is almost certainly too low; 150 is often a bare minimum and 300 or 600 is more standard. PDF or EPS is always best if you can produce your images in that format.

See this question on your attempt to scale the images.

Possible duplicate of What does the term "camera-ready" mean and why is it used?

Thanks. The journal does not specify DPI requirements, but now I also feel 96 DPI is too low. I am re-running my code to generate pdf figures. Actually, when I regenerated the figures in png files, I find there are some very tiny differences between the new pngs and old pngs, which is puzzling given that I am using the same data and the same code. Maybe this is due to I am using different computers/screens. Would this make sense?

@allen Maybe... what software are you using to generate the plots and what kind of differences are you seeing? I know in R(ggplot) changing the figure size can change the size of the labels etc. and requires some finessing.

@ekl I am using stata (graphic export). I am convinced now that it is likely be due to different computers/screens. I am plotting one year of daily data where I see a very tiny difference at one place of sharp transition. If I change the frequency of plotting to monthly, I see no difference at all, even at places with similar sharpness of transition.

There isn't any real, single standard as to what "camera-ready figures" means. Different journals/publishers may use different publishing processes and workflows, which can result in different requirements for file formats, resolution etc. (Or even color spaces.) However, 96 dpi is indeed quite low. 300 dpi is a more reasonable minimum guideline for raster images - but obviously vector graphics should be preferred whenever possible.
In lieu of a standard, we can look at typical recommendations. A review by J.H. Lee in Science Editing titled Handling digital images for publication states that

The most commonly recommended resolution for printing on paper depends on the nature of the images: 1) 300 dpi for color pictures, 2) 300 to 600 dpi for black and white pictures, 3) 600 to 900 dpi for combination art (photo and text), and 4) 900 to 1,200 dpi for line art.

Note that this is the printed dpi, which isn't necessarily the same dpi as seen in the submitted manuscript. The same author also suggests a universal guide to avoid issues with publishers rescaling figures etc.:

It is the opinion of this author that a universal recommendation could help authors prepare their images. The standard figure size of most academic journals is about 86 mm (single column). The standard pixels per inch for line art is 900 to 1,200 ppi. Therefore, an image file of 900 ppi and 4 inches is of sufficient quality for most publications; this means 3,600 pixels in a horizontal line. It is recommended that authors use this number as a universal guide.

Thanks. This is helpful. I will switch to vector image format, pdf.

Here is a rantswer: In my experience (limited to my field) it means "We're a cheap journal that doesn't care about graphics quality, so we let the authors do all the work even if the figures will be subpar." I have never had one of these journals complain about the quality of my figures.
On the other hand, when checking galley proofs, I have complained a few times that my Tikz figures ended up having the wrong font (because the production team changed the manuscript font but copypasted the figures rather than recompiling them). And, guess what, nothing happened.


text:
How to correctly cite a retracted paper?
I would like to cite a particular paper that has been retracted, due to a specific error the authors have initially overseen in their analysis.
Because this specific error is the subject of my discussion, I want to include it as an example.
Now, how do I cite it correctly? For example, ...

Should the citation appear in my list of references?
Am I supposed to use the general citation format; e.g. Smith et al. (2000)?
Should I or am I actually allowed to mention the author's names?
Can I be brief and simply write: Smith et al. (2000, Nature, retracted)?

Are you using a specific citation style (APA, MLA, etc...)?

If you cite the study, then the citation should appear in the list of references.
The exact way to note the retraction varies based on the citation style (e.g. APA, MLA, etc.), as Nate Eldredge mentions in his comment. However, the basic convention seems to be to note the retraction in parenthesis, as an additional part of the original reference. For example:
Ricaurte, G. A., Yuan, J., Hatzidimitriou, G., Cord, B. J., & McCann,
     U.D. (2002, September 27). Severe dopaminergic neurotoxicity in
     primates after a common recreational dose regimen of MDMA.
     Science, 297, 2260-2263. (Retraction published September 12,
     2003, Science, 301, p. 1454)
This example comes from http://blog.apastyle.org/apastyle/2013/01/retraction-action.html, which pertains specifically to APA.