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even if editor said they are prepared to accept the manuscript. but still possible to be rejected?
I submitted my manuscript this July and got comments from two reviewers and two editors. It seems like there was one reviewer no in favor of my manuscript although s/he did not directly say to reject my manuscript though. The other one was positive and said to accept mine with a minor revision. Overall, editors told me in the email that they are prepared to accept my paper. BUT it will be SUBJECT to how I revise the original manuscript. So since then, I have been revising the manuscript and responding to every single question that editors and reviewers raised.
I am trying to be meticulous and working on revising the manuscript thoroughly.
However, I don't want to get my hopes up. It's kind of self-defense mentality I guess.
According to the editors' comment, are there high chances that my manuscript will be accepted as long as I do my job decently? or I don't know, this is my first time to try to get a paper published, I have any idea on this. Is there still possibility of being rejected even if the revision is not so bad?

You're trying too hard to parse what the editor is saying because you think that an editor is some kind of black box that operates on its own rules. But in reality, an editor is just a person like you and I, and if that person says something in plain language, it's a reasonable approach to believe that what they say is actually what they mean. That is, if you got a reply that states...

that they are prepared to accept my paper. BUT it will be SUBJECT to how I revise the original manuscript

then that is exactly what you should assume: If you do a reasonably good job at revising the manuscript, then the editor will accept the paper. There is really not more to it than what it actually says -- read it as if your room mate said it.

Probably, I was trying too hard to understand what the editors said. But getting a paper published is very important and pretty hard in my field, which is why I am obsessed over tiny little things.. But thank you anyway

Yes, it is possible to still be rejected, but you are doing the right thing to make it less likely. "It ain't over 'til it's over" as Yogi Berra once said.
You are probably in good shape. Get a colleague to review your updates, perhaps for some advice on the overall product.

I will definitely hire(?) or ask someone to go over my revised manuscript. I am working on all cylinders so if it will be rejected, I am too depressed and frustrated. I hope that does not happen though. Thank you for your comment!


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PhD Frustration and plans
I have recently (a couple of months) started a Ph.D. in Germany in the field of reinforcement learning, which I try to combine with Optimal Control to give guarantees and /or analyze performance and convergence properties and the like, or at least that was the initial idea.
The thing is, I am not enjoying the experience so far. I was never interested or very good with theory and math proving, but I was applying to many machine learning Ph.D. programs last year, and that was the only one I got accepted in (or at least the first). Because the salary is tolerable and the overall program prestigious, I thought I might as well take the risk and plunge in and push myself out of my comfort zone, even though I was, and still am, very uncertain I would succeed.
I do not like it so far for several reasons, which I will provide for context. First, the lab itself: While the other Ph.D. students are likable people, and I have no issue with them, they are all essentially doing theoretical research in control theory, and one tries to combine it with deep learning. Besides that, there is no machine learning or even much data-driven work. Ergo, I am in a lab where I neither understand nor care about anyone's research, which feels isolating and, quite frankly, useless. There's also the issue of teaching assistance, which I have been told takes substantial time ("We don't have time to do research over an entire semester" time). I can experience it for myself already as I am supposed to be a TA at a theoretical optimization course with material I don't understand.
Then it is the issue of the supervisor. The lab's PI is a super senior Prof with tens of thousands of citations and over 10 Ph.D. students. Mine is a super junior Professor who just started on the tenure track a little over six months now and has two other Ph.D. students. I feel our mindsets don't match my Prof's because he's way too theoretical. At the same time, I am much more software-oriented and even feel he is trying to micromanage me by telling me how many hours I should spend on X course, always letting him know what I am working on, etc.
He is even opposed to the idea of me doing projects outside of work, like an entrepreneurship incubator, because "before I have results, this kind of work, as well as networking, are useless," which I honestly find idiotic. He even lectured me when I let him know I would join, even though I had asked him before applying because he said I should listen to him more and tell him these things like I would tell my friends and some other nonsense. While the program will last around six weeks and require my presence for six days, I still do not think that reaction was warranted or useful. Truth be said, I dislike him increasingly as time passes, and I am afraid I will hate him in a few months.
Finally, there is the issue of the work itself. I just don't find myself excited to try to make sense of papers all day. It feels dull and meaningless. I am still figuring out my exact research topic too. Still, I am thinking of going into more causality-based learning, which I am surprised the Prof sort of accepted after several attempts because while he constantly says he is flexible, the first few times I suggested some topics beyond the very initial rough ideas we had sort of agreed on, that is the theoretical analysis of RL algorithms, he has several times said he is more interested in staying the course on those initial ideas and not exploring more, which feels constricting. I mean, the whole point of a Ph.D. is to explore relevant topics freely, isn't it? Right now, I feel less free here than when working in the industry.
Therefore, and because I do not believe those problems can be overcome, or even that I want to overcome them, I have come up with the following plan: I will give this program some time so that I am confident beyond reasonable belief about these observations and to figure out I indeed do not enjoy or am good at this kind of thing. I want to clear any doubts I may still have while trying very hard to make it work and not have any thoughts about quitting without a fight.
I will minimize my time toiling on my Ph.D., working diligently during my 9-5 but no more. Instead, I will dedicate significant time to upgrading and expanding my data science and software engineering skills and preparing for technical interviews. Then, if in one year the situation has not dramatically improved, I will apply for jobs in the tech area in the US and quit the program after I have secured an offer. If I am asked by employers why I quit the Ph.D., I will sell it as the sort of thing I just realized is not for me, and I want to create value, work with code, etc.
What does the community here think about my thoughts and plan? Is there anything I need to improve or rethink?

This site is not intended for questions of the form "here is my situation, any comments?". That said, you absolutely shouldn't do a Ph.D. in a topic you are not interested in, especially if you don't relate to the research that the rest of the group is doing either. Moreover, if you find reading other people's papers dull and meaningless, it's not clear that doing any Ph.D. at all in CS is a good idea. Finally, it's not true that "the whole point of a Ph.D. is to explore relevant topics freely", and it is reasonable for the advisor to put some constraints on the direction of your research.

This is not the right forum for this type of "question". But for what it's worth, reading your complaints makes me think you're way too far away from where you'd need to be to succeed in your current position. Your goals and judgements seem barely connected to those in your environment. In fact they seem actual opposites. Don't try to fit a square peg through a round hole!

We can only go with what you wrote here, and given that: if you do seriously want to give it another year to decide whether this is for you, then you do need to reflect on and rethink how you view things.
If you are not interested in what anyone else is doing, if after six months you qualify suggestions from your supervisor as idiotic and if you deem a core part of academic research (reading papers) as dull AND if you are convinced that a PhD means unlimited freedom for a PhD student, then you are likely fully unaligned with your PI and your surroundings. It sounds like neither the lab nor the topic nor perhaps a PhD in general is what you want.
Bring this up with your PI as soon as possible. They will want to know your perspective and - especially if they are on a tenure track- there is as at least as much in it for them to make your PhD a success as it is for you. If you cannot come to a better understanding of your respective expectations and responsibilities then don’t prolong your PhD - this is not failure on anyone’s end, sometimes things simply don’t work out and it is in everyone’s interest in the long run to acknowledge that - as hard as that may be and as painful as some of the conversations you are going. to have may be.

Finally, there is the issue of the work itself. I just don't find myself excited to try to make sense of papers all day. It feels dull and meaningless. I am still figuring out my exact research topic too.

Voilà!! You unearthed underlying issue.
For a PhD, give this careful thought and work around and towards it.
Obviously, it's a continual learning/discovery.
In research, you need to make sense of (relevant) papers. Find a strategy that works.
You may check out

Amina Yonis' summarising research papers
Andy Stapleton's How to read and take notes like a PhD - easy, fast, and efficient.

There are tons out there.
Whatever you do, if you desire interest continuing your PhD, don't get to the point of hating your supervisor. You might just get self blocked and wander off ...

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Advisor getting involved in semi-pseudoscience
I am a final year PhD student and recently my advisor started collaborating with some people engaged in what I would call semi-pseudoscience. For the sake of anonymity, I won't give the details but his new collaborators are into various types of alternative medicine.
It's the kind of research that sometimes makes it into reputable venues - often as "letters to the editor" and other barely scholarly things but is mostly found in predatory and other low-quality journals.
And it's clearly connected to selling something - some alternative therapy of whatever.
My advisor has a track record of good research, I've really enjoyed working with him and he's a nice person. On the projects we've worked on together, he has always maintained a very high standard of scientific rigor. So this pseudoscience stuff is unexpected.
I feel like I should say something, but of course I don't want to sour my relationship with him, especially before I complete my PhD. However I'm worried that he might "go down the wrong path."
What should I do?

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

This is your problem, how? It would be interesting to hear how things have progressed in the last year plus.

My research program is based around a technique that I blew off as pseudoscience as a grad student!
In my case, I thought the technique, transcranial electrical stimulation, was unlikely to meaningfully affect brain activity, but a funding agency really wanted to know for sure. I figured that I could do some really careful experiments, drive a stake through the heart of a silly idea, and then move on. In fact, I was most interested in the control conditions, which would test out some other (safer, more conventional) ideas I wanted to work on. However, once the data started coming it, it became clear that it did do something! My initial skepticism wasn't totally unwarranted: the effects were different than some groups had claimed and I certainly wouldn't want to co-sign everything the field has done, some of which still seems dubious to me. Still, digging into how it acts has been a lot of fun. Beyond the science itself, helping nudge (in my own, small way) clinical work onto the "right" path has also been rewarding.
Your advisor may have something similar in mind. It could be an "adversarial collaboration": he and his new collaborators genuinely want to know whether the putative treatment works, and the best way to determine that (especially for skeptics like yourself), is to tackle it with the high standards of scientific rigor that you say your advisor is known for. It may be an indirect route towards something more aligned to his usual research. He may doubt that their green tea extract (or whatever) has any special properties, but the control data collected during these experiments might support his long-standing interest in placebo effects or adenosine receptors[1]. Of course, he could also suspect that there's something to it. "Natural products" have inspired—and indeed, are the actual physical source—of many conventional treatments. Treating pain with flowers sounds preposterous, but opioids like codeine and morphine are still among our best options (and biggest problems). Moreover, the natural source is often the best or only way of producing it. Total synthesis of morphine is possible but so inefficient that most of it is still derived from poppy plants [2].
Thus, consider having a friendly, low-key conversation with your advisor about it. What piqued his interest in this field? What is he hoping to do? How does this fit in with the rest of his research interests? It may be useful and edifying to see how a senior person develops a new line of research. Perhaps he will even persuade you that it's not as crazy as it seems!
Still not convinced? The good news is that it doesn't really matter much to you, personally. You're wrapping up your PhD and are presumably more comfortable with your own thesis topic. You can politely decline new projects in the interests of finishing up and submitting. In fact, you should probably do this anyway! If you are worried about future letters, you hopefully have a thesis committee who can also vouch for you. You should certainly firm up your relationship with them and this is also a good idea anyway too: many fellowships need multiple letters!
Good luck with the rest of your work!
[1] A target of caffeine.
[2] I think. I am neither a licit nor illicit pharmacologist.

"I figured that I could do some really careful experiments" and "In fact, I was most interested in the control conditions,"
Fantastic. If more people would do science based on these premises, and not on "I know what is science" or "my idea will solve the long-standing issue" or even "I know what is right, I just need the data" we would be centuries ahead wrt to where we are now ...

Already gave you thumbs up. You could make it even better by mentioning that some "traditional medicine" has something behind it since it has effects. It may be over-reported results in some cases. It may be placebo in some cases. And it may be very different from what the traditional folks claim. But there are lots of things discovered when these things are investigated. Even if just alternate sources of existing things. I recall an anecdote about a plant that produced sap with 20% caffeine. Locals were in the habit of chewing the twigs for the rush.

@BobaFit: There's also the nocebo effect, in case anyone is interested. Both placebo and nocebo can have significant genuine physiological effects. It's underestimated by many scientists, but of course they can't do anything beyond what the body can do to itself (e.g. neither of them can cure or cause cancer).

Thank you for the answer. We did end up talking about it a little bit. It sounds like he is sufficiently skeptical. He seems to think there is something interesting scientifically in the topic without necessarily buying into the connected miracle cure claims or whatever.

Your answer and the comments made me realize that I've seen lots of research that oversells itself or its applications. It's just that my research (and thus the papers I mostly read) is not connected to health, at least not in a curative way, so the stakes never seemed so high. I realize now that it must be pretty common for bad health advice to be given out based on speculative papers if at all possible.

What makes a field pseudo-scientific are the methods, not the subject. If you can openly discuss results with your advisor and both have high ethics standards, all questions are valid!

It may be worth mentioning that Isaac Newton spent a lot of time practicing alchemy (I'm not sure to what extent the Wikipedia article https://en.wikipedia.org/wiki/Isaac_Newton%27s_occult_studies is accurate, but there are plenty of writings of him on the subject that survived nonetheless). As long as your supervisor maintains good scientific standards in your joint projects and doesn't force you into the activity you find questionable, I would just let it go. Only if he insists on your participation in something that you find unscientific, unethical, or illegal, would it make sense to confront him and firmly but politely refuse.
Besides, some alternative medicine does work, so as long as it is not at the level of ghost busting and exorcism of evil spirits, I would certainly wait a bit before passing the final judgement. Also, remember that, in general, the main objective of interacting with people smarter or more knowledgeable than oneself is to learn from them, not to judge them (though, of course, one is always free to choose what to take and what not to take) ;-)

Side norte: we even have the final solutions to alchemy, it is possible to transform everything into gold. You just need an extreme amount of energy, but in principle we can reassemble neutrons and protons and electrons ;)
So in a sense Newton the physicist was just laying the foundation to solve the alchemy problem he was investigating and alchemy is a consequent problem to understanding physics.

@EarlGrey Sure, but that won't let you refine your soul into something like God. Alchemy had spiritual aspects as well as the physical ones.

"some alternative medicine does work". Well as the saying goes any alternative medicine that works is just called medicine.

@Voo I would add "after some period of time" to your sentence, but otherwise I agree :-).

And more recently a successor of Isaac Newton's at Trinity, Cambridge, namely Prof. Brian Josephson, has devoted most of his life since winning his Nobel Prize in physics to a study of the relationship of mind and matter that has taken him well into the realms of what most people consider quackery. But how do you know it's quackery if you don't study it properly?

@Voo I'm reminded of a quote from Prof A. B. Pippard who defined physics as "everything in science that we fully understand".

Science is a method, not a topic
The mere fact that a person investigates alleged phenomena in a particular field (e.g., alternative medicine) does not make their work scientific, pseudo-scientific or anti-scientific.  What matters is the approach and methodology they bring to the work.  The fact that you presume that working with others who are interested in alternative medicine means that your advisor is involved in pseudo-science means that you are in a poor position (in terms of scientific maturity) to judge this issue.
Experienced academics with good track records of research typically do not require career advice from upstart PhD candidates, notwithstanding the pretentions of the latter to adjudicate for them what is and isn't real science.  Your supervisor sounds experienced enough to make this judgment himself.

I agree with the sentiment, but this seems a bit harsh. Plus, I think the student does have a legit worry: if the prof is going off the rails, letters (etc) from him aren't going to be much help.

Fair enough.  I will leave the answer as is for now, since I think the critical sentiment reflects the reaction that many academics would have to this (and the OP needs to be on notice of that).

I wouldn't just call that statement "a bit harsh", but rather "utterly arrogant". It's important to inform the OP that his advisor may share that sentiment, but that does not necessarily make that sentiment true.

Intelligent and experienced people also make mistakes and are not above criticism. An arrogant appeal to authority does not give support to this point, on the contrary suggest there are no real substance to it other than appealing to a logical fallacy. Not a stereotypically "Academic" remark. (-1)

This statement is alarmingly arrogant, there are many well-known examples of extremely influential physicists going off on very ill-advised detours into pseudoscience later in life.  A few examples: Roger Penrose and Julian Schwinger.  Pascual Jordan invested a large amount of time into nonsensical theories of geology which he could (should?) have been persuaded to leave aside.

The answer does not preclude the possibility of an academic wandering into pseudo-science; it merely takes the view that experienced academics are better placed to judge this than grad-students.

And in the field of Biology which the OP is likely working in, consider the cases of Nobel laureates Kary Mullis and his support of Astrology and denial of AIDS, and Luc Montagnier and his support of homeopathy and the "memory of water". Sadly, experience, knowledge and intelligence seem to be no barrier to falling down a hole of pseudoscience.

I am aware of a PhD student that was severely affected by a supervisor that got them to investigate a pet theory that didn't stand up to cursory examination (I was one of those that pointed out to the supervisor in question, but was ignored).  IIRC they (the student) left academia.  Academic departments do have a responsibility to protect students from supervisors that have "gone emeritus".

Wow... This is about as arrogant as it comes, this statement (from the perspective of the academic) is essentially “I'm right and you're wrong, I'm big and you're small, and there's nothing you can do about it". Sure, PhD candidates are likely missing some context and experience, but it's ridiculous to write off the opinion of (by definition) some of the smartest people in the world just because you're old and have been doing this for a while. People later in their careers in all fields do stupid stuff that fresh talent can see is a bad idea miles off.

Thank god Linus Pauling revealed the magic of taking massive doses of vitamin C, and Michael Atiyah proved the Riemann Hypothesis without any "upstart PhD candidates" stopping them from making fools of themselves first

A truly experienced academic knows to take PhD students' concerns seriously, as they represent a fresh perspective and can help correct for the overconfidence of the advisor in their own ideas. (-1)

@Tom What are you referring to with Penrose and Schwinger?

Penrose - consciousness, Schwinger - cold fusion.

@Tom "consciousness" What about it?

@rhermans It's interesting that you're bringing up "appeal to authority" here. The accusation being made re: "alternative medicine" is itself an "appeal to authority", because it presupposes the only legitimate medicines are the "established" ones mass-produced by multinational pharmaceutical companies.

@llama It is highly inappropriate to bring up Atiyah. His "proof" announcement was in fact made just months before his death. It was obviously an age-related thing, not an evidence point that PhD students can and should determine what constitutes legitimate research for their advisor.

@DikranMarsupial ''gone emeritus'' haha I will have to use that some time.

@Tom I believe it comes from the book "The Languages of Pao" by Jack Vance https://en.wikipedia.org/wiki/The_Languages_of_Pao (which I quite enjoyed reading a while back)

As others have said, there are good reasons to investigate alternative claims.
The only worry is if the prof has become ensnared in something. The signs of this would include such things as being unduly euphoric about results seeming in favor of the alternative thing. Or if the prof were investing money in some scheme to sell the alternative thing as treatment. Or if there was some charismatic "Worm Tongue" whispering in his ear and pushing him into rash actions.
Another possible worrisome thing would be if the "usual" research were pushed aside or curtailed in favor of this alternative stuff. Derailing an established program of research in favor of something deeply speculative would be alarming. Adding a minor interest that does not stop the established work is not necessarily troubling.
So keep your eyes open for warning signs. Try very hard to stay objective. Try to be motivated by the search for the best understanding of the world that you can achieve. Try not to be an advocate for any position. Rather, try to interrogate the data to achieve better understanding.
So keep an open mind. Not so open your brain falls out, but still.
The usual way to do this is to set up an hypothesis and try to test it. Set up objective tests that can explore the hypothesis. Examine the tests carefully before they are performed to assure there is minimal chance of being confused or misled. Things like objective tests, careful stats, double-blind when appropriate, predictions before measurement, and so forth.
If the research is following proper principles of science, then go for it.

I'll try to just directly answer the question of "What should I do?" ('about my advisor getting involved in something I consider pseudo-science')

If its important enough, talk to them.

Polite conversation about the motivations and interest in the subject while trying not to start the conversation with "I'm obviously bias and view this as bad"
Segue into personal concerns (whatever they happen to be).

If you're going to dive into "I'm concerned about you, and what this might do to your career" then treat the topic with some care.  Like some answers have noted, many folks will often take that approach as rather pretentious.
If its "I'm concerned about your new research will do to me" then make sure you have a pretty good idea about what the supposed risk is.  Research has to be pretty bad to completely torpedo the value of recommendation letters from someone with a long track history in a field.
Reason I start with "have a polite conversation that's mostly curiosity and attempting to understand the situation" before diving into recommendations or concerns.

Read about the subject critically.

Is it all pseudo-science?
Are there possible research avenues that might be valid or might simply not have been explored?
Is there some issue with "accepted" approaches that's causing people to look for alternatives?

Ex: "We Hate chemotherapy and how it makes us feel, is there any other choice?"
"Why yes there is" says the Mayo Clinic and Medical News Today.

You can try acupuncture, aromatherapy, hypnosis, meditation, music therapy, ect... to try to deal with the symptoms.
You can try photodynamic therapy, laser therapy, immunotherapy, targeted therapy, or hormone therapy to try to deal with the tumors.

If its still bad after these, finish your PhD, without souring your relationship.

Do quality work you can be proud of
Have publications, references, and other support for your future life so you're not totally dependent on a recommendation from your advisor
Let your advisor worry about their own career (unless there's some "serious" ethical / legal issues)

Unless that was a deliberate pun: segue.

@keshlam Thanks, mentally doing the transliteration of (ˈsɛɡweɪ).  Changed.

I think it's a bit much to go telling your supervisor what research they can and can't do. Even if they were really going off the rails, did a load of fradulent work that totally trashed their reputation and then murdered a few people, I presume there would be other people in the department who could write letters and vouch for you in terms of future applications?
Also, there are plenty of important areas of research that were once widely considered pseudoscience. Cranial oscillations have been considered total crap for at least 100 years and now the MRI guys have developed the techniques to image them they're one of the hottest new discoveries in neuroanatomy.
Absence of evidence is not evidence of absense. That kind of mindset is how we ended up pretending that COVID wasn't airborne, masks woudln't help, and killing people all because of scientific arrogance.

I would imagine that personality structures are rather different in the life sciences than in physics, but my personal experience is that the distance in methodology, interpretation of results, and opinions on philosophy of science (not to mention the slippery things we call "facts") between academics can be mind-boggling without compromising their professional or personal relationships.
And that's a sure sign of a healthy scholastic process in my view---if anything but the most unequivocally crankish dissent is suppressed, de jure or de facto, it risks obstructing genuine improvements in methodology and philosophy. Even restricting to questions of "real science," induction must welcome all criticism, because arbitrarily dead hypotheses can (and do) resurrect: I recall hearing about some 5-sigma accelerator result that gradually evaporated into statistical noise. I can't imagine there have ever been enough people to conduct a medical study of that power, so I find the idea that mere investigation of alternative medicine would cast doubt on someone's academic credibility risible.
An excellent way to handle a situation like this is, individual dynamics permitting, making a meta-joke out of it. It can communicate the dissent in a way that strengthens the relationship, rather than compromises it. I recall stories from my advisor about mutual, good-natured ribbing between him and his advisor about their differences, contentual though they were. Sure enough, when I met the guy, he immediately cracked one about this old disagreement.

I actively avoided excessively soapboxing my discontent with medical methodology in my answer, but suffice it to say I find it concerning that y'all don't get likelihood values that demand measurement in dB...especially given how confident people and governments act with those results in hand.

tl;dr plus extrapolation : medicine is not a science, but quite a good approximation. Economic sciences, on the other hand, are quite a good approximation of crank science.

Cargo-cult science used to be Feymann's way to speak about his contemporary psychologists who did rat psychology. In Feynman's view, they were doing pseudoscience because they were following methods that are unlikely to
Whether or not something is pseudoscience depends on the methods of how it's investigated and not on the subject that's investigated.

I hate how the only thing anyone remembers from that story is "psychology=dumb", especially because it's about a thousand miles from the actual point.

It's not psychology = dumb but psychologists at that time = dumb. The voodoo neuroscience paper would be a more modern paper about a pseudoscience field.

You are a bit too simplistic in associating Cargo-cult with "contemporary psychlogist"
. See https://calteches.library.caltech.edu/51/2/CargoCult.htm . He even mentions that physics is behaving like Cargo-cult science (but of course the fault is on some overarching institutions, not in the people themselves like in Psychology ...) Feynman is right in his criticizing of the methods. Please cite him carefully (or let him rest in peace ... https://caltechletters.org/viewpoints/feynman-harassment-science )

@EarlGrey : I referred to those of his contemporary psychlogists who did rat psychology.

"following methods that are unlikely to": unlikely to what? Generate valid results?

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Extended abstract with references and citations
I am writing an extended abstract (8 000 characters) for a conference* and I am not sure how should I work with references and citations there.

On one hand, abstract is still an abstract, so I guess it should not contain references and in-text citations.
On the other hand, 8 000 characters seems as too many to describe the paper without referencing other papers.

The other problem is that my paper is mostly a review and one of its most important points is the critique of another paper. The rest is based on this, so I guess I should cite it and not dance around like "there was some scientific work before like this... which had mistakes, so...".
The question:
Should I cite it in text but skip references? Or are references allowed in case of extended abstract?

*I don't thing the conference has book of abstracts or conference proceedings, so it seems like the purpose of the abstract is just to provide information to the organizing committee

Since your profile mentions economics, I think this answer is relevant.

Actually, anything you publish that uses the work of others needs citations. Otherwise...misconduct.

@Buffy Yeah, but that is the problem, right... I need to cite other's work, however, abstracts usually must not contain citations... However, in extended abstract of review article, there seems as if there should be a citation. So there are like three opposing reasonings in here of how to approach this problem.

Hmmm. Who says "abstracts usually must not contain citations". Smells a lot like plagiarism if you aren't careful.

My understanding of the "no citations in abstracts" rule is that an abstract should not refer to a separate bibliography, because it might be used somewhere without the bibliography. If the bibliography is included in the abstract or if the cited work is completely identified in the abstract's text (as opposed to a separate bibliography), then I see no problem with such citations.

You definitely need in-line citations in an extended abstract. If I were reviewing conference proposals, I would like to see a full bibliography, but I would probably not reject if the paper didn’t include one and I liked it otherwise.
However, if the extended abstract was going to appear in a conference proceedings (sometimes the case with ASSA) then you will need to add the bibliography. I don’t know if it will be expected to fit within the 8000 characters. You could ask the program chair for a more definitive answer.


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Springer proceedings NOT indexed by Scopus
I am searching for a conference in economics and business. There is one conference that looks relatively OK (less probability of being predatory: according to papers which are published in its proceedings; furthemore, past proceedings were indexed by CPCI with 2 years delay). Importantly, the conference is published as a book by Springer.
I can either write there a paper or just present just an abstract. The thing is, for a work on paper to be justifiable for me, I need the conference proceedings to be either indexed by CPCI, Science, SS&H, or proceedings indexed in Scopus.
Therefore, I have followed this question on StackExchange which was relatively optimistic regarding Springer proceedings being indexed in Scopus.
When I tried to search in Scopus database for indexed conference proceedings in Economics and Business, though, I got only 15 results and proceedings from my conference were not among them. Nevertheless, when I searched Scimagojr I have found the proceedings on their site.
The question:

Is there a possibility of conference proceedings being published by Springer and not indexed by Scopus?
Does conference proceedings being listed on Scimagojr mean something?
How many conference proceedings are published by Springer and not indexed in Scopus?
How can I evaluate with certainty whether conference proceedings are indexed by CPCI, Science, SS&H, or indexed in Scopus?

The thing is, for a work on paper to be justifiable for me, I need the conference proceedings to be either indexed by CPCI, Science, SS&H, or proceedings indexed in Scopus.
You are in the unlucky positions that this conference is not what you formally need, you are bound to some stupid bureaucracy, go to any conference you deem interesting and discuss with your advisor the funding of the trip. For this trip and for the cheapest possible conference respecting the criteria you need to fullfill...

What is your goal? attend this conference because it is very interesting and relevant, or just to fullfill the bureaucratic requirements "attend and publish in a xzy conference"?

I want to think I would like to satisfy both criteria. However, the truth is, attending an interesting conference is just an optional goal now. This conference seems interesting, though, but if it does not meet the criteria I could go there for presentation only (it would not be viable to write a paper as the effort would not have paid out). Otherwise, if it meets them, I would send a whole paper.

Thanks for the explanation. Now you have 4 questions, when in reality the question is only one, i.e. "How can I be sure that a conference is indexed by CPCI, given that the previous one has been indexed with 2 years delay?"

The only relevant question you pose is the last one. And the answer is a boring ask "them" (both conference orgnaizers and indexers).
In your specific case:

furthemore, past proceedings were indexed by CPCI with 2 years delay)

This. Ask whatever CPCI is (and the conference organizers as well) if the conference proceedings will be indexed by CPCI.
If yes, then you have peace of mind (write a paper with them), if no or don't know, then you have peace of mind (of not writing a paper with them).

Thank you. The first question is also important to me, as I previously thought that Springer guarantees indexation in Scopus, but according to Scopus database itself, this might hold hold only in a limited amount of cases. So I wanted to be sure, whether I did not do something wrong during the search.

Springer is a big publisher, it does not mean that everything that Springer publishes is indexed by Scopus.
It may be that every journal published by Springer is indexed by Scopus, some conference proceedings are published as special issue of a certain journal or of a collection (therefore falling under the umbrella of some journal), and some conference proceedings are published as books and not indexed by S... and you can self-publish basically any book with at least a minimum of academic rigorousness with Springer (as an example: https://www.springer.com/gp/campaign/chemistry-book-2 ) ...


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Sending paper to a journal while proposing its shortening right away
The Setup
I hold a prepared and written manuscript (10 500 words of text) focused on argumenting about specific problem in my field of study. This paper has been rejected few times from the most reputable journals and now I stand before the decision to finally send it to the last remaining one of the reputable journals I took inspiration from. However, as this was my first paper I think I might have overreached and plugged almost everything I could in it that I considered relevent for the argument. Now, I start to think that this might be the problem and the reason for rejection, because the paper feels rather like two papers that could be separated.
The Problem
I am pretty confident that the first chapter (2 500 words) of the paper is its strongest point, there is the core of the argument, while the remaining chapters are just supportive evidence and classification of the possible outcomes of the argument. However, there is one substantial problem: The argument on its own is not sufficient for publications as it should contain implications as well (cannot just say: this definition is problematic for this and that reason; must include also, what to make of it). My most profound implication of the argument I present is that it effectively simplifies another argument. But... This implication is laid out in total of 3 chapters on multiple separate positions (around 1 500 words in total) - in the original paper it makes sense as I focus on too many things that are interconnected.
The Idea
And here's the thing... I could shorten the paper, use the first chapter, and rewrite the implication such that it is more compact. Or I could write a cover letter to editors explaining that I do not exactly know what should I let in the paper and propose the afformentioned reduction.
Conclusion:

Is writing a cover letter to editors proposing the shortening of the paper a good custom?
The reduced version of the paper would contain less information but would be more compact.
Shall I send the reduced version right away and just tell there is potentially more to it?

You write that your paper was rejected quite a few times already. What was the feedback that you received from those rejections? Did you address these properly? From what you have written it is not clear whether you bothered to include the suggestions from reviewers to improve your paper.

By mentioning chapters, are you by chance indicating sections of your manuscript?

Are you the only author? Do you have someone from your faculty to provide you feedback? It is better to ask someone established in your field to get involved. The feedback will be more specific compared to answers from this site!

@And: Yeah, I rewrite the paper when I get the rejection. I should have said that I got the desk rejections instead of classical review rejection. Sometimes the feedback was great (once I got 5 pages long reason), but mostly it is just one sentence, sometimes with kinda irrelevant reasons, which makes me think the paper itself is not good enough... To "semmyk": Yes, I meant sections...

@usr1234567 Well, the thing is, I am the only author and I within this paper I try to establish myself in a completely different field than the rest of my faculty, so I actually do not have many people to discuss the paper with. I thought there was the possibility to transfer this request to editors, but mostly the desk rejection is just one sentence long with the feedback being rather polite than sincere. Do you know if there are some services that provide "practice" peer-review feedback for money?

Of course I can't tell but have you considered that the paper may indeed not be good enough for the top level journals? Have you tried to find a more specialist journal with somewhat lower Impact factor that could be a more appropriate venue for your paper? These should still exist with OK reputation.  I think that the current trend that everyone submits to the top journals is bad for science as it creates lots of additional editor and reviewer work that would not be necessary if people would go as soon as possible for a level at which editors are happy to publish the work.

If you think your paper can be shortened by 1,500 words, it can probably be shortened by 3,000... To the extent it's possible, shorter is almost always better.

You shouldn't expect that you can write a paper to establish yourself in a different field - that's a terrible motivation to writing a paper. You need to first start with a deep understanding of some issues within a field, best guided by a mentor who has a lot of experience there, and then start to tackle issues on the edge of what the field knows.

You should not submit the paper to any more journals. Instead, focus on forming working relationships with one or more academics established in this field (at other institutions if there are none in your own), with whom you can test your ideas and writing. That is the only way you will get the feedback you need.

You should submit the best version of your paper that you are capable of submitting. Whether the shorter or longer version is the best version is up to you to figure out.
It's fine to ask editors about flexibility in policies like word counts or figure counts, but it's not their responsibility to read your paper and help you determine its length, only to decide whether the paper you submit is a potential good fit for their journal.
If you want feedback on the length, I'd recommend asking people in your professional network rather than expecting editors to help.

Don't do it. If you submit a paper and promise to shorten it, why not shorten it right away? The editor won't bother sending a draft paper out for review and an improved version of the same paper shortly after. It would just waste everyone's time.

At least in mathematics (my field) it would be normal to say in a cover letter to an editor/journal that "the paper can be substantially shortened, if necessary, at the expense of omitting some of the proofs which follow standard arguments." The reason is that some of the strongest math journals really do not like publishing papers that are over 30 page-long (the longer the paper, the harder to publish) and some journals even have hard cut-offs on the length of a paper.

Direct response: submit the 'shortened' manuscript and in the cover letter, indicate that there's potentially more to it. The trimmed down version should still be able to stand on it own.

I focus on too many things that are interconnected.

[1] Consider mapping out diagrammatically the interconnections. From there, see which are the main interconnecting pipes and filtered out the draining pipes. Your manuscript might get more concise.

[Edit] @Henning input, which I fully agree and align to:
... Don't include the diagram in your paper, but use it as an aid for revising it. It's a revising aid, a scaffolding. Do not include in the actual paper (at least not verbatim).
The purpose is to aid.

[2] Prepare for yourself a rebuttal based in previous rejections. With your earlier graphical view of your research argument and 'rebuttal', your manuscript should take shape more clearly (on key arguments).
[3] From there, get a four-eye-review from 'colleagues' in your discipline, amend accordingly and submit to the next (reputable) journal in line.

That's a good revising technique. Just to be sure: Don't include the diagram in your paper, but use it as an aid for revising it.

@henning ... Fully agree. It's a revising aid, a scaffolding. Do not include in the actual paper. ... If at all it's (remotely) included, it comes in as a conceptual visualisation of the research. Then refine it similar to a 'conceptual framework'. However, better drop it.– Use as a aid and drop it off.

Your situation sounds similar to mine: several rejections of a long-ish paper from top journals. A small number left to try before moving to lower tier.
This "answer" will use that as a guide to give you advice.
I have several relevant posts here about it. In my situation, it is a blessing because I found better arguments and now legitimately have more than one paper.
The comments and answers to my questions are probably relevant here: have capable and trusted readers give you honest and thorough feedback. That will help you decide what to leave out if anything (and generally how to improve the presentation).
Follow the standards of the discipline and the journal you wish to submit to. This includes the writing style and paper format. If it is typical for things to be left out, then do that. I do find that top journal papers often day things like "it is easy to see X" and I personally don't like that, but if that is the cultural standard, it is what it is and might be advised to follow it. But there is no guarantee that yours is treated exactly the same as other papers. You say this is your first paper, and that means there is an additional challenge due to lack of experience. My situation is similar--although I am mid career and have several papers, this is my first truly top-journal worthy result. The challenge is purely about presentation/style. I suspect that is a big factor here. "Style" could also be construed to include things like leaving out standard or simple arguments or the specific way/order things are owned in (the flow of the arguments). That will depend on discipline/journal to a degree too.
Much of this comes down to editor and referee subjective preference too. There is luck involved as well -so I have been told at least.
I was unable to get any thorough/careful qualified readers for my paper (the main thing people suggested I needed), but the extremely limited amount of feedback I got was IMMENSELY helpful (from real, even somewhat "famous" experts). That plus deep introspection, hard work, and much rewriting will vastly improve my paper. Plus presenting the work to an audience helped. Even if I still can't get it at a top journal, the paper will be accepted somewhere. It's for the love of the knowledge and sharing it that matters, even if it's not immediately (or ever) honored by those at the top.
I hope that is helpful and doesn't just come across me wanting to talk about myself. I truly get the situations were similar and that these comments might be helpful.
Best of luck!

Sometimes I write very long papers -- and am faced with similar difficulties. A wonderful method that has helped me on several occasions is to equip papers with long appendices. This enables one to explain in the main text the key results, in a terse manner, and to expand on them in appendices.
On a couple of occasions, even this trick was insufficient, because the total size of a paper, with appendices, was excessively large. So in those two cases we agreed with the Editor that I would put the full version on ArXiV.org and cite it in a shorter version to be published in the journal. But then, again, this happened to me in two cases only. Usually, the trick with appendices works out well.


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Interpreting frequent rejects from PhD workshops/conferences
I am already at the end of my 2nd year of PhD studies. Currently, I do not have a publication in a journal; however, I have few published proceedings from conferences. I have chosen my own research topic, which is not a traditional PhD topic in my discipline, and I work mostly independently on it. Just for the set up.
The thing is, there are many interesting PhD workshops (basically conferences - you need to send a working paper), where I would love to attend just for the opportunity to meet other young scientists, see what they are working on (mainly to be able to compare it with my own research), present my own work, and similarly... Nevertheless, when I submit my work to them, I get rejected, almost always. No feedback given, only something bland such as: "we had many brilliant works, we had to reject few of them".
Well, noone needs to give me the feedback, I know, I know... So where is the problem...? The problem is that, recently, I have written an article I really love and believe in. Most importantly, the article is currently under review in one of the most prestigeous journals (D1), so I guess it has a merit (knowing that this journal does not hold back with desk rejections, as that was the fate of my previous article).
So, I feel a certain cognitive disonance: I send this paper to PhD workshops and it gets rejected, however more prestigeous entity gives it a chance?
How shall I read this?

Is my paper bad and the journal just honors me with a review process since I already tried to send something there?
Is my research so specific that conference committees do not give it a chance but the journal does?
May committees focus primarilly on CVs? Do they accept only people who have already published in journal?
What do PhD workshops even look for?

Have you asked your advisor or at least run your work past them?

@BryanKrause Well, this would lead to an additional question, I suppose. :D So, in short, I study at a small department in a small country. My PhD advisor is from a different field (pure mathematics) than the one I would like to profile myself in (Philosophy/Economics). There are similarities between the fields and he still may be the best advisor I could realistically get, however, I cannot send him my papers, because he just cannot read/understand them due to lack of formulas (his words). That's why I need to work mostly independently... And search for feedback elsewhere.

The whole point of a PhD is getting training to develop as a researcher. I suspect you will struggle and should expect to fail, as would nearly anyone, without sufficient supervision. The situation you describe does not sound tenable; I think you are seeing the effects in not knowing why your work isn't seen as suitable in the field (or maybe these workshops are not suitable to your work). StackExchange won't be able to replace a competent advisor.

Additionally, who is going to decide you've earned your degree if your advisor cannot read your papers? I think this is an issue to resolve sooner rather than later, before you've put in too much more time.

You say you have published proceedings from conferences, good. Did you go and present (talk, poster) at those conferences? Anyway, there does seem to be some community that you fit into, so perhaps selecting events closer in topic to those conferences might have a better yield?

The idea that "the journal just honors me with a review process since I already tried to send something there" is definitely false. The notion that the second time you submit to a journal you won't get desk rejected because... it is already your second time submitting to the journal makes no sense. The idea that "they accept only people who have already published in journal" also sounds unlikely to me. Finally, I do not see a significant contradiction between the journal sending your paper out for review and workshops rejecting it. You may be reading too much into not getting desk rejected.

My best guess is that your papers are considered out of scope for the conference or workshop. That can easily happen without feedback. You also say the topic is non-traditional.
My experience (different field) is that your third bullet is incorrect. Committees I'm aware of take advice from reviews on the work itself.
I'd guess that most committee (or program) chairs would respond to a polite note asking why the paper was rejected. It might be just too many competitive papers, in which case you need better papers, but it might just be the scope issue above.
Your advisor might give you some feedback on that as well.

I always ask them when they reject me. The standard reply is that they cannot provide me with detailed feedback. Yes, they sometimes state that the workshop is highly competitive (the record was 30 spots for something around 250 submissions, with the usual being 20 spots for 100 submissions). But then, can I interpret this as my paper being bad, if it is in the review of prestigeous journal? On the other hand, can the journal be just nice?

Working without an effective advisor is very risky, I'll note. Not everyone can be successful at it.

I feel like I've experienced just the opposite. I rarely, and I am profoundly thankful of it, been rejected to a workshop and their funding. I did my PhD in biochemistry with computational biology. My system was profoundly basic science: protein folding. Despite the essence of my research, we even got the "paper of the year award" with the journal of my first paper. I have several colleagues and fellow candidates that were less lucky on that regard, and the difference I could clearly tell between our applications is how do you explain your problem to a broader audience, and how do you interest them in your solution.
Yeah, I know this is easy to say, but I think it is quite important to:

assume the people at the conferences are not experts in your topic. Sometimes they are, yet a highly specific and methodic paper usually pushes people's interest away. Try to give them the bigger picture, even if your problem is as elemental as mine.
make your solution reachable. I know writing a paper requires you to put the specifics of the methods. But we do that in length when we have plenty of space. When you are a bit more restrained in that term, try to just stick to the elementals of your approach, i.e. in my case 'molecular dynamics', 'computational approaches', 'biological modeling', so remember that the main point of an abstract/paper is to make yourself understood to everyone who is reading it, and not to confuse the reader with fancy words.

I think there is a learning curve, the more exposure you get, the more you learn how to interest people in your research, get contacts and essentially learn a lot, which is the main goal of a PhD. My advisor taught me plenty on how to do this, by reviewing my applications when I just started. He is still quite an interesting invitee to conferences, so that helped me a lot.
For us, third world resrarchers, going to a meeting in Europe or USA is quite expensive, and we normally lack the resources to do so. Thus, funding is really crucial to us and making good applications so important as well.
Don't give up, it is a struggle, it is frustrating, but if you stop exposing yourself then everything becomes just worse.
From your points, I just believe that you are not putting yourself out there in the best light. Again, it has nothing to do with intelligence nor how good is your research, but mostly with how interesting and approachable do you seem to other researchers/fellow students.
Sorry for the long reply, but I sincerely hope that I showed you that it is just experience and soft skills.
Bests of luck!

It might well be that your working papers get rejected there for very superficial reasons. The selection committee will often handle a huge amount of submissions and work hard at first whittling it down to a manageable size. They might first check whether your paper looks like it belongs to the field.
In economics conferences, you might run into trouble if you write in Word (in theoretical subfields), use a note citation style, or do your statistical analysis in SPSS. All these things shout that you are not part of the community. However, nobody will ever tell you that your paper was rejected for such reasons; these reasons do not look scientific enough. Journals might be willing to take more time to check whether there is something in an unconventional-looking submission.
During your PhD, you need not just learn the in and outs of your research topic, you also need to learn the in and outs of the research community. These are the people that will referee your work and decide about acceptance at conferences and journals. If they are not willing to buy, you will not be willing to sell. Usually, your advisor should serve as a guide to that community.

Papers for PhD workshops and journals are inherently different, at least in the field of computer science. There, the goal of a PhD workshop is not to present your latest results but your PhD project itself. Hence, your paper for a PhD workshop should provide

a general motivation for your project
some background explaining the basic techniques/concepts of your area
a literature review clarifying why your PhD project is novel
an overview of your (published) results so far
an outlook how your PhD project will advance the field

While the general ideas of each section are similar to a scientific paper, the scope of these sections is very wide (your whole project). This could be the reason why you got accepted at conferences and a review in the journal but rejected by PhD workshops.


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How do you indicate changes (deletions specifically) in a manuscript without using tracked changes or strikethrough?
I have a manuscript accepted with minor changes. I had to delete and rewrite some texts as the reviewers suggested. The journal specifically asked "Please highlight the changes to your manuscript within the document by using bold or coloured or highlighted text. Please do not use track changes or strikethrough text". But I can't seem to figure out how to indicate deletion without using strikethrough. Any thoughts on how to do this? Thanks a lot!

Suggestion: after deleting a word, highlight from the last letter of the previous word, to the first letter of the latter word. This should create a highlight of three characters (last letter->space->first letter) indicating where something was deleted.

Ask whoever instructed you. The journal is a much better point of contact than we are!

Style issues are going to be different from one journal to the next, even from one editor to the next. Seek advice from the journal, then keep that advice in your "toolkit" for future submissions. Maybe the journal even has an on-line style guide for such things.

There are times when one might just decide to ignore the rules. In your case, it sounds entirely reasonable to re-submit the document in two version: One that shows track changes including additions and deletions (struck through, if that's what your software does, or additions in blue and deletions in red), and one version that is the clean final product.
If they really really want to insist on their own rules, then you can still provide what they want. But in the end, you are satisfying the spirit of the request: To make it easy for anyone to see what you have changed. I'd give it a 95% chance that you can get away with that. In fact, I'd give it an about equally high chance that nobody who will handle your re-submission actually knows the rules well enough to know that they could, if they wanted to, call you out on the rules violation.

What you are returning is a new draft, not the final copy. Another version will eventually be required. Simply provide a key either within the document or as a separate note stating that words in a given color have been (are to be) deleted. Bolding is a bit less useful since it can have other interpretations.
Put (or mark) the key itself in the color you will use, indicating that it, too, will be removed eventually.
Alternatively, ask for more specific instructions from the editor.


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Choice of undergraduate courses impact in Computer Science PhD application
I’m currently a junior majoring in Computer Science with a Mathematics minor on a t20 school. Since sophomore year, I have been active in a ML research group and I’m considering in applying to grad school for a PhD lwith a focus in AI/ML. Therefore, do the courses that you take as an undergrad, matters a lot in your grad school application? And should I be focusing on taking all AI/ML related courses?
I’ve been thinking of doing a second major in Math to take more advanced courses, but they are unrelated to AI/ML.
Will it be better for me to take additional AI/ML CS courses instead of pursuing the second major? Thank you.

We deal with general Academia questions. Your question is specific to ML/AI.

Instead of another major, I would think a minor in a statistics would be more helpful overall - it would be much easier to handle while doing undergrad research and would give you the requisite rigorous mathematical background in AI/ML

A Ph.D. admission committee wants to find reasons to believe that the applicant can do Ph.D. work. Taking hard classes and doing well in them (especially in Math) is good, but what exactly these classes offer is of secondary importance. Working on research and either getting papers or good recommendation letters is even better. In the US, there is no pressure for new Ph.D. students to immediately become research-productive, so students who need certain knowledge (e.g. Linear algebra or Optimization for ML) are expected to get it during their studies.
Based on this, I would advise you to prefer a research experience over additional course work or even a second major.


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Do I need to list a school I attended as a non-degree seeking student on CV?
I am currently applying for some graduate programs and got a question regarding my CV. I took one course at a different institution than the university I am graduating from. I attended the college as a non-degree seeking student and did not transfer the credits I earned at the college to my university. I am pretty sure that I need to send a transcript from the college, but I have no idea whether and how I list the college on my CV. I appreciate any helpful info in advance!

Requirements vary. Is this for the US?

Yes, I only apply to the universities in the States

You are almost certainly right about the need to send a transcript; nearly every U.S. college and university requires transcripts from all institutions the applicant has attended.
That said, an admissions reviewer with transcript in hand will wonder why it's not on the CV.  It makes sense to list it, noting that you were not seeking a degree.  You need not go into detail.

That sounds reasonable. Thank you!


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Change of University Marie Curie program
Hello I'm in a cofunded PhD program with the University X (This means that the University X pays half of my salary) but my suepervisor decided to quit the project and I couldn't find a supervisor inside the University or doctoral school.
So i found a supervisor in the University Z but I don't understand yet what is happening because my coordinator is asking me to apply for the University Z and I wouldn't be student in the University X although it would pay half of my salary. Is that possible??
What can I do?

How can anyone here possible tell you what to do if you yourself don't understand your own situation well enough to describe it in clear terms? You should ask your supervisor at University Z if you are unclear about what they are proposing. You can also talk to the Director of Graduate Studies at your university (or whatever equivalent position you have there).

How can anyone tell?? Is so simple, you just know how it could works or not. I'm asking if it is possible or not and what can I do.... Your answer is not helpful but thanks anyway...

As a research administrator in the US, I will just say that when we receive Marie Curies, we all groan.  It's not an experience anyone wants to have.  I would advise you to ask within your own institutions.  They are going to have terms and conditions that we don't have access to.  This program is very specific, and I would consult the administrators for help.  The other thing is that even if something is possible, the universities don't have to agree to do the administration for you.  You should consult the universities to find out what is the best course of action.


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Thesis: How to mark variables from software in text?
I am writing a thesis about a web application that I developed. I sometimes need to reference a variable or type from the code. This happens quite a lot in the maintenance guide that I am also writing. They appear in the middle of the text so creating a code block for them is no option.
Does anyone know the proper way to mark them?
I came up with these ideas:

The "greenhouseData" needs to....
The greenhouseData needs to....
The <greenhouseData> needs to....

Every editor/school/office etc. will have their own ideas. For "mechanical" style issues such as this you should look for style guidance from the place your document will get published. A thesis for example should check with the department/school. Check how others have done it. Check for official style guidance from the school. But I did give thumbs up to mh333's answer.

Commonly this is done by using a monospaced font - often the same font as used in your code blocks.
Example:
The greenhouseData needs to....
See also here:
What are the conventions for indicating programming variables within text?
and maybe also
Proper way to format computer code included in a thesis/dissertation


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Possible to pursue physics Phd after applied physics masters?
My goal is to pursue a PhD in physics. I went to a pretty prestigious undergrad in the US, but I didn't stand out very much and I suspect I was mostly average. I did some decent research with one publication and two strong recommendation letters, and an ok GPA of 3.71.
I think what may have significantly hurt me is that I took several years after undergrad before applying for PhD programs. In my first round I was waitlisted at my first choice, but I was admitted into a program that is ~ top 20 nationally (top 10 in my subfield). However after extensively researching the program I decided it would definitely be a bad fit for me, and I decided to try again. In my second round I applied to fewer schools and was not very successful, with only a waitlist that went nowhere.
I am wondering if it would be a good idea to pursue a masters first in a related subject (since there aren't any masters in physics). Specifically, I'm hoping that if I do well in a masters in applied physics (or maybe EE or math) at a top program, then it would benefit me in my PhD applications.
All of my top choice schools have both a physics and an applied physics program which are run by separate departments. My question is, would a masters in AP at one of these schools benefit me in an application to a physics PhD at the same school (or a different one)? Would I have to start the PhD program from scratch or could my years in a masters possibly carry over? Furthermore, do I even have any hope of getting into a top masters program in AP? I know masters are generally less competitive than PhD, but with only one PhD acceptance to my name, I am pretty nervous about it.

I had several colleagues that were just average or even bellow average undergrad students and now they are super successful researchers. You should choose where to apply for a PhD based on the research area and supervisor, university ranking is irrelevant.

Why is it so important to you that you get into a top ranked program that you accept "nothing" as an alternative? You are defeating yourself.

since there aren't any masters in physics --- Did you misstate this? There surely must be more than one hundred universities in the U.S. that offer a masters in physics. I found 5 or 6 in the top 10 hits when googling {masters + degree + physics} -- e.g. San Francisco State University AND Arizona State University AND Texas A & M University

@DaveLRenfro - I think it would be fair to say that at least some top physics programs do not admit students for a masters program. They have PhD admissions, and while they will grant a masters (say after prelims), that is supposed to be on the way to a PhD. (Data point: Princeton).

Or, from Cornell: "Note on Ph.D. and M.S. Degrees
Students admitted to graduate study in physics at Cornell are enrolled in the Doctoral program. There is no Master’s program in Physics. Most students are awarded a Master’s degree at the time of advancement to candidacy, as an in-progress degree."

I think you may be shooting yourself in the foot here by prolonging the process. The further you get from your undergraduate while being away from academia altogether, the worse your prospects look for being able to succeed as a student. It's a difficult mindset to get back into once you are away for a while.
In the US, I would venture to say that within the top 100 ranked physics programs, there are good people doing good work. In the top 25 or so, there are many exceptional PIs, but as you go down into lower ranked program, by virtue of the fact that there are many exceptionally trained scientists coming out of the top programs/groups, and few academic jobs, there are typically at least a few very good researchers in every department. I would focus on just getting into a good group with a supportive PI doing research you find interesting. If you do well, aim for a top-5 postdoc to round out your CV. This is better than waiting for an ideal situation to materialize, which may turn out to be less than ideal once you get there.


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How long does it take for a admissions decision to be made after a P.h.D interview
how long does it take to get an admission decision after a Ph.D. interview? I had an interview for a P.h.D position in a school in the US with two professors in the faculty(neuroscience) and I was asked about my areas of research interest, I stated. one of the members on the panel is part of the department on which I intend to focus my research on. but I am not quite interested in her research, so I was asked if I went through her work I responded yes but I added that I found it a little complex and did not quite understand. is this a big red flag for me getting admitted?

The question title and the body of the question contain different questions.

This ultimately depends on the school, department, and temperament of the faculty involved, and could be anything from days to weeks to longer. You're best served reaching out to admissions at the school you're applying to, or the department in question, and asking for a loose timeline. They won't be offended by such a request, and if they are unable to answer they'll tell you so.
As to the interview, most research is at least a little complex and difficult to understand. Academics are used to being told that, especially by incoming students. Much of the early part of one's PhD education is learning how to decipher the work of others in your field, so to expect somebody who hasn't even started that process to understand it fully is usually a stretch. The attempt is respected, however, and is a good sign for someone who took steps to prepare for their panel, even if they didn't fully grasp all of the details.


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Is this a form of plagiarism?
Recently, I had an author contact me regarding naming me as a consultant on a project of theirs, rather than co-author, if I was to contribute. No fee was discussed at all.
Was it a form of plagiarism to avoid naming me as "author"?
For some reason, they seemingly did not want to cite my published research (which they have ended up doing anyway since I declined the invitation).
Does anyone please have an opinion as to why they tried to avoid the citation in the first place?

Whatever it is, it isn't plagiarism. Without a lot more information we can't begin to guess what it is.

Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.

From what I could gather, the intention was to report results from an existing study I wrote, change them slightly to incorporate different literature and then name themselves as an author, and myself, as a consultant.

Unless the group that contacted you plan to represent your work as their own, it is not plagiarism.  Even if they don't do that, there may still be ethical issues that aren't plagiarism.
You have the right to ask, before you agree to anything, how your work will be credited in publication.  If you don't like the answer they give you, then request modification, or back out of doing the work.  Before you start, you should also understand very clearly if there will be any compensation, monetary or otherwise, in exchange for the work.
My suspicion is that the want to offer you an "acknowledgement" in the papers that result.  You should ask about the parameters of the whole project, and if you think your part of it would merit authorship, say so.
Get all of this hashed out before you make any commitment.

Thanks Scott. I attempted to get as much detail as possible but they simply stopped replying which kind of told me everything I needed to know.


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Is wanting to quit part of the "PhD experience?"
Do most PhD students want to quit grad school at some point, or is this a thought that only the most miserable students entertain?

I think this question is too broad to answer. We can't ask most PhD students in the world.

Possible duplicate of How should I deal with discouragement as a graduate student?

If at any time you feel

You are not understanding what supervisor is saying.
You are not on the right path.
Your colleagues are performing better than you.
Only you don't understand a thing and lagging behind in deadlines.
Your supervisor is not happy with your work.
Your advisor is rude to you but you saw him laughing with another student.
Your work seems easy but others' work is very impressive.
You just want to quit.
You can't quit because of social pressure.
You just wanna go with flow.

Any other symptoms like above mean you are doing PhD and almost every student get such mood swings any time.  I almost gone through all but when I talked with my colleagues they were thinking exactly like me, some even saying my work is very nice and their work is easy etc... So don't worry just work and read.

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Undergrad studies in Physics: Europe vs America?
I'm currently in my first year of undergrad in Physics in Leipzig, and was just wondering, does a 3 year undergrad program make it necessary for one to pursue MSc instead of going straight to Grad school for a PhD like most American Physics undergrads do?
P.S. My interest is inclined towards theoretical particle physics.

Do you mean going to do a PhD in the US or in Europe? I suspect the answer is that different countries/institutions will vary. At least across the UK, different universities (and potentially different departments within the universities) have different requirements for PhD applicants.

An undergraduate degree in physics in Germany will usually leave you better prepared for PhD work than an undergraduate degree in the U.S.  Of course there are plenty of people who are individual exceptions, but what I'm saying is that the two degrees are not perfectly aligned.  You need to keep in mind that the German equivalent of the U.S. high school is not perfectly aligned with the U.S. high school "diploma" either.  You would have to do U.S. high school plus one or two years of U.S. college to be at a comparable level to the entering first-year college physics student in Germany.
I am basing this answer on what I have heard from my spouse who studied physics in Germany, and my spouse's comments over the years about what our son did in high school and college (physics major) in the U.S. where we live.
But the best way to check if my answer still holds would be to compare programs of study, course descriptions, and syllabi.
Bottom line, for physics, at least, you can probably go comfortably from a German undergraduate degree to a U.S. PhD program.

Oh. Thank you so much, that had got me worried. Apparently most European universities ( Such as Oxford) require a Masters before getting a doctorate. Please do thank your wife as well! Would you mind if I asked where she received her degree in Germany?

You should note that there is a difference in what is contained in PhD programmes as well - my experience is in maths, but from looking into the US you'd start a PhD programme by taking some courses and tests and eventually getting to the stage or starting research, while in UK and I assume the rest of Europe you'd be expected to start a PhD ready to begin research immediately.

I know this is an old question, however, I can personally say your physics undergrad education in Germany is probably far superior to an American. I studied at Uni Freiburg as well as MSU and FU Berlin and it's ridiculous how much Americans pay for such an incomplete education. If you choose to move to the states, be aware that you will have to take qualifying exams during your first 1-2 years of grad school, during your 'masters' work. This was a turn-off for many of my friends in Germany, who could just apply for their masters program and start working at a Fraunhofer somewhere.
Also, don't think of it as 'master's' and 'PhD' as much as the first 2-ish years and then research. Universities handle this differently: For instance, I've heard of universities that accept way more masters students than they have PhD positions for and if you aren't working with a professor by the time your first couple years is over, you're out of luck. Others only accept as many as they can promise PhD positions to, which is not many, but if you talk about your course work and labs, you shouldn't have a problem.

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How to escalate a complaint about errors produced by a journal from the Nature publishing group when Editor doesn't respond
We have a scientific paper that was published at the beginning of this year in "Scientific Reports", an open-access journal by the Nature publishing group. However, upon publication, as authors we were shocked to see some of the figures (which were uploaded to the journal's website during submission) altered in an unacceptable way that changes the scientific meaning of the paper. It was clearly a "production" error during the final processing of the manuscript by the publishing team.
We have since been complaining to the journal and its Chief Editor (for several months now), but without any meaningful response from them; the Editor never bothered replying and another assistant promised to fix the errors but nothing happened.
As authors we are very frustrated to see our work being distorted online (in front of the readership) and we don't know how to complain about such negative experience and get the errors fixed.  Any advice on who to complain to or who can escalate this seriously with the editor/team of this journal would be appreciated?

@ndpl The errors were not present in the proofs provided, nor in the original files we uploaded. Somehow, the errors were produced later by the journal just before publishing.

This journal is labelled as "a mess" by many colleagues. So the situation doesn't surprise me. I suggest you contact the Publisher instead of slippery paid editors.

Didn't we have this question the other day? can't seem to find it though....

@SolarMike Something similar, I believe

@Scientist How do I contact the publisher? I couldn't find an email that sounded like the right person, and when I emailed Editors of sister journals under the same publisher for advice, no reply either. Any suggestions?

@user135626 Try "contact us" from the publisher website. For instance: https://support.nature.com/support/solutions/articles/6000206179-contacting-us

As authors we are very frustrated to see our work being distorted online (in front of the readership)

Release a technical report which doesn't contain these mistakes and explain in the report that the errors were made by the publishing team.

we don't know how to...get the errors fixed.

It seems you have exhausted the usual, informal routes. Perhaps you can escalate with your university's legal team, since there's surely a breach of contract which reflects badly upon the university. A strongly worded legal letter will hopefully prompt action.

Thanks for your answer. Regarding the suggested release of a Technical Report with the errors removed, where can I publish such a report (I don't think the same journal has such type of publications)? And will it go through peer-reviewing delay again?  Also, do you think it will be enough to alert the readers to the errors in the original article?  I tried actually to notify the readers through a "comment" I inserted in the comments box below the article, but not sure if this sufficient.

where can I publish [a technical] report arxiv (or similar), your university's technical report repository, your website, ... will it go through peer-review no will [it] be enough to alert the readers depends what you want I [added] a "comment"...in the comments box below the article I doubt many will read


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Effect of work experience in gaining PHD acceptance
I am a senior in water resources engineering. I graduated in master degree in 2008. After that I have worked in cosulting companies to now in my expertise. Recently, I am intrested in studying in water resource,PHD. Is having work experience positive point in gaining acceptace for PHD or not?

What's a "senior"?

It depends on your experience. While the academical and research-based works through your consulting profession would be interesting, the typical works are not positive in the academical settings.
If you can explain your earlier experiences through research and development elements and illustrate your ambition to solve the profession challenges as the main cause for entering the PhD course, then it would be a strong positive impact on the acceptance in the interview of the PhD.


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Is it possible to publish research paper independently?
Is it possible to publish independent research paper without any academic or industrial affiliation in a reputed journal?


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Can I approach a new professor from another University?
I am a Masters student.
After two years of research, I could not able to meet the standard of my professor.
I have tried a lot but he said I am not good enough at writing papers. I would not be able to graduate. But I think I have research potential. I will lose my confidence if I woud not be able to finish my research.
Is it a good idea to approach a new professor by describing my current situation from another University and start over again?

Why "not good enough at writing papers" implies "not be able to graduate"?

As my department rule, to graduate, I have to publish paper or attend the conference at least three times.

Are you sure you didn't misunderstand the rule?

My professor confirmed me the rule.

Maybe your supervisor misunderstood (or invented) the rule?

If your problem is not being able to write, then that is the problem you need to tackle. Going to another university and starting over does not solve that problem.
Writing is something that can be learned. All the universities I have been had hat courses or workshops or other forms of help available. So that is what I would do.

Thank you for your reply. Could you please tell me how can I get your help?

You can't. The point of my answer is that you have to look at the resources available at your own university.

Going to another supervisor might be part of the solution, however, since it is also the supervisor who should teach a student how to write papers, be it through direct feedback, or by providing students with resources and directions that allow them to learn it.


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How much must I change a table to be clear of any copyright issues?
I am writing a chapter where I want to include a copyrighted table from a published article as an example of how some test analysis was performed and presented.
On one hand, the closer the table is to the original, the better the example it would make I figure, on the other, the editors and publisher have explicitly told us to avoid using copyrighted material as far as possible.
I am the original author of the table and it is trivial to copy-paste it in Latex form from the original manuscript to the chapter manuscript. So I wonder how much change is needed for it to be considered a "new", non-copyrighted, table?
Possible options include for instance: replacing actual data with dummy data, only including parts of it, changing background color, changing font, changing headings, or changing margins and width (no work for me since the chapter has different margins than the article).

Generally, the entries in the table (data) are not copyrightable, only the presentation of the table overall.

Who owns the copyright? What did you sign when you published the original work?  I would speak to the copyright holder (which may well be you!).  Also the press where the new chapter is published may have some rules.

If you don’t need the actual data (possible option to "replacing actual data with dummy data") nor the structure (… and "changing headings") why use that table at all?

@JonCuster That is my understanding, but replacing the data or removing parts of it could arguably change the presentation of the table.

@Elin The journal is the copyright holder, and while I can still reproduce the material for my own work, it does not include work that will be published by a publisher for instance, like these chapters.

@MisterMiyagi I want to use the table as it is an example of how the data has been analyzed and presented.

@JohanPI I would understand that if replacing the data and structure were not fine by you. Since it is, what exactly is left there that makes it a unique example?

In most places this would be a judgement call and subject to civil law. You could get sued. The changes you suggest are inessential to the information you are presenting in the figure. That is problematic, but up to the copyright holder to decide.
But it sounds like you are deliberately trying to circumvent copyright and that, in itself is problematic.
Suppose you take a #1 selling novel and republish it changing background color, font, headings, margins, and width. Does that sound appropriate? Safe? The things you suggest changing are not, in almost every case, the thing that makes the work copyrightable.
Moreover, since figures can contain a lot of information (creativity) in a small space, they are judged differently than taking a sentence from a copyrighted work.
If you are the original author, then it should be possible to get permission for reuse of the original. In fact, you may already have a license for some uses from when you turned over copyright. And "as much as possible" is a judgement call. In this case it may not be possible.
And, citation is, of course, required.
Do the right thing. (Mookie, from the movie with the same name)

I don't really understand this answer. Assuming this concerns a table of (numerical) data, the suggested cosmetic changes are indeed inessential to the information, but they are also likely to address precisely the elements protected under copyright law in many jurisdictions. The text of a novel is quite different from the data in such a table, being a quintessential creative work.

My understanding is that the data is inessential to the copyright (though it is both numerical and text), but should naturally be cited properly. The copyright transfer allows me to reproduce e.g. tables in work that I publish, but not that someone else does.


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After almost three years of research, I am at my wits' end. What should I do now?
After I got my masters, I started my PhD project three years ago. My start coincided with the start of the pandemic. I spent many many months all on my own with little to no help and no equipment at an almost deserted research lab. I would write to my supervisor and sometimes talk to him but their initial ideas just wouldn't work out and somehow I wasn't able to convince them it wasn't for lack of trying. I did my best with the little things I had access to. Since the subject was also out of their usual scope, no one had any knowledge to support me or direct me to the appropriate literature.
After almost a whole year I had the annual talk with my supervisor and he was like you haven't progressed much and when I told him I am sorry but I wasn't even given a frickin camera until last month to record anything and was working with my smartphone camera he told me he wasn't aware of it!!!! I had asked for a camera repeatedly but their answer always was others have priority you will be given a camera once one is free.
I was working at a research center and everyone else was at a university lab about 20 km away. No one was there to witness my struggles or suggest anything. I was hoping that once the pandemic was over things would get better. But nothing happened. This would perhaps be more acceptable if the other PhDs would have gotten the same treatment but they were all sitting at the university lab with their and my supervisor and had easy access to everyone and everything. Once I asked if I could switch my workplace to the university lab and my supervisor told me we can't take everyone to university. Mind you, everyone else starting their phd was given a place at university and I was literally the only phd in this external lab with some postdocs, if they ever bothered to show up that is. Eventually my supervisor and the professor in my project had to accept that what they initially thought, would not work and I had to work on other things.
After three years of struggling, constant desperation, overwhelming feelings of inadequacy and being entirely ignored, I was notified the other day that my funding would not be guaranteed anymore. The professor told me I should start writing my dissertation.
Today, I came to work but I started crying in the bus and have been crying since in the lab.
I have just submitted one research paper and that's still under review. I can probably come up with one more paper but that's it. I haven't been to a single conference. I haven't had one single undergrad student to supervise. I haven't met anyone and never made any connections. I was literally forgotten and ignored. I just can't anymore... At times I felt like I was kept away because I reminded my supervisor of his failure to be a supervisor.
My dissertation will be thin with not enough material to fill the pages because whatever I did was just repeating one single experiment over and over and over again for the past 2 years.
I just wanna go home to my parents and forget I ever wanted to work on a PhD.
I have an appointment with ny direct supervisor next week to talk about my dissertation but I am so so mad atm that i can't imagine talking to him.
What can I do? Should I throw in the towel and forget about the three years I wasted?

This is more venting than question. It's hard for anyone to give good answers.

When someone is having big problems (or problems that seem big to them) and feeling very bad like this, I don't think we should tell them that they are "venting". That word suggests someone who is expressing frustration about a minor issue.

I don't know if I have good advice, but here are some thoughts.
It sounds like you have had an extremely difficult time in your PhD and didn't get the support and advice you needed.
If you have submitted one paper and might submit another, you have done better than many people (especially if you take into account the difficult circumstances you have had).
I don't know your field but I think it is common in some fields for people to repeat an experiment for two years and not get it to work and it is definitely not their fault.
Does your professor think you can write your dissertation and pass? Do you think it is possible that you will be able to do that?
I recommend trying to be on good terms with your professor. You can remind him or her that you have had great difficulties due to the pandemic, being isolated in that lab, not getting the equipment you needed, and the experiment not working (which was not your fault). Maybe ask for advice or support. Try not to blame him or her. You might have to be prepared for him or her to argue back a bit and say you should have asked for help sooner or something like that. I don't know what they will say. But just stay calm and tell them what you have done, and try to figure out together what is best for you to do now.
I also recommend talking to a therapist or doctor about stress, anxiety, or depression. You could just tell them what you have written in your question here and they might be able to give some helpful advice. For a start they might be able to give you some reassurance and encouragement. Maybe your university has a student welfare department, for example.

Also, there are other questions on this site by people who have had very difficult problems during their PhDs, so if you search for them you might find useful ideas


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How to keep my mind clear during competitive math exams
I've been training for the mathematical olympiad for a while now and from what I've gathered from my past exams, I feel like I'm alright in terms of knowing my theorems and formulae, but I struggle to keep my mind clear during the exams. By that, I mean I can solve 2 or 3 problems, then for the rest of the exam I can't seem to concentrate and think properly, especially if I'm in a time crunch. In my most recent olympiad exam, I solved only half of the problems which I should've been able to solve because I wasn't able to concentrate after solving 2-3 problems (Yet, I was able to solve almost the entire question set fairly easily at home). Anyone know how I can tackle this?

It seems to me as if the problem with the question is that the context is not about academia. If you change it from the mathematical olympiad to exams in general, I believe that it would be on topic - there are certainly enough people who have similar problems in university. I'm pretty new here myself, however, so take this with a grain of salt.

The combination of time pressure and pressure for results can be a lot of stress. What often helps is to get familiar with the situation causing the stress, but with lower stakes.
Personally I find it helps me a lot if

I know that I am capable of solving that kind of problem
I have a good feeling for how long I can spend on a single problem

Now it sounds like you already have point 1 covered.
So get used to the time pressure. When you are practicing don't just solve the problems, also set yourself a hard deadline. Evaluate your results once the time runs out, not once you have solved everything. Try to find a balance between speed and results.
If practicing on your own doesn't cause you enough pressure you can raise the stakes otherwise (I find my own pride usually does it for me).
For example you can practice together with friends who also want to participate in the exam. Do a mock exam and grade each other. Compete for bragging rights or for whoever has to buy the pizza.
Or maybe for you it's some other aspect that causes the stress - for example the location or the amount of people around you. Try to figure out what it is and replicate it when you're preparing.