text:
Have applied to, and been rejected from, a number of PhD positions; are they really so difficult to get?
I am a student who graduated with a Master from a German university in April this year, majored in materials science, willing to further pursue a PHD degree in a European university (or possibly a university in the USA if I can not get anything in the EU). I have already applied to a certain amount of universities´ PHD studentship programs.
I admit that there hardly are positions exactly fitting the thesis work and research activity I had in my Master study program, because materials science is a very diverse and gargantuan subject. Each different university has its own research preference and inclination. Sometimes you may say you can find between 20%-40% overlap with your past experiences, including the similarity of research content, or the techniques being used. So I tried to apply to all of them, the replies were mostly like this: "You can not fit the best of criteria.."  It has been several months, there is still no slight improvement of my application.
My GPA is 3.4/4 (no publications so far), but according to the PhD advertisements I have viewed, some universities have rules about the basic grade requirement you need to have for PhD enrollment, some do not have. The universities I had finished my Master and Bachelor study have certain reputation in their own region or country. My Master degree is Master of science(M.Sc.), Master thesis is about metal-oxide nanostructures synthesis and its application (basically using different approach trying and trying again, compare the final results), on the one hand I am afraid of the simple and even boring thesis work could give people wrong impression about my research experiences that is poor and rudimentary, Professor will have some doubts about whether I am truly quantifying to do some sophisticated PhD work, on the other hand, if I stick to doing metal-oxide fabrication research or related in my PhD study, you need to have solid background in chemistry, which also is what I am lack of.
Unfortunately I do not have too much contact with my professor (thesis advisor) except having some discusses related to my Master thesis, because our group is very big one and each PhD student is responsible for supervising master students for their thesis work, so Professor could have time and energy doing other things, I only asked my professor for recommendation letter once, maybe I also need his suggestion about my applications.
After I have accepted some rejected letters, I started to think which kind of project could fit my profile, not only I can be accepted by them but I can also enjoy my project and stretch my muscle, doing some useful in materials science field.
Sometimes I am confounded by various projects and their fancy names offered in the webpages, and do not know what to do next. but I still  have a dream about one day I could leave my fingerprints on the TEM machine and my thoughts on the scientific papers.If you are a PHD student (have successful application experiences) majored in materials science or related area, I kindly ask for suggestion (any suggestion and any opinions will be useful to me).

Hi Daniel, welcome to Academia.SE! I have rolled back your last edit because asking for recommendations for specific universities ("shopping") is not allowed here.

@ff524  Ok...thanks for heads-up, but "no recommendations for specific universities is not allowed", it sounds too strict, but anyway it is OK...:)

You can read this post if you'd like to understand the reason for this policy. Basically, it's that questions asking "What are good Xs for Y?" are not considered a good fit for a question and answer site that's meant to be a canonical reference for future users with the same question (as opposed to, say, a discussion forum where they'd be OK)

@ff524   OK....I understand...

@BenCrowell thanks for your concerns, this is the titles someone edited for me, it is not what I really meant, I actually applied to several positions (not "a large number", that is too much exaggerated) related to materials science, what I  needed is good suggestion from PhD students in materials science who can give me certain direction or good advice..

General requests for "suggestions" tend to be too broad to get answered here. If you highlight a very specific, answerable question, you will probably get more useful advice. As you can see, we're having some trouble understanding what your specific question is.

For example, both @Jigg and I thought from your statement that you "tried to apply to all of them" that you had sent out a lot of applications.

It depends on how qualified you are.

I am surprised there has been no mention of your Master's thesis advisor.  Judging from my humble experience, your advisor's support can be very important for finding your next position.
This support could come from their scientific network (e.g. by establishing contact to a group you want to apply to), writing letters of recommendation, or even just looking over your CV and cover letter.  They will know better what a “good” application should look like in your field.
Of course, all that is assuming that you have a good working relationship to your advisor.  If not, maybe another professor / experienced researcher would be prepared to help you.  You say you already graduated in April, so I do not know how much contact there has been since then …

thanks for your insight, my advisor is a little bit of busy and "lazy", sometimes it is even difficult to locate him, but anyway I will try to contact with him for my PhD application.

@Daniel you best bet for getting a Phd position is to convince those who are supposed to offer the position, that you posses the basic requirements to become an established researcher/scientist. Looking at your grades, I assume throughout your studies you have had some projects and seminars where you could have convinced you supervisors that you are capable of doing research. Now is the time to ask those supervisors to write recommendation letters (not general ones, which just substitute the name) emphasizing your research performance and capabilities

@WolfgangKuehne thanks for your comment, yes, you are right, I will do like this..

As for the question in your title (which originally was: "Is it really that difficult finding a funded PHD position?") the answer is it depends on the field and the country. As an engineer, in countries with a well-developed industry, the job opportunities for graduates outside academia are good, thus diminishing the competition for PhD positions. This being said, a grad student is not just hired to lay bricks because there is a wall to be built. It represents a substantial investment for professors who will thus rather have no student than a not-so-good one.
To the point, previous experience in the specific field of the PhD study is almost never a requirement, so I doubt it's the limiting factor in your case. Your grades might be though, or your written english proficiency, but these are guesses.
I think your strategy might be inefficient. From your text it sounds like you sent a large number of applications and are waiting for someone to bite the bait. A personal interaction with people in the labs you are interested in would be a better approach, for example via an internship or a visit, if you can afford it.
So I would narrow it down to a few places where you really would like to work, gather the reasons why you like them, and start establishing a contact via email, say what you like about their approach or research topic and how you think you could fit in. They will then be able to let you know what is needed to be accepted in the graduate program (note that you will still have to comply to the department, university or graduate school requirements in order to be accepted).

Thanks Jigg for your advice, it is very useful to me.....

Mostly depends on your GRE score (if below 1000, try again), and your letter of intent. Add those up with some good recommendation letters and it should not that hard to get a scholarship (unless you are aiming for top 10 schools).
The topic of your MSc is not the limiting factor, looking at your courses list, they should get an idea of your background and educational knowledge. Maybe it is good to contact the professors that you are interested in first, and afterwards let them know that you will apply. Worked for me.

Is GRE used in Europe? I had never heard of it (and still not sure what it is) before I moved to America.

(or possibly a university in the USA)... and I can only speak about the US PhD system, but it might be an option to look into if EU does not work. Entry into the program is not so much focussing on how well you know the professors... :) GRE is not used in Europe and in US it is testing your basic knowledge (all grad school prospects have to take it)

'Entry into the program is not so much focussing on how well you know the professors' I don't understand this sentence. Where is graduate school admission focussed on how well you know a professor?

@user20087  ok thanks for your answer..one small question though, from uni´s official website I know that we only can apply to US graduate school for summer-semester or winter-semester PhD program, not like in Europe we can apply at any time only if there is vacant position available, is that true?

Yes, rather fall and spring admission though (september or January), but most admissions are with the fall admission.

@Jigg, Belgium and Holland to name some places.

You yourself know what you are falling short of! You have specified yourself about your interests, your research work till today and expectations. You would score an accept letter if you apply to a PhD position that better suits your profile and your future expectations! It is like finding a job. You cannot be a doctor if you studied history!
Yes, PhD admission is competitive. It depends on you whether to make it difficult or easy. The PhD programmes are looking for researchers who deserve to be in that place, not for random people asking for acceptance. Your graduate advisor might help with the selection and application. The PhD supervisors during your MS thesis, might also be good guides. Identify the weaknesses of your profile and improve them before you fall into the abyss of rejection into PhD!
Wish you the best!

thanks for your insight and words of encouragement, it is very nice of you, I also wish you best...


text:
Do referees get to see each other's reports?
I have submitted a paper to a physics journal. Two referees reviewed it, and I got their reports.
My questions are the following: Does each referee see another one's report? If yes, at which stage - response to the referees, or even before?

Is this for an APS journal? (Seems likely but not guaranteed based on your previous questions.)

@Anyon : yes, it is.

I don’t think this makes sense without actually naming a specific journal. Even "physics" is huge with wildly different branches and customs.

I don't know of a journal that would send the other referees reports before that referee has submitted their own. It seems like it would be a potential source of referee bias, because other referees reviews are going to influence your own, especially if you're early career and think your other referees are more knowledgeable than you.

@Crazymoomin I have a vague recollection of a question where OP had noticed that the online system (probably for a conference?) gave them access to other reports before submitting their own, but I cannot find it now.

As stated by @Buzz in a comment,

In physics, referees almost always get to see all the reports.

In the case of the Physical Review family of journals published by American Physical Society (APS), my experience is that this usually happens when authors have submitted a response or when the editor considers the process in the current journal finished (e.g., after enough referees recommend rejection or transfer to a specialized journal instead of publication in Physical Review Letters). If a given referee is invited to review the paper again, the invitation email can contain phrases such as

We append copies of reports from you and the other referee on the
previous version of the manuscript and of the author's response.
Is the response of the authors to all the previous recommendations
satisfactory?

Conversely, if a reviewer isn't invited to the second round, the previous reports may be sent to a new referee. If the reviews and would-be responses are "trivial" in some sense (e.g., all reviewers recommend acceptance in the second round) one might receive just the decision summary instead of the reports. I've also on occasion been asked to break the tie between reviewers that had already submitted reports. In those cases, the previous referee reports were included in the invitation.

Also for Nature the other reports are visible to all refs after the authors response.

It depends on the journal. Some journals send editor decisions, along with all referee reports, to all reviewers. Most don't.
Generally, if authors write their reply to reviewers, they copy-past most of the reviews into a document so they can address individual points. Reviewers get to see this document in the second round, and at that point they see what others reviewers wrote (or at least the part that was copy-pasted).

I suspect the practice of "most" journals varies by field.  In physics, referees almost always get to see all the reports.

Yes, I usually see my co-referee's reports at the same time the authors do. How closely I read it varies, mostly on paper quality.

I cannot second the "Generally, …" part at all. I’m used to systems that provide separate responses to each reviewer, for example. Heck, even the idea that there is a second round isn’t a universal standard in the reviews I was involved in from either side.

Just to echo others, int he ~10 different journals I reviewed in my career, never have I not seen other reviewers report always got bcc'd (or forwarded) the email sent to the authors.

This varies by journal (or more likely, editorial management system). The full spectrum is possible, from "they never see each other's reviews", to "you can see the other reviews once the paper is accepted, to "you can see the other reviews once you submit your review". Some EMSes require the authors to respond to each reviewer separately, in which case the reviewers might not have access to the other reviews at all. Other EMSes don't, and the authors simply upload a "response to reviewers" file, whereupon the reviewers can see what other reviewers said. (But unless the authors copy/pasted the reviewer's comments, they might still be in the dark over the exact words of the other reviews.)
One constant is that referees don't usually see other reviews before they submit their review, since that can bias the review. Therefore, the earliest a reviewer might see other reviews is after they submit their review.

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text:
How come I haven't been accepted as a reviewer for Physical Review D?
A few months ago, I applied to become a referee in Physical Reviews D. I have seven publications there.
However, I still have not received any update on the status of the application. Could you please tell me if I miss something because of which I may be not eligible?

I don't think I got a request to referee for Physical Review D until I had published about twenty papers there.

@Buzz : I know people who only have two papers but are already referees.

There is no way that we can know whether or not you might, or might not, be eligible

To become a reviewer for Phys. Rev., it is usually enough that someone who is already a reviewer there recommends you. Whenever I get some article for review which I have no time to review or don't feel it is in my area of expertise, I can recommend an alternative reviewer. The editors usually follow these recommendations, and they are very interested in extending their pool of reviewers. You can just ask your former or current PI to forward you some papers in this way, and then you will start getting new submissions from the journal.
Edit: I recommend that you check your account at referees.aps.org and see if it shows you as "available for review" and also contains enough keywords under "Expertise" to make sure that papers get assigned to you. This is done semi-automatically, assuming your profile is set up properly.

For some reason, the link you mention returns just You are unauthorized to view this page. But I get the point; thanks!

Try https://referees.aps.org/Referrals/login/new

This is what it writes me: ```You are currently logged in with APS Journal account *****
If you have been invited to referee a paper and cannot view this page, please contact help@aps.org for assistance. Typically this is because your APS Journal Account has not yet been properly linked to the referral.```
Maybe something is wrong with my application then...

It should show a login page where you can either log in (if you already have an account) or press "Create an account" if you don't have one yet.

OK, then probably your referee account has not been created yet, you have account as an author but not as a referee. You have to wait when someone sends you a paper for review, as I said, and your accounts will be linked automatically. It could just take time, and the simplest way to speed it up is to ask someone you know to give you the paper they were asked to referee.

As with most such questions about relationships to journals you should ask them. If there is a problem they will let you know, but, I suspect that they would have already done so.
More likely, I think, is that they have made a profile for you (subfield, interests, ...), which takes some time. And, once the profile is complete you won't get a request to review until a paper arrives that fits your profile. Moreover, if they already have several trusted reviewers with a similar profile, it might take even longer for you to get a first request.
I can't promise that this is the actual reason, but if you ask, you will probably learn.

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text:
Why do so many papers state the obvious?
There is a pattern I keep seeing and I'm very curious about the reason behind it.
Let's say you're going to read a paper on astronomy: In order to understand it, you need to know some basics about the topic. Similarly, a paper on electronics will require some basic knowledge of the topic if the reader wants to have any chance of understanding it.
But I keep seeing research where, at the introduction the prerequisite knowledge is defined, as if the reader was unaware.
At first, I was assuming that it might be similar to legal documents where you will define the terms when it comes to their meaning, coverage and exclusion, but the more documents I read, the more I realize this is not the case.
Let me take some simple examples here, about sleep apnea:

(1) Obstructive sleep apnea-hypopnea (OSAH) is characterized by episodes of complete or partial upper airway obstruction during sleep.
(2) OSA occurs when there is obstruction of the upper airway causing cessation of airflow
(3) ... is characterized by momentary
cessations in breathing (apnea) or significant reductions in breath-
ing amplitude (hypopnea) caused by an obstructed or collapsed
upper airway

I can find many many links exhibiting this and it seems a lot more prevalent in medical literature.
For example, when reading a paper about technology, you don't find a paragraph starting with "electricity results from the existence of charged particles...": there is an assumption you know what electricity is.
Content space, and the reader's time, are wasted to define the basics even though the contents are usually incomprehensible to anyone that wouldn't know the basics anyways.
Can anyone explain why this seems to happen more in some disciplines than others?

Removed some answers-in-comments and ensuing discussion. Please answer in answers :)

That's what an introduction is. A good introduction will (1) start with the basics that everyone knows, (2) present the problem that we're trying to solve, and then (3) set up the rest of the paper (how this is done may be field dependent -- it could be a summary, or just an overview of the paper's organization).
These introductions should be concise, and they are not necessarily intended to be comprehensible to a general audience. For example, your first article defines central sleep apnea as follows:

Central sleep apnea (CSA) syndrome is characterised by recurrent episodes of apnea in the absence of upper airway obstruction during sleep which can occur in association with alveolar hypoventilation (i.e., hypercapnic), or it can be normocapnic or hypocapnic

Anyone interested in this study likely knows what CSA is, but seeing this definition stated gives me a good orientation -- I now know exactly what we're talking about and am ready to "drill down" to the specific things this study considered. It's also helpful to see the definition stated using the same language that the paper is going to use. But note that this definition is not really intended for non-experts: "normocapnic" and "hypocapnic" are not words that most people know.
Next you say:

For example, when reading a paper about technology, you don't find a paragraph starting with "electricity results from the existence of charged particles...": there is an assumption you know what electricity is....Can anyone explain why this seems to happen more in some disciplines than others?

I disagree with your premise. Sure, physicists probably don't define electricity just like the doctors in the above study didn't define sleep. But a well-written introduction does start with "the basics that everyone knows." For example, I pulled up the first link from the first open-access electronics journal that google returned, which led me to this article, the introduction of which begins:

The increasing global energy demand over the last 20 years means that electric energy is gaining more and more importance in our daily lives [1–3]. Furthermore, when
taking into account the imminent emergence of the electric vehicle (EV) [4–6], there is no
doubt that the electric energy sector will be of great importance in the immediate future.
Inside the electric energy sector, the power converter is a key device whose design and
behavior directly affect its efficiency, its cost, and the size of the final solution

All of this is definitely "the basics that everyone knows" -- in fact, this seems even more accessible than the sleep apnea introduction.
One last comment: not all introductions are well-written, so occasionally, your observations can be explained by "this author did a bad job." One example that comes to mind is papers about neural networks (especially deep convolutional neural networks, and especially in journals that are not "about machine learning"). Giving a clear explanation of what these neural networks are and how they work is very difficult, and most authors do not want to allocate many lines to the task. So, the result is exactly as you say: they give a thoroughly useless explanation which is incomprehensible if you don't already know how such networks work, and not needed if you do already know. One must make judicious choices in deciding what material to present in the paper versus what material should be left to references.

+1. A common advice is that introductions should be "funnel-shaped": start broad, then narrow things down to the concrete problem statement and an overview of the solution.

Good answer. I'll also note that many methodologies are widely applicable regardless of the domain area, whether working in medicine, business, pure science, etc. A statistician or someone designing an experiment may well be interested in the approaches taken in the example manuscript, even if they know absolutely nothing about CSA specifically. The domain background can be very useful for those who work across domains.

I think this definition "handshake" is useful in ANY kind of technical conversation, not just papers.  Half the job for any good IT helpdesk engineer is making sure they're speaking the same language as the caller

Incidentally, let me suggest that common sense sentences as those related to "increasing global energy demand" are OK in the Introduction but definitely out of line in the abstract, where space is precious.

Well said. I'd add that the introduction is a key part of the paper in that you should be following the "tell them what you're going to tell them; tell them; then tell them what you told them" model.

I was thinking: do definition change over time? If this is not so uncommon in medicine it might be good to include it.

Content space, and the reader's time, are wasted to define the basics even though the contents are usually incomprehensible to anyone that wouldn't know the basics anyways.

Do you remember when you were an undergraduate (or even worse, high school student) reading your first research paper? If your experience was anything like mine then you might have had thoughts such as "I have no idea what this means" or "I understand this paper up to exactly this point since I have seen that equation in my textbook, but I don't understand anything beyond that at all", or even "Why do authors use such complicated sentences instead of plain English?"
Have some mercy on people less expert than you - you can skip past things that are obvious much faster than they can learn things which are not obvious.

Similar experience even for experts, especially when reading outside their area(s) of expertise. I thoroughly appreciate earnest introductions that don't assume knowledge and which provide enough for a layperson to comprehend what is discussed. As Einstein (apocryphally?) said: "If you can't explain it to a six year old, you don't understand it yourself".

This is particularly true in medicine, where conditions frequently straddle the line between multiple specialties and require doctors to occasionally dip their toe into new areas.  They learned these terms/concepts in school but don't encounter them every day, so a quick reminder of basic terms/concepts can be enough to jog the brain and get them on the same track as the writer.

That'd be the entire damn undergrad. And usually it goes like "Consider 2+2=4" me, confidence boosted: "I'm with you so far". The paper would then continue "This can be viewed as a factorization of a pseudo-Riemannian manifold using Ruse-Lanczos
identity (a bunch more jargon goes in there)". Me, a poor undergrad: .... It is not too bad if this change happens in two paragraphs and not just two sentences - at least then you get a shot at extracting some keywords and looking them up.

Understanding a paper is not a binary. I challenge the assumption of the question that someone who doesn't already know the "obvious" facts won't understand a good part of the study.
I'm no medic, and before reading I knew very little about sleep apnea ("it's some problem that makes people sleep badly and snore I think...") but I opened  one of the papers you link, and after just a quick scan I have a reasonable idea what they were trying to do and what they found. If pressed I could probably offer a summary that could go in a funding request or something.
I don't know the context of the study in the wider field. I wouldn't spot any shortcomings, aside from perhaps botched statistical analysis. I would only have a basic idea about how to compare it with another study. And certainly, nobody is going to rely on me to review it. However, all that said, it's not hieroglyphs to me, and I learnt something reading it.
In addition, if I found I wanted to know a bit more, the author has given me some terms that I could search to fill out my knowledge further. So that was helpful.
As mentioned in the other answers, these statements can serve to ensure other expert readers know what basic definitions you are using. But they do also expand the group of people who may read the paper and make some sense of it. You don't need to understand every last detail of a paper to get something useful from it. What with most of us being publicly funded, perhaps we have a duty to take some steps to make research accessible, and basic definitions are easy to provide.

This would likely be very different if you presented a paper on say, knot theory. But I'd be interested to see if papers on knot theory did the "broad intro" thing at all....

Despite my years as a boy scout and a sailor, I'd never heard of knot theory as an academic field.  So I looked it up.  The first couple of paragraphs in Wikipedia (https://en.wikipedia.org/wiki/Knot_theory) do an excellent job of providing a very quick overview/introduction to the subject, understandable to my sailor/boy scout mind.  The broad intro thing is possible

@Flydog57 yes, that is a very nice intro. The point of the comment was that papers on the subject don't often even try; https://arxiv.org/pdf/1806.05168.pdf Perhaps because even if they did, I don't think I'd get much from the rest. In this regard, knot theory is knot like medicine.....

The definitions of medical terms (and terms in other disciplines) are reasonably likely to change over time, so even if every reader today knows the meaning of a term, it does not follow that every reader in the future will know the same meaning.
That said, any paper (or really any verbal explanation of anything) should include some statements of things the explainee already knows, because the way humans learn is by associating new ideas with things we already understand, and so an explanation needs to tell you which old ideas the new idea is (or should be) associated with.
Consider a mathematical proof: these often contain a statement of something the reader already knows (e.g. a definition or theorem), because although the reader knows it already, the reader doesn't know a priori that that particular definition or theorem is the one that justifies some later step in the proof. And that's not just true in mathematics; every paper is practically an argument for why its conclusion is correct, and arguments should state their premises, even if the premises are well-known facts, so that the reader can follow the reasoning of the argument.

Consider a mathematical proof: you start by stating definitions - A lot of presentations of proofs I see in math papers don't start with definitions.  Is this what you meant?

@Kimball: As I'm sure you know, the definitions are usually not just before proofs, but incorporated into the introductory material (examples for a recent notion), although for what it's worth, older papers (I'm talking about 50 or more years) often sprinkled definitions of terms throughout the paper as needed, which sometimes made it difficult to find such a definition when encountering the term in a later section of a paper that you're only browsing through for something or other.

(+1) especially for first sentence. I was thinking this myself when I read the question (yesterday), especially given the OP's medical example, as I suspect these types of terms are not decades old and are also likely to be different in a few decades, although I suppose in this field (as opposed to mathematics, for example) people aren't going to be paying much attention to papers several decades old. My guess is that it's mostly inertia from conventions in the field, rather than explicit considerations given in the comments/answers here, that mostly drive what one finds in publications.

@Kimball Indeed, many mathematical proofs don't begin by stating any definitions, and I'm not specifically thinking of proofs in research papers, where space is more limited. Nonetheless, it's very typical for mathematical proofs to begin by stating the definitions which the later steps in the proof derive from.

My point was the question is about writing papers, which means how to present something.  So if you're comparing writing a paper to presenting a proof, I think you need to explicate the analogy a little more to explain why the introduction of a paper should start with (or just contain?) definitions, at least from this mathematician's point of view.  (FYI many math papers don't start with definitions in the intro, though many do.)

@Kimball The question is about why people do write this way, not about how they should write; I'm not proposing that mathematical proofs should begin by stating definitions, just observing that they typically do. Surely not all of them do. If a definition isn't used in a proof then there is no need to state it; imagine a proof of the form "all foos are bars, and no bars are bazzes, therefore no foos are bazzes"; the reasoning does not depend on the definition of a foo, a bar or a baz, so there is no need to state those definitions, but nonetheless the premises are stated even if everyone ...

... knows that all foos are bars. I have said that arguments "should" state their premises and explanations "should" include statements of things the reader already knows, but I only mention mathematical proofs as an example of this being done (where definitions are the things the reader knows), not to say that definitions "should" be the things the reader already knows in a mathematical proof.

I've just edited that paragraph to hopefully make it clearer what I'm trying to say.

Simply, it is that it is both standard practice and wise to define the technical terms you intend to use in a paper so that there is less chance of misinterpretation. What is obvious to you will not be obvious to others and, you need to admit, that in come cases, what you think is "obvious" is actually wrong.
Each element of the medical term you describe is essential in some way and should be stated. Alternatively, such terminology can be introduced by citing another work in which the definitions occur.
To do otherwise is probably malpractice.

I'll also note that some things are "common knowledge", such as most things taught in an undergraduate curriculum and certainly anything taught in most secondary schools. These things don't don't normally need definition when used as the definitions are both standard and easily available to anyone. There are exceptional cases, of course, in which even the definition of electricity needs to be specified, such as when it is used in some esoteric (non common knowledge) way. Scholars are familiar with the concept of common knowledge because such doesn't normally need referencing or citation in a paper.

I disagree that things taught in undergraduate curriculum are "common knowledge". Or more accurately, I disagree that the conventions, names and notations regarding things taught in undergraduate curriculum are common knowledge. Researchers assume too often that the way they were taught things is the only way. It's never the only way. There is always a different convention used somewhere else, and not stating the convention at the beginning of a paper is always bad and makes things confusing for no reason.

Along similar lines to @Stef: which undergraduate curriculum? Careers aren't always linear and people can drift e.g. chemistry<->physics<->engineering.  Also even if the definitions are common, they can still be necessary to establish that the writer is using the common definition and not a technically correct but confusing one.  This is especially true where industrial usage conflicts with research usage. (+1)

@Stef, "common knowledge" doesn't mean that everyone knows it, just that it is widely available and generally agreed upon. If you can capture it in a textbook then is is almost always common knowledge.

@Buffy I suspect most of us have seen at least one textbook apparently written with an intended audience of 20 students. In that case I suspect the contents would only be common knowledge in that classroom.

I see this from a slightly different perspective than many of the other responses (from my cursory glance at them). The three examples you chose each has a slightly different definition. That's important. Though it seems they are repeating the same thing, they actually aren't. Why is this important? Because the exact definition may be the determining factor in what the study is trying to resolve. As mentioned by another, they are not defining "sleep." The kick is, they COULD have defined sleep if they had a specific reason for the type/kind of "sleep" they were concentrating on for the purposes of the study.
Consider this: Write a paper regarding something in your field of work or study. Write it as you wish papers were written, skipping all the "common sense" terms and concepts. Now, give that paper to someone who may have a general idea about the topic, but no where near what you have. Or better, give it to someone who has NO idea. Get their reaction. Did they understand it? Did they want/need foundational information to help with comprehension?

When papers "state the obvious" it often appears weird and unhelpful, as you noticed. Yet this awkwardness does not come from "stating the obvious" but rather from immediately thereafter assuming the non-obvious. Let's consider your first example, along with the sentences that follow it:

Obstructive sleep apnea-hypopnea (OSAH) is characterized by episodes of complete or partial upper airway obstruction during sleep. Conditions associated with worsening severity of events include supine body position and rapid eye movement (REM) sleep. The therapeutic response to continuous positive airway pressure (CPAP) is usually complete.

Central sleep apnea (CSA) syndrome is characterised by recurrent episodes of apnea in the absence of upper airway obstruction during sleep which can occur in association with alveolar hypoventilation (i.e., hypercapnic), or it can be normocapnic or hypocapnic.

Merely three sentences after defining sleep apnea, the paper assumes the reader already understands "alveolar hypoventilation". How many people don't know what apnea is, but do know what "alveolar hypoventilation" is?
Introductions should be funnel-shaped, starting out broad and then gradually narrowing. They should provide prerequisite knowledge that a typical reader might not know. But when introductions narrow sharply, they seem faintly ridiculous. And when introductions provide prerequisite knowledge that most high school graduates know, but fail to provide prerequisite knowledge that first-year graduate students might not know, they are rather unhelpful. It is this unfortunately common practice that makes you (and many other readers of academic literature) doubt the value of introductions.

Journals can be odd things.  Often, they publish papers in very narrow areas that can still be of interest to their wider general readership.  This is particularly true of clinical literature, but it comes up everywhere.
Other times, especially where a paper takes common knowledge in one field and presents it to a broad readership in an adjacent area, basic explanations are quite necessary.  For example, while apparently apnea impacts circulation in a way that it might interest the general readership of Circulation Research (one of your examples comes from there) it would be a mistake to assume that the general readership knows what sleep apnea is.
I suggest that what you call "obvious" may not be obvious when you consider a wider readership than what you apparently assume to be the case, necessitating more basic material than what would be required by an expert in a narrow area.


text:
Do I know my GRE scores when I choose to send them on test day?
I haven't started preparing for the GRE and I have my exam in a week's time (15th Oct.). I know I'll get a low score which is why I don't want to report the score to any university. So, I have two options:

Reschedule the exam to something like 10th Nov.
Take the exam on 15th Oct. and take it again after 21 days.

I will go with option two if reporting the scores is optional after taking the exams since reporting the score is my only fear in regard to my question.
Do I have to report my score when I take the GRE? Do I know my scores before I choose?

Have you tried googling to see what the GRE's policy on score reporting is?

Hi Ronak, welcome to Academia.SE. I tried to edit your question to make it a bit more generalizable. Let me know if I changed your question too much.

When you finish the GRE, at least a computer-delivered GRE, you will be asked if you want to report  or cancel your scores. If you choose "cancel," you don't get to see them or report them. If you choose "report," you get your unofficial scores, then are asked to report them.
According to ETS (emphasis added):

On test day, after completing the test and viewing your unofficial Verbal Reasoning and Quantitative Reasoning scores, you will be asked to designate which score recipients you want to receive your General Test scores.

At this point, reporting is optional, you don't have to report to anyone at this point.

As for whether you personally should reschedule or retake it after 21 days, that's a question we can't answer, but hopefully this information helps you decide.

Thanks for the detailed explaination! It answered all my queries!

@RonakSharma if that answer was the most helpful to you, then you should accept it using the check mark on the left.

Regarding your first question - yes, you will be prompted after you have finished your GRE to decide whether or not you wish to see your score. If you select "yes," you are provided scores on your verbal and quantitative reasoning, but not the analytical writing section (which must be graded). The full score sheet becomes available to you within a few weeks of taking the test. If you decide to take the test twice, it is possible that your first test's scores will come in by the time you are eligible to take the GRE again, which would allow you to reflect on the areas you need to work on the hardest.
Regarding your two options - this is completely up to you and a personal decision since you know your own academic capabilities and strengths far better than we do, but something to consider - depending on your field and program, taking it twice (despite the pain to your wallet) doesn't hurt. I have found that many people, like myself, performed far better the second time taking the test, whether they studied more or less. Taking it this first time could allow you to get comfortable with the testing facility and test structure/format, and then you could take it a second time with more preparation. I studied extremely hard for a year prior to taking my first GRE. The second time, I did not have much time to review, but I felt far more comfortable because I had nothing to lose (especially thanks to Score Select). I ended up scoring several quartiles higher in the verbal reasoning category and even exceeding the recommended score that institutions had suggested for my program.
Others might say to hold off, which is also valid because the GRE is testing you on your ability to work methodologically through their questions in a manner that, realistically, requires some practice, even for the best and brightest test takers. The free Kaplan practice test helped me assess my strengths and weaknesses, but despite how much my study resources helped in the long run, neither practice tests nor all of my studying could have prepared me for how the test was structured in the actual testing facility, except for just going ahead and taking it.
Regardless of your choice, keep graduate coordinators or any other relevant parties in the loop, if the timing of your tests is something that they need to be told about. Best of luck!

Thanks for the explanation and sharing your experience. I'll definitely keep that in mind before taking any decision.


text:
Where I can post a supplementary video for my published paper?
I have a paper submitted and accepted in a journal (Biology and Environmental Sciences) and it has a supplementary file which is a short video coverage, however, the journal does not support this but I have uploaded the video to Vimeo. Do you have any suggestions where I can store the video and generate a DOI (like other journals) then attach it to my paper?

I'm not sure you can have doi for that kind of media. Do you have personal website? You might consider putting the video there.

You can't generate the DOI just like that. It has to be published after peer review by a journal. Otherwise, the best place is the personal/institutional web page. and give a link to your publication in a video frame itself.

No DOI, but Vimeo should be fine.  If you put it there, it may be around longer than your current personal web site.

@Coder actually, any organisation that meets the contractual obligations of the DOI system and is willing to pay to become a member of the system can assign DOIs (https://en.wikipedia.org/wiki/Digital_object_identifier). It doesn't indicate peer review.

Keep in mind that most people will google it (name of the paper, maybe part of author's name + video), especially when showing it to other people. Most of the time, the actual place the video is doesn't really matter that much.

Videos are among the file types accepted by Figshare, which is an online digital repository operated by Macmillan Publishers. You can create an account for free, and you will get a DOI when uploading files which you can then cite in your paper.

Fantastic! This is helpful. I will check this.

@xavier no problem - happy to help. :)

the "among the file types" link seems to be broken, perhaps this would work instead? https://help.figshare.com/article/item-types It mentions "audio or 3D representations" which suggests this might (or might not) be applicable to Scientific paper with 3D scatterplot in supplementary information; I can add a video but how to let readers rotate/zoom interactively?

Also have a look at Zenodo, a research data (including movies) and text repository operated by CERN and OpenAIRE.
Like Figshare, Zenodo will generate a DOI for your publication.
Unlike Figshare, Zenodo is not owned by a big corporation.

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


text:
Cannot present paper at conference. Instructor wants to move me to second author
Due to unforeseen circumstances, I am not able to present my paper at a Computer Science conference. Without the presentation the paper will not be published. My instructor has said that she will present the paper instead, but wants to move me from the primary author to the second author. I did all the work as a graduate student while she reviewed and gave general feedback. What is the proper etiquette here? Is it okay to move her to primary because I cannot present?
UPDATE
In the interest of fairness to the professor, I want to provide some more background. This started off as a end-of-semester project. Each student needed to come up with an idea, then propose, implement, present and write a paper on it. I initially proposed a vague concept of using PSO to train neural nets. My instructor said her lab is working on something similar and if I wanted, I could tackle an extension to their algorithm, which depending on the outcome could lead to a published paper. During the course of the semester, my instructor offered little to no help for the project, presumably because that would give me an unfair advantage. All the work, code, paper, the specifics of the algorithm extension are all mine, and all I had was the published paper of the previous algorithm to work on.
After the semester was over, I decided to see if I could get it published. I noticed a lot of mistakes I made with my implementation during the tight semester time-frame and spent several months iterating and refining my process and results. I was put in touch with the previous researchers who offered little help with the exception of getting a portion of their source code, which was also of little help to me. I would venture to say that my professor's role in this was mostly advisory, although at the end of it, I would send my paper to her to proofread it.
Fast-forward to now, my instructor is claiming that because I am not presenting, I am not taking ownership of my work. She is also claiming that the work was her idea and based on her lab's previous work. She gave me a choice of swapping authors or withdrawing the paper. Note that a camera-ready version of the paper has already been submitted. I offered to withdraw from the conference. She then tells me that she has already registered the paper so I shouldn't withdraw, but she wants the source files for my work (I assume latex files?).
She has now invoked university policy and copyright law, saying that since both our names are on the paper, I cannot withdraw without her consent, which she has not given. Since she shares ownership of the paper, she claims she is also entitled to the source materials of the paper. She has offered not to change the author order.
That is the majority of the story. The actual email conversation was not as civil. I have graduated and moved on... we never actually met face to face since this was an online class. So... given the above story, have I done anything wrong? Is the instructor entitled to the source material for the paper? This is for the IEEE WCCI conference this summer. We are the only two authors on this paper. This is my first paper, this is not her first paper.

In which field is this? Something like computer science, where conferences are the main publications, or biology, where they are secondary?

Computer Science.

Sounds 100% wrong. If your adviser's doing this either he's inexperienced or abusive. If you think it's the former, you could politely let him know that you weren't aware this is standard practice; is it? If you think it's the latter then go up to your department chair or ombudsperson and complain. It's part of their job to handle stuff like this. (To me it sounds like the latter.)

yep, sounds like abusive behavior. as others already said, presentation of a paper and authorship have nothing to do with eachother. all conferences that I have seen require one of the authors (regardless of the position) to present the paper and that's it. you should ask your instrcutor, why she would want to change the order of the authors, but stay polite and professional when doing that. maybe ask coworkers, if they had similar experiences with this very instructor. good luck.

The correct response is "on your bike sunshine" and report them to your institution's ethics committee. This sounds like a blatant breach of ethics and an attempt to steal credit from a student.

I will politely decline to move the order of authorship. Let's see what she says.

@Sandra I would be interested in hearing what happens next regarding your instructor

Is anyone else mentioned in the paper? Did anyone else assist with the work? In short, can anyone other than you or your instructor plausibly present the paper? If push comes to shove you can threaten to let someone else present it. (This is not really a good plan, it's just something to think about so you don't feel completely cornered.)

What's wrong with a pre-recorded video presentation? (Or maybe even live video, but those tend to cut off in the most important parts ;-) It is computer science

@beta: "one of the authors" - or not even that. If none of the authors can attend, a colleague may fill in and present instead. In no way can that imply adding the colleague as an additional author.

I have added an update and more background to the situation.

@Sandra The update changes A LOT about the question. It's no longer about the presentation. You should really create another question to address it. This sounds like clearly unethical behavior and you ought to contact both the University and the conference about it.

@Ric I plan on contacting my university about it, but I just wanted to know beforehand if this behavior really isn't normal.

Did you sign any agreements when starting grad school giving the University intellectual property rights to your work? Were you paid by the university as a TA or an RA? Specifically while working on this project? The edit brings in a lot of legal questions and I'm not really sure that the edit is "in the interest of fairness to the professor." It is a one-sided account of the history. I'm not saying that it is inaccurate, but it is definitely your view of the situation.

@Xen2050 The conference doesn't get a registration fee out of you :) (plus you can't answer audience questions)

@mikeazo You're right it is a one-sided view. I only have the emails of our exchange which I will share with my university when asking for their advice. I didn't sign any agreements although I wouldn't be surprised if there was some clause as part of my education. I went to school part-time at night, there was no subsidy from the school.

"She has now invoked university policy and copyright law, saying that since both our names are on the paper, I cannot withdraw without her consent, which she has not given." -- I'm unsure about your university's policy but is the reverse not more true for most publications? i.e. the consent of all authors is required in order to publish (therefore a single author is always able to contest/veto the publishing of a paper, as opposed to the opposite of a single author being able to publish without the consent of all the remaining authors as suggested in the quote)?

this makes me angry: my instructor is claiming that because I am not presenting, I am not taking ownership of my work. A has nothing to do with B.

I just want to add one angle here--for you to put her as primary author would be an ethical breach on your part.  It is not true.  in no way is she a  primary author.  DO NOT give her the source files.

When you say "Without the presentation the paper will not be published.", what you mean is that the organization you are working with now will not publish it, right?  Does that mean that you could submit it at some other point?

It happened to me twice (not be able to go to the conference --- and not for lack of will; once was for a death in my family.) Both times, the second author presented the paper. No one ever even hinted to a change in authorship.

I think handing her the source material is the last thing you should do, or in other words, DON'T do it!

I am interested in how the situation was resolved. @Sandra, would you mind sharing?

Who presents a work should not affect its authorship.
Authorship is determined by the contribution to the publication.  That work is complete at the time when the publication is accepted and the camera-ready is submitted.  Now, it is entirely reasonable (and in fact common) for a paper to be presented by somebody other than the first author, and it's quite normal for the presenter to highlight their name in the presentation.  In no way, however, should that change the authorship of the paper.

+1 This a 1000 times. It is mainly the OP's paper and that should not change. The OP might also prepare the presentation for the advisor. But the author order must remain the same.

Can you confirm that your answer is speaking from a computer science perspective? Authorship order issues are discipline specific, and you make statements that can be interpreted as universal generalizations. Does the answer change if the the paper is not an independent publication, but rather a write-up of the talk in a "conference proceedings" journal? (Which it sounds like it may be, given "without the presentation the paper will not be published".)

@R.M. I am speaking as a computer scientist.  "Without the presentations, the paper will not be published" is actually a standard clause in many computer science conferences, used to prevent people from submitting a publication and then not turning up to present (see, for example, my recent answer about IEEE publications chair responsibilities)

This is for an IEEE conference in Computer Science.

No, certainly it is not okay to change order of authorship reflecting levels of contribution to a paper, because of not contributing to its presentation.
You should ask very politely your advisor about this sensitive issue. (Try smiling.)

Contrary to the other answers, in theoretical Computer Science, it is customary to list authors in alphabetical order, not by contribution (so what applies to you depends on what exact field you're in). That said, it is possible to deviate from this (for instance, placing the student as first author when they did an overwhelming majority of the work) but who presents the work shouldn't have any bearing on the author order.
Since the order was already agreed upon, whether alphabetical, by contribution or not, I see no reason to change it.

This is true in theoretical CS but not in applied CS (it is of course the main way to measure how theoretical a conference is).

I would say that this is not contrary to the other answer to the OP's question: all answers, including yours, state that it is very common for someone other than the first author to present the paper.

The paper was accepted with this order, no matter who was about to present it. Unethical behavior in line from the supervisor. In some cases, conferences and journals won't accept a change in order after accepted.
The question is: how important is it for you, is it possible for you to resist?
The first thing to check is whether the conference forbids paper or name order change. If it does, you are saved.
If not, that is another question.

I'm not following "The question is:" part...

While other answers have given what I also consider the morally/ethically correct answer, that does not help you much. You can bask in the warm glow of being in the right, it won't get you forward in life. Question is: What will?

You mentioned "circumstances" prevent you from presenting the paper. Try changing them. I mean seriously try. If it costs you some money, pay it. If you have to break a promise to someone, let them be the one hearing "due to unforeseen circumstances". Go out of your way (not too crazy, but out of your way) to make it there.
If you really can't make it there, get someone else to go in your stead. Again, that may mean paying - even if only for their plane ticket / conference attendence. You might get this money back, but probably not. Yet, that's not an unreasonable sacrifice given the amount of time and effort you've spent. Who can do it in your stead? Another graduate student, or even someone you know who's going to the conference and not presenting himself that day. Or if you have a grad student acquaintance or collaborator at that university, try to get them to do it. Make super-professional slides for them to use. Tell them they're saving your ass and that you'd be eternally grateful. I actually wouldn't officially tell the organizers I'm not coming - let your replacement show up and tell the session chair that due to grave personal circumstances you could not make it and asked him/her to present in your stead. This is not unheard of, and is relatively well accepted - in my limited experience. (Of course, I might be overestimating the importance of the acceptance.)
Get the head of the lab or other researchers there (or your advisor like others suggested) to lean on that instructor. It's extremely poor form (although not uncommon) to try to hijack credit for something which grew out of a student's course project, and your instructor should know better. If you have a graduate researcher / all-levels academic staff union, consult them about it and maybe they can bring some discreet pressure to bear.
She's acting in a very underhanded way. So, if worse comes to worst, consider replying in kind. For example, you could promise her you'll ask for the switch, but fail to send the email; or email the wrong person; or misspell the address slightly. Or you could even write the same person earlier, describing (some of) the situation, telling him you might be forced to relinquish credit against your will and asking him/her to politely refuse when they get the request. Alternatively, if you get her on record essentially blackmailing you - either by email, but better perhaps by voice recording - you could, right after she makes the presentation, demand that she undo any request you have made for the switch, and threaten to publicly denounce her and/or file a disciplinary complaint against her. These last suggestions are more risky, so think about the pros and cons and don't follow them without careful consideration. Another, safer, offensive measure is getting your union to do something like the above on your behalf - but unfortunately many/most universities aren't unionized that way.

I considered it over a weekend before letting my professor know. I did not make this decision lightly. 2) I don't really know anyone who can do this for me. 3) I plan on consulting with my school, although, she was an adjunct (I think) from another school. 4) I don't want to do this. I would rather go through my dean.

@Sandra: 1) I didn't think you had. But other people in your situation may want to rethink the decision given the circumstances and give put more weights on one side of the scale. 2) Try asking someone you don't know well enough, or asking people you do know for people you don't know. While this is a big favor, you could be paying for someone's conference trip, which a lot of people would appreciate. 3) I feel sorry for the adjuncts, being driven to such underhanded behavior. 4) Fair enough. But.. perhaps think about what you would rather not-regret rather than what you would rather not-do.

Er... if you promise her to switch the order, she can tell the conference that you've mutually agreed to the change....

@cfr: They won't accept such a communication from a non-corresponding author who wants to become the first listed.

Do we know who the corresponding author is? Maybe I missed that in the question.

@cfr: OP said he did all the work and was the only one with the motivation essentially, so I assumed OP made the submission.

I plan on contacting my university about it, but I just wanted to know beforehand if this behavior really isn't normal.

Is it "normal?" Well professors can be egotistical and pull all sorts of shenanigans (just like any other group of people). So perhaps normal in the sense that situations like this are not uncommon. But the professors actions, as described, are inappropriate and potentially violating of academic standards of publication.
From the way you describe the situation, such as this being an end of term project, it does not sound like you are a graduate student. If have any relationships with faculty who you trust, especially ones involved in research, I would consider talking to them, perhaps even before "the university."
However, if you plan on continuing in academia as a grad student, preventing bad relations is something to think about, as @einpoklum says. So try to find as win-win a solution as possible.
I am confused about one thing. You said "my instructor said her lab" (emphasis mine) but also said that you think she is an adjunct. Those two don't jibe. If she has a lab, then she has an appointment at a university, and would not be an adjunct.

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


text:
How much should poster/talk prizes be spread at a symposium?
I am one of a group of students organising an institute-wide symposium (by and) for PhD students.
PhD students will be invited to apply to give a short talk (about 8 spaces in total) or to present a poster (~40 perhaps).
We intend to award prizes for best talk and best poster. It is my view that it is fairer and kinder to have two runners-up in each category and to spread the prize so that more individuals are recognised for their good work and effort. To me, awarding prizes only for 1st place, or 1st and 2nd, ends up assigning reward in a noisy fashion or according to bias in the judging, which ignores the fact that there are many good students doing diverse work at the institute.
My peers did not seem to find this nor the format of judging important - but I feel that spending institute money on rewards in a competition style ought to be done thoughtfully and properly. Having a narrow prize spread acts as a greater incentive in tournament theory; but in my mind the symposium is an infrequent instance of recognition, not incentive, and assigning the prize will be noisy or biased which is smoothed out by spreading the prize.
How much prize spreading do you think is appropriate or optimal? Also, how much monetary value of prize do you think is appropriate in this setting? £100 for first place talk has been suggested. Is this better/worse than a £25/£25/£50 spread? I'd like to hear about people's previous experience with running these competitions and/or winning one of these awards.

Minor nitpick. Instead of calling them "Runner-Up", possibly call this "Honorable Mention."

@Compass - I disagree.  Runner-up means "something".  Honorable mention sounds like some crap ribbon you get for "trying".

I am a volunteer with the IEEE in Connecticut, USA.  Each year, we give prizes to EE-related projects at the Connecticut Science & Engineering Fair at Quinnipiac University. This is a fair for High School students (mostly) to present their projects.
What we do is award a first place for each of the Senior and Junior sections of the fair. This prize is worth $200.  Then we award $100 prizes to 6 other students as "Honorable Mentions".  These other six tend to be 3 for the Seniors and 3 for the Juniors, but it depends on the relative quality of each pool.

To answer your question is a little hard. Here is the full list of science project abstracts at this year's fair. Not all of those (or even half) are EE-related. My guess is that we'd start with a list of about 100 projects (50 each in Senior vs Junior) and then make a determination from there.

Thanks Peter! Could you give me an indication of the proportion of rewarded students out of the whole pool of participants?
In our case awarding 3 would give ~3/8 for talks and <1/10 for posters.

@Teige: Some attempt made.


text:
Include reference strictly at first occurrence, or in detailed discussion?
I'm writing a paper detailing a workflow which makes use of some software tools.
I have a sentence very early on in the introduction, which says something like the following.

The tools to use include: Tool One, Tool Two, and Tool Three.

At the moment, this is where the references to the respective papers are, like the following.

The tools to use include: Tool One (Lorem, 2014), Tool Two (Ipsum, 2011), and Tool Three (Ipsum et al., 2015).

Each tool has "its own" section in the paper, where it is discussed in detail. I've a gut feeling that it'd make more sense to include the reference there, although I think that including the reference where the respective tool is first mentioned is the "correct" thing to do.
The editors don't give any preferences, and I think that something like this is assumed to be common knowledge (which unfortunately I don't seem to have).
Is there a documented "best practice" for when a reference needs to be included, i.e., whether it should rigorously follow the first occurrence of the referenced?
The domain is CS/linguistics, in case there are some specific practices I'm not aware of...

Why not have a reference in both places?

The best thing to do is probably to reference them in both locations.

Reference upon first mentioning is a standard convention, which helps your reader because it makes it clear that the term references something that previously exists, not something that you are introducing in this paper.
When you discuss again after a significant gap, you should cite the paper again, as discussed in this question.


text:
How do journals improve their impact factor?
I would like to know how journals improve their impact score? It seems that great journals have almost always been great and second tier journals have always been second tier. How does a journal go from obscurity to highly respected?

The traditional way is: publish great papers.

Darrin, I would suggest that your closing question ("from obscurity to highly respected") is not always the same as your starting question ("hoe journals improve their impact score"). Could you please confirm which of these two is your intended meaning?

@GEdgar that's good, but not enough unless you also desk reject the irrelevant, redundant and other junk contributions.

Do you mean impact factor?

I am an Associate Editor with a journal that has improved its IF from a little over 1 to more than 4.5 over the past decade. Some of the things that we have done to achieve this have been:

Better defining our unique niche within the field. Part of this has been placing an emphasis on publishing papers with finding that are generalisable across sub-fields, not specific only to a narrowly defined group of specialists.
Publishing Position Papers that help set the standards within the field. These Position Papers are designed to help scientists in our field improve their procedures, practises and assessment of their own work. They quickly become standard references, so they receive a lot of citations themselves, but are also something we can point authors to for guidance if their work needs improving to meet the standards of our journal.
When asking for revisions, working hard to make sure the feedback is as useful as possible and designed to help authors improve the impact of their papers. We try to get four reviews of each paper, usually including some comments from an editor about how to make the paper more impactful. The feedback that we have from authors is that, although our review process is longer than they'd like, they do find the extra feedback helps to make their papers better.
Inviting contributions from scientists who we feel can help us to improve the profile of our journal.
Changing the way we handle special issues. Like many journals, we used to let guest editors handle the review and acceptance of papers for special issues alone, with candidate papers taken from a group of invited authors after a workshop or major project. Now, guest editors must work with regular editors who know our standards and what we are looking for, and the opportunity to submit to the issue must be advertised generally, not just to workshop participants. We also make sure the special issue topics are broad enough to be of wide interest.

There are right ways and wrong ways to go about increasing a journal's IF. I think the above points are the right way. Some "wrong ways" that I have heard of include asking authors to cite more of the journal's previously published papers, and coming to agreements with related journals to encourage cross-citations between the two.

The general argument is to publish great articles. However, the challenge is that in many fields, authors will send their work to the most prestigious outlet that they think might accept the manuscript. So if you have a second tier journal, it will typically receive the work that has  been rejected by higher ranking journals (or where the authors felt that the work would have been rejected by higher ranking journals, so they didn't bother submitting).
Here are a bunch of approaches for increasing impact factor from the ethical to the unethical.
Ethical approaches

Publish quality over quantity. Of course, a journal needs a certain number of publications per year in order to receive an impact factor. But in general, higher quality publications will receive more citations. And impact factor is a ratio of citations to publications.
Create belief in authors that impact factor will rise. Having a great editorial board or being from a prestigious publisher can create a belief in authors that the impact factor will be high in the future. I've noticed this particularly for new journals that are released by established publishers or by a group of famous academics. Authors know that the journal doesn't have an impact factor yet. But that given the profile of the editorial board or publisher, it soon will be a respected journal, and therefore, it is worth submitting work to the journal.
Make the submission process more pleasant for authors. A pleasant review experience will encourage people to submit their work. I.e., allow different file formats, give quick initial feedback, get good reviewers, etc.
Use editorial process to improve articles. This relies on having good reviewers.
Make articles easier to find. Make sure that articles are well indexed by relevant scholarly search engines.
Make articles free and open access or at least have a liberal copyright policy. You want readers to be able to find your articles. Allowing authors to post copies online or making articles open access will facilitate this. Of course, author publishing fees will discourage submission.
Find a niche. As @significance mentions, it can be helpful to find a niche. I.e., rather than being the 4th ranked journal on a more general topic, your journal can be the best or 2nd ranked journal or a more refined topic.

Questionable approaches

Delay the time between online publication and final paginated publication. I'm not sure if this works, but the idea is that by the time a paper is counted in the impact factor metric, it has already accrued citations.
Think about types of papers that might attract more citations (e.g., reviews, special issues, etc.) and use this citation potential as a criteria for acceptance.

Generally unethical approaches:

Encourage authors to cite the journal. Of course, at a basic level, citing articles from a journal is an indication that the article is on topic, but this has the potential to be abused. See this discussion of coercive citation practices.
Encourage editors to cite articles from the journal in their other work irrespective of relevance.
Collaborate with editors from related journals to encourage citations of each others journals

I don't know about your field, but in mine (where the publication process is notoriously slow, and IFs never get too big) you would probably have better luck with the opposite of your first questionable approach.  Journals being fast can attract higher quality papers.

And you might note the unethical approaches are punished with with lower/no IF scores when discovered.

@Kimball +1 good point. I imagine there must be a spectrum of practices. In particular, more subtle forms are likely to go undetected (e.g., editors choosing to cite their journal where they have a choice, but only where it seems appropriate in the context).

@Kimball Has there really been a case in which the impact factor of a journal has been altered or retracted after proof of citation fraud? I never heard about it but I would be interested.

@Federico I feel like I've heard about this a few times. Here's one news post about a few journals that were noted for citation irregularities: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0101-20612013000300001

@FedericoPoloni As I recall, examples are given in the links in the answer and comment here: http://academia.stackexchange.com/a/44918/19607

How does delaying publication help, if the article will be cited at some point anyway?

@JDługosz I think the idea is that the article is posted to an "online first" or "early access" section. But it only gets official page numbers some time later. So, the paper exists for a while, before it enters into the date range used for impact factor calculation (which I think uses the official publication  with page number date). So readers become aware of the paper and it gets a chance to build up traction. So that by the time it actually has page numbers, it is already attracting citations. At least, that's how it works in theory.

But if it was published in paper earlier and attracted citations, wouldn't it have the same score anyway at time X whether it was officially published at X or was published earlier?

@JDługosz So 2015 impact factor is calculated in 2016 as the number of citations given by 2015 publications in any included journal divided by the number of publications in the focal journal in 2013 and 2014. So say the journal publishes an article online first in 2012, but doesn't publish it officially with pages until 2013. Now also assume that the citations a this article will receive will on average be greater in 2015 than in 2014 because of this strategy (i.e. because an article receives few citations straight away because it takes time for people to read it and then incorporate it).

I see. I didn’t realize it had a fixed time window for which citations it counted.

You're asking two different, but related questions:

"How do journals improve their impact scores?"
"How do journals go from obscurity to highly respected?"

Those are related, but distinct questions.
For impact scores, they can begin targeting highly cited/citable papers. For example, some medical/public health journals allow for the publication of a "cohort profile" that goes over the basic recruitment strategy, underlying demographics, etc. of a cohort of patients. This paper will be cited continually by the papers that come out of that cohort, taking advantage of "...the details of recruitment may be found elsewhere [cite]."
One can also deliberately promote citations, for example by having lots of commentaries focusing on one or more papers in that journal. The International Journal of Epidemiology did this to great effect - while they were already publishing good papers, they were now publishing good papers and an accompanying commentary from someone fairly visible in the field.
In terms of obscurity to highly respected - by publishing and attracting high quality papers. That includes having the editorial team try to get good papers in their journals, sponsoring sessions at conferences with accompanying publications, etc.

Of course if you go too far with deliberately promoting citations, you will lose your impact factor.

Indeed - IJE's approach was an ethical version of this, but there's some very dangerous ones if all you want to do is tweak IF at the cost of everything else.


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Providing Methodological Support to Colleagues Outside One's Expertise a Career Killer?
I have a friend who works at a small university with limited resources. Since he has a gift for methodology and statistics he frequently supports colleagues with their studies. He helps with the methodology and data analysis often. It is not uncommon for him to support people in Education (his field), English, TESOL, and Business since to do simple studies in these fields involves descriptive stats, regression, ANOVA, etc. In other words, basic research methods
In exchange for his support, he gets to be second author on these papers.
His concern is all this wide variety in research on his CV. His own research is focused when he's the lead but whatever his friends want to study is up to them. There aren't too many others available to help out with the technical aspects where he works at. Therefore, If he ever applies for a job somewhere else, what would a committee think of such a chaotic CV?

My understanding is that this sort of cross-disciplinary consultation, leading to second authorship, is particularly common for statisticians, so I don't think hiring committees would be at all surprised.  As Wolfgang's answer says, though, this isn't a substitute for doing his own research.

I'm in exactly this situation, and I have separate sections in my CV on my "core" specialty (forecasting) and my "service" activities (inferential statistics for psychologists). One point is that coauthorships as a statistician come with rather little effort, and I'll have five such "service" coauthorships for every "core" paper I coauthor, so the CV sections are pretty unbalanced in length. Then again, I can't say what a hiring committee would say to this, being in industry.

I can't think of a case where research or publications outside one's core area would have hurt an applicant, and would think that most departments actually think positively about it. What's important, though, is that the research and publication record within one's core area remains strong and prolific. If you only publish a paper every other year in your own area, but 2 every year with people outside your area, then a department might legitimately question how much you actually bring to their table.


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How to anonymize research software in an abstract?
I'm writing an abstract for submission to a conference aimed at a rather small research community. The abstract should be submitted anonymously for double-blind review purposes.
The problem is that in the paper I describe a set of interoperable software tools which are fairly well-known within that community (thus, it would be reasonably simple for reviewers to infer authorship when acquainted with the software).
How can I anonymize the tools properly?
I need to go into engineering details, so I have thought about simply referring to tools by function, e.g., data processing tool, data analysis tool, data conversion tool, etc. (references would in reality a little more domain-specific). However, as the set of tools forms a relatively unique combination, reviewers may still be able to infer authorship.

Confidentiality and anonymity are different things.  There is no way at all of guaranteeing anonymity.  When you discuss the extremely enlightening experience of an unnamed one-legged Spanish lesbian lion-tamer in Sheffield, you have pretty much made certain that someone could identify her.
If it is important to your professional community, however, that community should protect that person's rights not to be discussed in public.
For peer-review purposes, I would suggest that it might be best to offer alternative terms for the concepts that you describe if that can be done smoothly, but otherwise to trust the community to be judicious and conscientious.  If we can't respectfully do that, we will never get anywhere with anything.

Thank you, I agree. However, I'm only concerned with anonymity for peer-review purposes, the tools will be named in the camera-ready version. I should've made that clearer in the question. The anonymity of the tools should serve to circumvent the constitution of any possible political or scientific prejudices on the side of the reviewers of course (not entirely unlikely in small communities where resources for tools are often fought over). Your last paragraph reads very sensible to me and supports my intuition.


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What is a suitable job title for someone responsible for data and software in a research project?
My PI has just asked me what she should call me when introducing me to visiting researchers. I couldn't give her a definite answer.
I work in a research project where I supervise its research data in terms of versioning, formats, conversion, storage, etc. In this function I've, e.g., written a data management plan. I also (and this is the gros of my work) develop software which is used within the project but is also generic enough to target other researchers. And finally, I work on my PhD thesis, albeit not in a structured PhD programme (in my neck of the woods you can write a thesis as long as you have one or more supervisors with the right to supervise PhD theses.
As of now, I've usually been introduced as the "project's programmer", which my PI finds is somewhat dismissive of my actual work and responsibilities.
What would be a good title then, one that could also be printed on business cards?

I've never done the job, or spoken to anyone that has, but the description you've given resembles the sorts of job descriptions I typically see for Lab Manager positions.

Do you want to continue your career doing this type of work?

@Ian_Fin: I'm in the humanities, where there are hardly any labs though.

@RemcoGerlich: Yes, I do. At least the software development/engineering part. Once that's what I'm doing exclusively, I could start calling myself an RSE (Research Software Engineer) I guess.

@Ian_Fin, depending on the organization, a "lab manager" may be either a very high-level or very low-level position.  For example, when I was at IBM, the entire organization at a whole facility reported to the lab manager.  But at the university where I work now, a lab manager is a technician who orders scope probes and parts kits for our student labs.

@NicoleHamilton I suspect it varies from field to field. In my field a lab manager would manage data, develop tools, consult on methodological issues for those working in the lab, and potentially contribute to grant applications. It would probably help if the OP specified the field they work in.

No it's just a different definition of 'lab', thus making one a manager of people, and the other of stuff.

How about "research software engineer"? There's a growing movement to recognise this as a valid academic career track - see, for example, http://www.rse.ac.uk/who.html

Yes, I'm aware of the RSE title (have in fact been at a related workshop recently). However, I thought that RSE wouldn't really reflect the data portion of my job.

@remcogerlich fair. "RSE and Data Manager"? I think you either have to pick the one you feel is best, or adopt an unwieldy hybrid title ;-)

This sounds essentially like my position: research programmer
It encompasses a lot, but perhaps 80% of it is helping researchers who know what they want to accomplish but have no idea how to get there.  It can include things like web scraping or cleaning up very ugly code, or translating a project to a different codebase, or writing simulations, or running models.  Version control often comes into play, along with data storage - I'm often teaching researchers about GitHub or S3, for example.  It also tends to involve data vis and data presentation (like on the web).
It also has an element of data science, where a researcher gets access to some data that has what they want but is too big for them to know how to work with or manage.  But I wouldn't call yourself a data scientist; it's a whole separate field with its own methods that often diverge from traditional research.
It sounds like "research programmer" encompasses everything you're doing, but sound a bit more grand and more accurate than what you're using now.  It's also one that is in official use elsewhere (in my case, the policy and think tank world), so that's a bonus.

He also manages all their data, so he could add "and data manager".

I am sitting with some people in a similar position, their official title is research engineers.
They actually follow a similar path to research scientists, including a PhD, postdocs, and permanent positions, but focused on producing high quality code and infrastructure rather than actual scientific results.

Hm, interesting. What's your field if I may ask?

@s.d I am in Bioinformatics. The developers work mostly on handling biological data from experiments and running simulations.

In the UK I would interpret "research engineer" as somebody who does research in engineering (not software engineering).

When I had this position, I was a research analyst. For what it's worth, the terms listed in all these answers are virtually identical from a resume standpoint.
Note that you should definitely consult with your HR department to find out what your official title is. Some places are sticklers about only using proper titles on business cards.

You could be introduced as the project's
data analyst.
This sounds more high level than programmer.

The data-related tasks the OP describes are data management, not data analysis. Unless there's something the OP is leaving out, this would be misleading.

@ff524 - Perhaps I'm reading too much into OP's job duties.  But then I reread "I develop software which is used within the project but is also generic enough to target other researchers."  How do we know this does not include data analysis?


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Accepting two conditional offers
I got two conditional offers for postgradute courses from two universities. The English requirements are a bit lower for one university (IELTS 6 with 5.5 in each section) than for the other (IELTS 6.5 with 6 in each section).
Since I will know my IELTS results next month at the earliest, I do not know which offer I should accept because I have to decide by the end of this month.
Is it acceptable to accept both offers? I am fine with paying the deposit or other fees even if they are unrefundable.

Couldn't you just tell them exactly that? "I am waiting for my IELTS results and cannot definitely accept your offer yet, but I am certainly still interested." I would not firmly accept and then still weasel out.

Since your offers are conditional, what do their rules say about accepting an offer and finding out later that you can't fulfill the conditions?

@Lawrence I suspect that Elastic Lamb is asking about the consequences of accepting the lower IELTS offer. If they fulfill the higher offer, then they will also have fulfilled the lower offer.

@MJeffryes Thanks, that makes sense. I don't see an ethical problem with the OP using the other uni as a safety net, especially since he/she is willing to bear any financial penalties for backing out after accepting. The terms of the offer should explain any other consequences, but the OP should consider contacting the uni to clarify this.


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Email to potential PhD supervisor
I am a PhD applicant and I am preparing to send an introductory email to a potential supervisor.
I have two questions:

I am self-funded. Should I mention this in the initial email?
Is the following sentence grammatically correct?

I would be delighted to undertake a research project under your supervision, kindly let me know if this might be a possibility; I have attached my CV and academic transcript for your consideration.

Are you self-funded because you are independently wealthy or because you carry funding you earned on your own?

About 30% from earning post-university and 70% from my family.

Which country(ies) are you applying in?

The UK only (I live here)

From discussion with some UK academics, self-funded PhDs seem to frequently be frowned upon ("I don't see that this person should get to do a PhD just because they're rich!"). So, it might totally be a good idea to conceal this fact, and, better, reconsider your decision. Being self-funded doesn't help you and can actually hurt you.

I remember meeting with a potential supervisor who told me he was very concerned about students being self funded, particularly in fields like computer science, as typically there is enough funding that if something is worth doing, it'll almost certainly be able to be funded in one way or another. If you're in humanities that's obviously a different kettle of fish, so I think whether you mention this depends on your field.
I would never personally use the phrase "kindly let me know" as it may come off as accidentally abrupt, but perhaps something like "please could you let me know if this would be a possibility based on x, y and z?". I'm assuming this is only a small part of a wider email, so be sure to appeal to their own research, and explain why they're a good fit to your future work.

You could mention self funding or not. However, it is important that you give some indication of why you are interested in this person and what it is in your background that might interest him/her in you. Mentioning past research projects in the same specialty would be helpful. Your statement is fine, but only as an opening.
In particular, you should investigate the background of the potential supervisor, including publications and past students. In mathematics, for example, the Genealogy project can give you information about where the person fits - advisor and students. For famous people, even wikipedia will give you information.

Don't mention self-funding. First, find out if the prof is interested - they may have some funding available. Any PhD that is worth doing is worthing being paid for by a studentship or other funding and offering to be self-funded has the danger of underselling yourself.

Thanks, yes it is just part of more detailed email - should have said above. Re funding, I understand it's better not to mention it. Does this also apply for enquiring about potential MRes projects too?

I think a good introductory email should highlight your strengths and your project.
A PhD is your task, a supervisor in my experience will advise, but it is down to you to come up with the research ideas etc.
I would mention that you're self-funded as it can only increase your chances of them looking for funding.
Use the website www.jobs.ac.uk and show some initiative and that Professor may help you get some funding you have already introduced.
Be proactive and best of luck!


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What's the meaning of "Topics in ... "?
I have seen some courses in the university that start with "Topics in this ... Topics in that ...", I have also seen some books that use that word "Topics in Algebraic Graph Theory", "Topics in Structural Graph Theory", so, I've been thinking, what is the difference beetween a book of "Algebraic Graph Theory" and one of "Topics in Algebraic Graph Theory"?, What is the meaning of the word "Topic" in academia context?

Also "Special Topics"

I suggest this Question belongs not to Academia, but to English Language Learners.
If you insist "Algebraic Graph Theory" and any kind of "Topics in Algebraic Graph Theory" are different, can you explain how, please?

I think it belongs here, because I am asking about how the concept is applied in this context, not the word itself, in my native language, topics is translated as "topicos" and there are some courses in my university like "Topicos en Teoria cuantica de campos", "Topicos en aquello" and I still really wouldn't know how the word "Tópicos" is used. The meaning of topic in a dictionay is: "a matter dealt with in a text", but I guess in every book there's always a matter dealt in the text, so from the definition it may look like a pleonasm

@RobbieGoodwin I don't know what algebraic graph theory is, but a "Topics in Language Acquisition" would probably delve into a professor's favorite research topic, for example  how bilingual English/Spanish kids learn English and Spanish syntax.

"Topics in" usually means that the content is

not meant to be introductory (i.e., the reader is assumed to already have some prior familiarity with the subject), and

not meant to cover "all the important things", but can focus on a selection of (well) topics the author is interested in.

For example, a "Topics in Representation Theory" course can afford to skip both the basic properties of finite group representations (as it is not introductory) and focus (e.g.) on quiver and Hopf algebras. Often, books will have more precise titles than "Topics in...", but lecture notes often take their titles from those of the classes, which are often intentionally vague so they don't have to be changed every year depending on the lecturer. For a department, calling a class "Topics in Algebra" is an easy way to offer a course that will be on something different each year without the trouble of having to rename it every year.

To elaborate on the last point, the department will often rotate the local specialists in subject X through the "Topics in X" course from year to year, with each of them teaching their favored perspective. So you might want to ask who is teaching it this year and what they plan to do.

This answer matches my experience, but it also has a corollary that's often important. Ordinarily, a student cannot take the same class more than once for credit. But that rule doesn't apply to topics courses because (even) university administrators understand that such a course will be about different topics in different semesters.

It may also mean that the course will not progress linearly through things that build on one another, but rather cover disparate, self-contained aspects of the broader subject.

It also means the lecturer doesn't have a good idea of what they're going to teach yet ...

@Andreas: Your administrators > my administrators, then. We were not allowed to retake "topics" courses more than once, because they all had the same course number. Once you have a course number in your record, you can't retake it. Even if it's with different professors, and a different syllabus.

@Inkblot When a new course is proposed at my university (or at least in my college) the paperwork includes a lot of questions about its administrative aspects, and one of those is whether the course can be repeated for credit. Since the paperwork is filled out by (or at least in consultation with) the faculty who are likely to teach the course, the answers are usually reasonable. Officially, the higher administration can change these things (or indeed can change the syllabus), their usual practice is to approve anything that isn't obviously bad.


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Should I include my StackExchange profile in my CV?
I've been thinking that sometimes here on Stack Exchange, people make very good questions and give very good answers, in my case, I have learnt a lot from the community and when I post a question I try to make an effort to formulate it in a proper manner to avoid downvoting, so, when applying for a job or an academic position, would be correct to also make a reference of your Stack Exchange profile?
I believe that people that are hiring you, may have a better glimpse of you interests, what you know and what you don't know from the answers and questions that you make, so, is it a good idea to also show it?

Nobody cares, but are you sure you want anyone to be able to look at every post you made with a fine toothed comb?

What field? ...

well,  I was thinking in physics, math, programming, electrical engineering ... I don't now, at least, those are my interests

my question seems to be a duplicate. Do I delete it?

You may get a small bump by being a good answerer on the technical stacks, like Physics or Cross Validated. I've heard MathOverflow in particular has a decent recognition among mathematicians. Especially if you are applying for a teaching position, showing a good track record wouldn't hurt, even if only 1 in 25 people have heard of Stack Exchange (which would be a very high proportion in my experience).
By "good" I'm thinking of rep north of 5,000 at least, but I'm not familiar with the standards of those Stacks in particular.
That said, your thought about:

I have learnt a lot from the community and when I post a question I try to make an effort to formulate it in a proper manner to avoid downvoting

... is, I'm sorry to say, pretty meaningless and confusing to explain to someone looking to hire you in an academic position. No one cares that you didn't get downvoted when asking a question online. That is basically the bare minimum to participate in these sites, even though I do acknowledge the communities can sometimes be harsh.