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What is a healthy DFW rate?
DFW rate stands for the proportion of students in a class or group of classes who earn a D, an F, or Withdraw. This has become a trendy metric in recent years due, in part, to its negative correlation with retention. A search for DFW on the Chronicle of Higher Ed site, for example, returns 10 hits since 2018 - several of which mention retention as well. As a professor of mathematics at a small, public university in the US with a focus on the liberal arts, I've found myself thinking about our DFW rate and found that I don't really know the answer to the question:

What is a healthy DFW rate?

Such an answer would certainly be multifaceted (balancing faculty expectations with those of the administration) and would also depend on the student body. Since this is not a discussion site, though, let me be clear that I'm specifically wondering:

Are there any authoritative publications on the question?
Is there any publicly available data that would allow us to compute or estimate DFW rates for specific classes at a wide variety of schools?

Note that I have found some papers (like those in the Chronicle) that discuss DFW rate. They all tend to be very isolated, though, dealing with one or two anecdotal cases without mentioning any specific goals for DFW rates.
With regard to question 2, I should mention that I'm quite adept at dealing with IPEDS and, while there's plenty of data surrounding grades and retention, there doesn't appear to be any data of sufficient granularity to compute, say, the DFW rate for Introductory Calculus.

What's IPEDS? .

I think this question is about the content of your research and should be closed.  You should be looking in higher ed research journals, not the Chronicle.  There is no simple answer to this question as there are many variables which relate to student success.

Also, it's a mistake to study student success using only one metric.

@AnonymousPhysicist I am a mathematician so this question is definitely does not concern my research; rather, it concerns my experience in academia. I do agree that just one metric is insufficient to measure overall student success. This just happens to be the one I'm curious about with regard to this specific question.

The funny thing about this question is that it is hugely culturally variable.  Various European countries seem to regard as optimal DFW rates (say 60%) that would be considered completely unacceptable in the US, and this is despite having strict qualifiers for who should go to university.

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

@AzorAhai-him-:  The Integrated Postsecondary Education Data System, a clearinghouse for US government statistics on colleges & universities.

@AlexanderWoo Yes, you're absolutely right about the cultural variability. I apologize. I did add that I'm in the US and I think that the reference to the Chronicle of Higher Ed contextualizes that a bit as well. Thanks.

Healthy for what purposes? What goals are being considered? For example, if the course entrance selection criteria were perfect the DFW rate should be zero.

This is too variable and opinion-based (healthy???) for a good answer here. My preferred rate is as close to zero as I can make it since my philosophy requires teaching every student. There are a few, unfortunately, who don't really care enough to do the work.

@Dan: You can't have a zero W rate, even with perfect course entrance criteria (sooner or later, someone is going to get hospitalized or drop out or something). Realistically, you also can't have perfect entrance criteria, and targeting a zero DF rate is likely to result in locking out some people who otherwise would have benefited from the course. The real question is the extent to which that is compatible with your pedagogical goals.

At some schools (or faculties or subjects, a university is usually a too coarse thing to look at) some courses are basically sieves. Many students consider to do perfectly fine if they managed to pass them.  These often includes stuff like calculus, mathematics, anatomy. Once they get their diploma, it does not really matter what grades they received i their courses. They passed they were admitted to the their final state exams and they passed them and that is what counts. In such cases half of the students that passed may have the lowest grade and a third of the overall crowd may fail.

Determining a healthy DWF (or DFW or DWFI, adding Incomplete) rate is a policy question, since it depends on how your university would define "healthy." For instance, is "healthy" a matter of sustainable enrollment delivering tuition dollars that keep the university budget sound; is "healthy" a matter of outcomes for students who want to graduate in 4 or 6 years; is "healthy" a matter for departments who want to ensure they have enough students progressing into and through their majors and minors; is "healthy" a comparative measure between your institution and institutions like it (small liberal arts colleges, R1s, community colleges); is "healthy" a question of programmatic rigor? It's likely that an academic affairs unit will consider several factors at once if they are determining a target measure.
As a result, the literature usually doesn't refer to a single numerical "healthy" rate. Indeed, I have seldom seen "healthy" used with DWF. Instead, I usually see "high DWF" or "low DWF," which are set relative to expectations within a specific context. For instance, how is one course's DWF rate as compared to expectation or to an average of similar courses, or how is one university's DWF rate compared to its peers? For example:

Mutanyatta-Comar & Mooring. (2019). Evaluation of a peer-led team
learning-flipped classroom reform in large enrollment organic
chemistry courses. From general to organic chemistry: Courses and
curricula to enhance student retention. American Chemical Society:

The course presents conceptual challenges for many students in these large sections resulting in a high DWF rate (approximately a 30% DWF rate).

Ferri et al. (2019). Three models for blending classes in a multisection course. Blended Learning in Practice : A Guide for Practitioners and Researchers. The MIT Press.

The DFW rates, another department-centered metric for the course, falls in the range of 12% to 14%, which is comparable to other required junior-level courses in the department.

Tallarico & Wisniewski, M. A. (2015). A better way to teach principles of microeconomics? Evidence from the classroom. Journal of the Academy of Business Education, 16, 21–38.

The method of assessment had a clear impact on the DWF rate, increasing from 10 percent when using the quiz method to 56.67 percent when using the exam method.

So beyond the general definition of what the measure looks at (failure, withdrawal), there isn't a standard way to interpret the rate.
Finally, it's possible that program chairs and other leaders have a gut idea of what a good DWF rate looks like in their context. For instance, in mine (large public university with an access mission in the United States), lower than 10% is low / good and higher than 30% is high / bad. But if I had to argue one was high or low in a research or assessment context, I would always carefully define compared to what because those terms don't mean much by themselves.

You are correct to emphasize that none of these citations talk about a healthy rate. Just an observed rate.

@TaliesinMerlin Yes, you're exactly right - it's policy question. I was motivated to ask the question because we (our math dept) have been asked by our administration to lower our DFW rate without clear policy on what a reasonable rate might be - let alone data support such a rate.  Thanks!

@MarkMcClure: You might want to consider one of my observations about universities: the political and economic context pushes most universities in the direction of becoming a diploma mill.

authors: Vladimir F Героям слава


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Am I supposed to submit my application only by email, or by post as well, or do I query? Job posting for reference/ language below
The job application description states: "Interested candidates must submit, by email ..... Send this and two LORs to:
[Enter snail mail]
[Enter email address]
I want to both; email and send my application by post since the dossier is long, almost 50 plus pages. Do I query if that is acceptable or do I just send by email?

If you do both, make sure the snail mail says that there's email too. Separate point: are you sure that 50+ pages is appropriate? No recruitment committee I ever served on would expect or read that much material at the start of a search.

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

@EthanBolker: How many pages are appropriate is probably a very culture depend thing. In my experience (pure maths in Germany), 50 pages is not uncommon. One reason for this is that many people like to attach teaching evaluations, which might already be 20 or 30 pages. Of course, nobody will read all of those 50 pages - but different members of the committee are sometimes interested in different parts of the application (and they might read more of it during later stages of the process).

It's hard to gather from the context of only the snippets you've provided, but my guess is that the application is to be sent via email, whereas the LORs are sent by recommenders directly either by mail or email (at the recommenders' preference). If you read the instructions with that thought in mind, do they make sense?

A comment I once (probably about 10 years ago) heard from a computer scientist about a job applicant who sent his application by snail mail: "What world is he living in?" Of course the situation may be different in the humanities.

Someone mailed  me a letter from US in the middle of December. Today is Feb. 3, I have not received it yet.

If they give you the option of emailing or uploading PDFs, you can pretty safely assume that's what they prefer.  If you send paper (especially 50+ pages!), someone's going to have to scan it so it can be shared with the entire search committee or posted on their internal website for the rest of the faculty in the department to weigh in on.  Save them the trouble.

source: Stack Exchange

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sort: votes


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Supervisor not allowing to submit Thesis
I am in very tense situation. My supervisor is not allowing me to submit my Master by Research thesis.
I have already told him that I have some potential fully funded PhD opportunity and he initially agreed but now he is creating problems. Earlier he wanted me to do PhD with him which I refused now I feel he took his personal and creating hurdles for me.
On the other hand, potential supervisor who offered me PhD wants me to join ASAP and I can lose this opportunity if I will not join in 2months.
I am thinking to withdraw Masters and join PhD? Is it a good decision? I have spent 2yrs and worked hard for this but now he is offended and creating issues.
I tried to change supervisor but 2-3 supervisors refused after knowing name of my current supervisor..he doesn't have good relationship with other faculty members.
Please advise what I should do?

What is the official reason that your supervisor gives you for refusing your submission?

I would look up your university policy regarding thesis submission.  At my university, we have strict policies for your situation.  In a nutshell, the student has the power to submit without the supervisor's permission.  However, as this is going against the supervisor's judgement, then a thesis may fail.  So only take this route if you know for sure you'll pass.

Are you able to get a second opinion about your Masters thesis at all? If you have evidence that it is of an adequate standard and you are convinced yourself that it is worth the risk of submission on your own then do so

My co-supervisor is happy with my work and thesis. Unfortunately, both my supervisors don't have a good relationship with eachother. And I am suffering from it. Moreover, as per University policy, only main(principal) supervisor has the authority to accept the thesis and recommend external reviewers.

@Erwan there is no official reason. Unfortunately, University gives all rights to supervisors which is not good sometimes.

Can you change which advisor is principal?

I tried alot but no one in the department want to do it because of having issues with him

Perhaps you can employ a double track strategy. If the new supervisor is willing, agree to join them and do what is necessary to do so. They should be made aware that it is possible that the masters won't be awarded.
Simultaneously pursue some sort of action at your current place to "force" your current advisor to relent and let you finish. This might require a petition to higher authority with a claim of unfairness. This sort of thing can get messy if you don't have any alternatives, but in this case you have a good one.
So, rather than withdrawing, put the responsibility on your current university to do the right thing. Perhaps they will, but only if you make it a bit uncomfortable for them to not treat you fairly.
But, I would first, you could just inform the current advisor that you are joining the other. You don't need to go beyond that. Perhaps he will relent, but if not, press your case with someone higher in the hierarchy.

Thanks for your suggestions. Actually I won't be able to join PhD if I will be enrolled in Masters. I can only join PhD either by getting completion letter for Master or by withdrawing.    Yes, escalation to higher authorities can help but it can delay and make things more ugly n complicated.   I got conditional offer for PhD where they asked me to give completion letter of Masters....(I still need to check if they can accept me without Masters by withdrawing Masters)

A much harder situation then. Good luck with it.

But, as you state it, it seems a mistake to continue with your current advisor. The future doesn't seem rosy there.

Yes Right. Planning to discuss and negotiate things with him once politely before taking and bug decision.

I had a late thought. Explore the requirements for an MS at the new institution. It isn't outside the realm of possibility that you could just move your current degree there. The new advisor might need to be involved. I can't predict success, but it might be worth an exploration.

@All... after waiting for more than a month, he replied and highlighted some issues which are already mentioned in the thesis in detail. My work is accepted in a ToP rank conference without his name on it but he is still not happy with it. Also, political problem between my main and co-supervisor also affecting me. I am afraid may be I will have to withdraw my master and join PhD in other insitutute. All my hardwork and efforsts of 2years will be wasted.

Since your supervisor doesn't give you any reason (and according to your comment doesn't even have to), it means that he could potentially postpone your diploma forever out of spite. You shouldn't have to withdraw from your Master just because of your supervisor's ego. His behavior is obviously unfair and unethical, so I think you should consider contacting the ombudsman or director of studies in your institution. Before that ask him again explicitly, preferably in writing, why he doesn't want you to submit. If he gives you a flimsy reason or no reason at all, it will be easier to make your case with the ombudsman.

@All... after waiting for more than a month, he replied and highlighted some issues which are already mentioned in the thesis in detail. My work is accepted in a ToP rank conference without his name on it but he is still not happy with it. Also, political problem between my main and co-supervisor also affecting me. I am afraid may be I will have to withdraw my master and join PhD in other insitutute. All my hardwork and efforsts of 2years will be wasted.

@Kevin as I said I think you should contact the ombudsman in your institution, or at least the student union, maybe they can give you advice. From what you describe it looks like a blatant abuse of power.This is why I think you need to escalate this: this supervisor is abusing his authority, he's unlikely to stop by himself. Ultimately the institution is responsible, and they certainly have rules against this.

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Best template for Poster presentation :First time(Conference)
My paper has been accepted in a conference related to computer science.
I need to prepare a Poster for presentation. This is my first time, I tried to find some good templates but ended up nothing. I am confused. Could you please advise some good templates where I can prepare a poster? and please give some suggestions to prepare a good poster. Thanks

I am afraid a good answer should cover too many aspects. Could be possible that you look at old posters from the group,  or even you work on that with a colleague eventually presenting at the same conference? At least from a graphical pov having homogeneity is good for the recognition, though it mainly concerns the group head.

Your institute might have a poster template available

Definitely worthwhile looking at previous posters from your conferences and other plus hunting around for posters from your department and team. There are some good sites that go through the background and with more concrete suggestions.
For a more traditional style of poster - https://colinpurrington.com/tips/poster-design/
There has been a spate of new poster styles if you are feeling adventurous - London School of Economics
-

Correct me if I'm wrong – but don't the last two links basically feature identical content?

Sorry didn't realise that. I will delete Rossi's one.

There is no “one size fits all” presentation template...
List the headings for what you need to say and cover then go from there.
So:
1. Bio

Intro
Etc

You need to anticipate what questions may be asked and that helps focus on what you should cover. Usually the issues and solutions are interesting...

Can you explain what "Bio" is?

@user114084 your BIOgraphy - who you are...

Thank you! I waa thinking about biology:)


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APA citation of two articles with no author, no date, and the same title?
I'm looking to cite both of the following articles:
https://www.sourcewatch.org/index.php/Institute_for_Free_Speech
https://ballotpedia.org/Institute_for_Free_Speech
For web pages like this, my understanding is the citation should look like this:
[Title]. [Web Site]. Retrieved from [URL]
Since both have the same title, how should I distinguish between the two in in-text citations? Should I list both the title and web site somehow?

Pretty sure those articles do have dates, because they’re wiki articles that you should be able to check the edit history for?

Curious: What sort of publication is it that requires formal citations yet allows wiki articles as sources?

For citing wiki content, which is likely to change over time, it's generally best to cite to a specific dated version of the page. For instance, rather than the URL you give, I'd cite to https://www.sourcewatch.org/index.php?title=Institute_for_Free_Speech&oldid=745869 and specify "22:22, 15 February 2019" in the citation. Otherwise, a later edit might change the page so that it no longer says what you cited it as saying, and then where are you?

@puppetsockreinstateMonica Wiki cites can be appropriate for illustrating how an issue is popularly discussed/represented (e.g. the two links in the OP give very different pictures of the same organisation - that difference of representations may be of interest in itself) or when definitions are changing faster than more conventional sources can keep up. See e.g. this article - it's in a judicial context but a lot of it is applicable to academia.

("Title of the page", n.d.a) and ("Title of the page", n.d.b) would combine:

naming the title in quotation marks "Article Title" due to the unavailability of an author; and
the n.d. (no date) due to the unavailable date; and
the letter that is added to the date because of multiple same-titles and same-dates (a, b ...).

However, your case is special as the first link is a Wiki. As Geoffrey Brent wrote in a comment, in case of a Wiki, you can click on "View history" and find a permalink to an article's current version with a date attribution. You can then link to that versioned permalink with the date. Here is an example of a version history page pertaining to your first link; the permalink to the most recent version (Feb. 2019) is this one: https://www.sourcewatch.org/index.php?title=Institute_for_Free_Speech&oldid=745869 (you can find this link by clicking on the most recent date listed in the version history page).


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How do I cite this old postcard?
https://digitalcollections.nypl.org/items/510d47de-036a-a3d9-e040-e00a18064a99
I would like to block-quote this postcard in APA style. The web site has prepared references citation, but it doesn't use the author's name which is clearly shown in the image itself. And if I'm not supposed to use the original author's name in the references citation, how do I format the in-text citation?

Can't help but link to this: https://www.chronicle.com/article/Citation-Obsession-Get-Over/129575

Forget for a moment APA style and ask what a citation is: A way for a reader to find the source you used so that they can check themselves. APA and other styles provide sort of a general format to do this, but the essence and end-all is not that you slavishly follow the style, but that you follow the spirit of making a resource retrievable with the information you provide.
In the current context, that means that whether or not you provide the author's name doesn't really matter: Knowing the author doesn't help anyone find the postcard. So just go with what is suggested on the website to cite the document.


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Discussing one's working ideas and possible research projects in PHD application
I am a senior year undergraduate student in Computer Science, graduating in a year and looking forward to pursuing a PhD. I have a good experience with the research topic I want to work on, with a couple of papers published and a couple of more getting lined up for publication. As I will be applying for PhD programs to the research groups of my interests, will it be a safer bet to reveal my research ideas for the next couple of years with them, which I believe are capable of publishing in academic conferences or journals? It would obviously be a point of strength in my Statement of Purpose to demonstrate a clear research path and vision, but then how worthy are those possible research gaps I might possibly hint towards in my application. I would love to do them under the Principal Investigator who might be interested in it, and who might eventually accept me as his student, but I would be applying to a few of them and leaving off research ideas to someone who you won't be working with eventually sounds a bit scary to me. Obviously there would be some layer of abstraction with which I will be pitching my research vision in my Statement of Purpose, but should I be too much careful regarding it?
Any idea regarding how this works would be really helpful.

will it be a safer bet to reveal my research ideas for the next couple of years with them, which I believe are capable of publishing in academic conferences or journals?

This is the entire point of doing a PhD - you are supposed to share your ideas with your collaborators! If you deeply distrust your potential research group to the extent that you worry that they'll steal your ideas without crediting you, you should probably not join them.

Obviously there would be some layer of abstraction with which I will be pitching my research vision in my Statement of Purpose, but should I be too much careful regarding it?

The scenario you are concerned with is highly unlikely. Professors would probably not steal your ideas from your applications, but rather actively fight to get you into the program so that they can start working with you (if indeed you have a very good idea).
If you truly have good, novel, ideas that you feel are worth publishing, and are worried about them being stolen, how about working them out into a two-page note which you can then put up online/on ArXiv, and then reference? This leaves no doubt as to the ownership of the idea, and gives professors a chance to assess your work and your capacity to convey it in writing. However, if that is really the case, you should probably contact professors individually (via email) with your manuscript and have them evaluate it. That way your emails act as evidence that the idea is yours.


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The Page Rank effect of Academic recommendations for Graduate School
I am an undergraduate who comes from a relatively small department, with moderate research activities being done around. We don’t have any research lab or dedicated research personnels in my field of interest at our school. I have developed an interest on my own regarding the topic and I’ve been working on it for the past one and half years. I have 2 publications and 3 more working papers , and I am pretty sure that I want to pursue this topic going ahead for graduate school. An essential component of graduate school application is Letters of Recommendations. I have learnt from many research groups homepage and some of my friends from natural sciences department that If I want to work with professors who are the leaders in research of  ‘XYZ’ , only the Professor who have made significant contributions in the field ‘XYZ’ or who is a collaborator of the potential advisor have a strong case on the letter of recommendation. I have been supervised by two different professors, who are very much unrelated to the field( as I’d discovered my interest on my own ). I have demonstrated research and other parts of applications to back me up , but I’m worried if Letters of Recommendations not coming from the same ‘XYZ’ area Professor will not help my case. Is the Page-Rank type effect which I fear really true in academia ?

I’m worried if Letters of Recommendations not coming from the same ‘XYZ’ area Professor will not help my case.

While a letter from someone who is an expert in the subject of your doctoral research is better, it's much more important that the letter writer know about your research record.
Sensible graduate admissions committees know that not all universities have faculty in every research area.  They care more about what the letter says than who wrote it.


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Professor expressed interest in working together, is not responding to emails?
Recently I received contact info for a professor close to me, with similar interests (Professor B), from another professor I have a long-standing working relationship with (Professor A).
I spoke with her at the beginning of the month, and had what I thought to be a great call.  She expressed interest in having me work with her on an upcoming grant remotely, in preparation for applying to her graduate program in the upcoming application cycle.  We ended the call with the decision to have me touch base with her in a week, when she would know more about her grant.
The next week, I sent her an email to follow-up, and set up a call to talk more about the project and set up time to visit her lab (something we discussed on the call.  No response for one week.
I sent another email, and received a one sentence response: "Things are hectic now, please touch base in a few days".  I waited 4 days and sent another short message.  It has now been a few days and I still haven't gotten a response.
What are my best next steps?  Should I write this lead off, and not bother sending anymore emails if I don't hear back?
EDIT: That is to say, how long should I wait for a response before reaching out again?  I don't want to be bothersome, but I also don't want too much time to elapse and this project to possibly be scrapped or forgotten.
I also have the option of going to Professor A and starting some work on the project while Professor B is otherwise occupied.  But at the same time, I don't want to seem like I'm "going around" or otherwise excluding Professor B.

Thank you for your reply.  I definitely don't need a response right away, but understanding the competitiveness of my chosen field, it will be extremely difficult to get into a program without having worked with a professor in said program directly.  With that understanding, I do need to know the status of this project so I can make alternate arrangements if it will not work out.
A better Q is: how long should I wait for a response before reaching out again?  I don't want to be bothersome but I also don't want too much time to elapse and this project to possibly be forgotten.

"Ignoring" your email is a very different thing than "too busy to respond".  Her reply clearly signaled the latter.  I think the title is misleading.

It's normal for professors to be extremely busy for an extended period, and not be able to respond to anything that requires significant thought or planning.  I would not say that she is "ignoring" your emails.
I would wait about a week from your last message, and then send one more message with a deadline.

Dear Professor B,
Just wanted to touch base again regarding my application and our discussion about working on Project X.  I am trying to make plans for the next few months, so if we are going to move ahead on this, I would need to know by date MM/DD.  I really hope it works out and look forward to hearing from you soon.

After that, do not send any further messages unless you get a substantive response from her.  If you don't get a response by the deadline, move on and look for other opportunities; either she isn't interested, or she hasn't been able to make time to evaluate your request, which would itself be an indication that she wouldn't be easy to work with.

Thank you for your advice.  I understand professors are often extremely busy and can't respond to all inquiries right away.  However, I do feel like I'm being bothersome when I am having to check win weekly about a subject with little, if any, feedback.  I, and many colleagues, have frequently experienced non-response as a way to decline academic inquiries in the past, so I believe my unease is justified.

That is why I am suggesting only one last message, with a deadline.  This removes ambiguity and makes it clear to her that you will interpret non-response as negative.  If you'd put a deadline in your previous message, you wouldn't need to send this one.

You made good points but it takes less than a minute to send an email saying that you're a little busy and will respond as soon as you're able.  That really should be a basic courtesy in any professional setting.

@G.Allen: If you have a different suggestion, please feel free to post your own answer.

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Withdrawing a manuscript after reviews - acknowledging reviewers in new submission
My coauthors and I have submitted a paper to a fairly prestigious journal. We have received favorable reviews and were in the process of incorporating the reviewer's suggestions into the final revision.
Unfortunately, a few days ago a crank paper was published in the very same journal. The paper received a whole lot of publicity, and has severely damaged the journal's reputation. We no longer have confidence in it.
We plan to withdraw our paper and submit it to another, more reputable journal. However, we are not sure how to go about this, since the current version of the paper already contains acknowledgements pertaining to the anonymous reviewers (who have done stellar work) and their suggestions.

What's the appropriate way to acknowledge these reviewers in the new submission? Should we submit a new version of the paper to the new journal, leaving out the acknowledgements to avoid confusion? Should we leave them in and write a letter to the editor of the new journal explaining the circumstances? Something else altogether?

Not a duplicate but quite closely related such that the answer in essence applies here too. https://academia.stackexchange.com/questions/18027/how-to-acknowledge-contributions-of-anonymous-referee-in-new-paper

You acknowledge the referees by writing "We thank anonymous reviewers for important and insightful comments on an earlier version of this manuscript."
This is no different whether your paper was previously rejected from another journal, you withdrew it from another journal, or whether the reviewers worked for the journal where your work is ultimately published.

I would not rush to withdraw the paper. "A few days" does not seem to me time enough to know that the "prestigious journal"'s reputation will be "severely damaged".
Since the paper has not been finally accepted, it can't be published until you submit the revised version. Wait a while to see the dust settle. Talk to colleagues. Then decide whether to withdraw.
If you do withdraw and resubmit elsewhere you can acknowledge the contribution of reviewers of an early version of your paper.

I upvoted. I am showing my age here, but it used to take more than “a few days” for a “prestigious journal” to do the death spiral down the porcelain convenience.

I appreciate the suggestion, and you for comment @EdV. But in this case my specific question is not whether we should withdraw the paper, or whether our assessment regarding the future of the journal is correct. It's only and strictly "What's the appropriate way to acknowledge these reviewers in the new submission?"

Just thank the reviewers for their exceptionally helpful work on an earlier version of the manuscript. No need for details.

@Z.A.K.My recommendation is in the last paragraph of my  answer. But I do think you should wait.

@Ed V: ... it used to take more than “a few days” for a “prestigious journal” to do the death spiral down the porcelain convenience --- I'm fining it difficult to reconcile "a prestigious journal" and "a crank paper was published in the very same journal". I don't know the OP's field (later -- it's math), but (in mathematics) I find it hard to believe a crank paper would be published in something like Annals of Mathematics, and even if so (by some weird accident), that this would within ONLY a few days undo nearly 140 years of excellence.

It's a fairly prestigious journal in my specific field. Not a top journal in mathematics in general by any means. The Annals could obviously survive a case of publishing high-profile crankery. The journal in question won't. That said, I'm really not interested in discussing or debating the specific case, whether our judgment about the fate of the journal is right, or whether withdraw our paper is wise (and this is not a discussion forum anyway). Was merely interested in the proper procedure of acknowledging the previous anonymous reviewers.

@Z. A. K.: I don't see a problem with acknowledging the referees of an earlier version, as Ethan Bolker suggests. I suppose the real issue is how to state this in a way that clearly indicates the earlier referees were not associated with the submission to the later journal, specifically doing this in a non-awkward way and in a way that doesn't provide any clues as to why the  later journal is different from the journal for the earlier version.

@DaveLRenfro Indeed, that is precisely what I intended to ask about.

It is utopian to expect that a journal never makes a mistake. A single cranky paper is likely to be dealt with in time: retraction, correction, etc.

Not if the author is also the journal's editor. Related math.SE question: https://mathoverflow.net/questions/433278/czelakowskis-claimed-proof-of-the-twin-prime-conjecture

If the editor who handled the paper is an editor at multiple journals, you could ask if they would consider let you withdraw and submit it at their other journal in which case they would just use the same referee reports. It's not unusual for referee reports to be transferred like this. You could also ask for them to send the referee info to another editor at another journal, but that's a little riskier because they could be offended.

That would raise a conflict of interest for the editor unless the journals have the same "corporate" parent. And ethical editor would refuse any such request.


text:
Documenting and publishing an algorithm with zero experience
Apologies if this is a loaded question, the closest thing I can find is this post and while some of the answers were helpful, I feel I'm not close to solving my problem, hopefully this thread can become a guide for people like me in the future.
Let me start by saying I'm not an academic, at least not traditionally speaking...
I'm a self-taught, hobbyist programmer, I've been working with cellular-automata for a while now, and in my quest to improve performance, I developed an algorithm that in short, minimizes the number of cells that require iteration every step, greatly reducing overhead, instead of iterating over the entire grid cell-by-cell as it's done traditionally.
What I want to do is document the algorithm in a paper and publish it, my reasons for wanting to do this are:

Because I genuinely believe it can be useful to other people working with cellular automata.

To get credit for it.

Because I think it'll look good on my résumé and help me with job hunting.

So, I've been learning about how papers written, formatted and published, as well as studying other papers as examples and frankly the whole process seems daunting.
Let's start with the writing, this is something that's brought up here a lot, but research papers use complex language in their writing, to my understanding, the reasons for that are conciseness, and because the papers are written by researchers, for other researchers...
First of all, I want my paper to be accessible to the average Joe like me, and I know I can concisely communicate my idea using (mostly) plain English, but I'm still worried about whether or not that will acceptable.
Secondly, what of the contents of my paper? I understand the general structure of a paper, starting with an abstract, keywords and an introduction, and ending with conclusions and references, but what about the actual body of the paper? I mean, I have a general idea of what I'll talk about (Briefly go over the general structure of a CA, provide pseudo-code, flowcharts, algorithm analysis of HOW performance is actually improved, talk about additional nuances like chunk size, neighborhoods and which values to prioritize as input, etc...), but how do I order all of that? And what other points should I address?
And finally, where do I go to publish? ResearchGate might be a bit too ambitious, plus the process of submission and review seems to be quite lengthy, I got my eye on arXiv, which does require you to either be a registered author or be endorsed by one, but I do have hope I can get endorsed if my paper is good enough, plus according to this answer, I can submit to arXiv and then submit to ResearchGate at a later date, one concern I have is I've seen people (mostly on ResearchGate) mistrusting arXiv moderators for megalomania and even plagiarism, I guess I can protect myself against the latter by either uploading a preprint to my personal portfolio or even documenting the algorithm on Youtube before anything else, to prove it's my original idea.
So to summarize: I'm a hobbyist who developed an algorithm, I want to document it in a paper and publish it somewhere reputable, how do I go about doing that?

A [tag:preprint] isn't a "publication" in most fields; arXiv hosts preprints. ResearchGate is a social media site catering to academics; they'd like people to upload manuscripts published elsewhere, but again, that's not "publication" per se.

@BryanKrause I guess I'm confused about the entire process of publication, so I'm guessing I directly contact whatever journal I want to submit my paper, but I can also just upload a preprint to arXiv if I didn't feel like waiting.

I would guess: before submitting to journal X, look at recent papers in that journal which "document an algorithm".  Understand the format and methods used in those papers, and do the same for your paper.  Also "upload to arXiv" is not as simple as you make it sound: arXiv has some barriers in place to reduce the cranks posting there.  If this is your first paper, you will need (one or more) endorsers.

@GEdgar I'm aware it's not that simple, I'm hoping I can write something get enough to get endorsed as I said in my post.

Before you can publish you need to be sure you have something to publish.
In your case I think that means at least two more steps in your research.
First, you say

iterating over the entire grid cell-by-cell as it's done
traditionally.

People have been programming cellular automata for a long time. You must find a way to check the literature to make sure you know the current state of the art.
Second, the only way to convincingly demonstrate that your algorithm is significantly better than existing ones is to run  benchmarks on seriously large examples comparing your algorithm's performance with standard ones.
When you have done both of these things then you can think about where and how to publish.

"Second, the only way to convincingly demonstrate that your algorithm is significantly better than existing ones is to run benchmarks on seriously large examples comparing your algorithm's performance with standard ones." - you could also do a theoretical analysis (which might be enough, if finding the relevant grid-cells is efficient)

I already did a cursory search and what I found was either basic optimizations (Using smallest possible data types, etc...) , or highly specialized for very specific models, and even those were rare, my algorithm is general, and depending on certain configurations can improve performance with near 100% efficiency, I don't think a benchmark is needed, but an analysis will be included in the paper.

Where you publish will depend on a lot of things.

Are you prepared to pay publication charges? These can be substantial for some journals.
Are you associated with any university or research institute? Could you lean on contacts to get an "in" at one?
Do you guess you might have more to publish on a similar line?
How much leg work are you prepared to put into this?

If you can get accesss to a university library you can probably find a lot of journals to investigate. You could contact the university department most closely associated with your work.
To pick a journal to put in the "possible" pile, you should go look at the kind of papers that get published there. If you can, browse a few issues and at least look at the titles. If you see useful titles, read some of the abstracts. Consider whether your work would look "at home" with that work. If they look like they are in the same general subject area as your work, that journal is a posisble.
That will also give you some examples of the makeup of articles that the journal publishes. You can get an idea about how terse they need to be, how long they can be, what they like about tables and figures and so on. The journal probably prints some advice on these issues. Also probably has a web site you should take a look at.
The librarians should be able to help you with possible journals to try first. They can probably suggest profs who work in the area in that university, if there are any.
Then you can investigate things like their page charges for publication. If the costs are just not possible, you can put that journal in the "oh well, maybe not" pile. You can also look for things like their policy on who can submit articles, and what the process is.
If you can get an associate in the university they can often guide you as to the best practices for publication. If you might have several papers to publish then it is conceivable you could get some kind of official connection to the university and so be able to put that on your submitted article. Just make sure they really do agree with that plan first.

Let's just say that money is out of the question, I live in a country where online monetary transactions are pretty much impossible, plus I'm short on cash anyway, I'm also not associated with any university, like I said, I'm not an academic, just a hobbyist.
What options does that leave me?


text:
Cautions while writing non-specialist/lay versions of scientific articles
I would like to write engaging summaries/discussions of research papers in my field for non-specialists. These summaries/discussions would be posted on my personal website. The original article, authors, and journal would be transparently and prominently cited.
The objectives are two-fold:
(1) To improve my communication skills, specifically the effective communication of complex ideas.
(2) To develop more traction for my own work in specific and my area of work in general [I am an early career researcher].
Is this an acceptable and encouraged practice? Specifically, are there any cautions I should take to avoid copyright violations or ruffling feathers?

This is certainly acceptable. It is  probably a good way to practice your communication skills.
Unless it is really  well done and turns out to be useful for others
I think it unlikely that it will develop much traction for your own work.
The only downside might be using too much of your time on this instead of that work.
If you carefully cite all the sources you use and don't cut and paste large chunks of words you are   unlikely to ruffle feathers or encounter copyright problems. You should ask before reproducing images.

Thanks, the point about spending too much time is well-taken.

One person who is very well known for communicating difficult technical subjects is Richard Feynman. He wrote a book on QED that was intended for non-physics folks. It's a classic. But note, he wrote it after he did the Nobel-earning work on the subject. He wrote several books on various aspects of physics from a personal point of view, semi-biographical, to detailed technical stuff.
He did lots of other teaching material for non-specialists. He wrote a book called Six Easy Pieces about (Surprise!) six ideas from physics. And another Six Not-So-Easy Pieces. And nearly ever undergrad in physics is pushed to read The Feynman Lectures on Physics.
His remarks on these books included the idea that they were some of the hardest work he ever did. And, that he was never satisfied with the job he did, especially for the students who read his lecture series. Maybe it's because he was very far out on the curve of expert knowledge and capability. He may have been feeling frustrated that he could not get everybody up to his level.
But they did get him a huge following and popularity.

Along with the good advice in other answers here, cautioning about spending too much valuable time on this, let me suggest:

Know your audience.

If you want to write for a particular audience, spend some time trying to understand what they already know and are interested in.
There has been some discussion here recently on the Curse of Knowledge in which one person fails to take account of the knowledge of another in some conversation and "speaks past them".
It may take a while to find that level of discourse that satisfies both you and your readers, but it may also be a valuable thing to do if you want to eventually teach at the university level.


text:
How can an undergraduate student conducting mathematical research with a professor expect to contribute?
I am currently an undergraduate student majoring in Applied Math. I have been reading recent papers published by two of my professors who I admire and I'm wondering what it would be like to conduct research with them. In what ways can an undergraduate student contribute to mathematical research? In what ways could I prepare myself to conduct mathematical research?
To be more specific, my academic background is in History and Social Sciences which I studied intensely from High School through my first two years in college. I conducted research at University of Arizona my junior year of high school analyzing a large set of longitudinal data on a group of high schools in NYC.
My interest in math, specifically applied math, started when I took a Computer Science class because I was curious. Since then, I've taken calculus courses, applied combinatorics, probability courses, and I'm currently enrolled in a computational geometry course and an operations research course. The reason I'm interested in pursuing undergraduate mathematical research is because I enjoyed the experience a lot when I was studying social sciences. My concern is that I don't have a strong enough background to contribute to the research my professors currently conduct. I get good grades in my classes, but I'm concerned with my lack of background for a Junior in an applied math major. Recent publications from my professors are difficult for me to understand, so I'm questioning whether I'm ready to conduct research with them.
I'm hoping you may be able to offer insight into whether my background is sufficient for conducting research and how I may be able to strengthen my skills. I take my school work seriously and think I have a good understanding of the material I'm taught. Thank you for your time.

You don't really prepare yourself to do research - you just do it.  It helps to find a professor who is interested in working with you. But, about your question: it might be a duplicate of the one here: http://academia.stackexchange.com/questions/44695/how-should-i-start-undergraduate-research-in-mathematics . Could you edit the question, if that one does not answer it, to explain what else in particular you'd like to know?

Go ask them directly if they have some (easy) problems you can try your hand on, look around for journals publishing undergraduate's papers where you might publish results, ,,,

@OswaldVeblen, thank you for your response. I'm new to Stack Exchange so I'll be sure to look out for duplicate questions before posting in the future. The question you linked has some good general advice, but I see the question was specific, so I'm hoping adding more details to my question could result in more personally tailored advice. Thanks again!

@vonbrand, that's a good idea. I've been to my professor's office hours before and I think he would be willing to introduce me to extra curricular problems. Maybe that will show him I'm a good candidate for research.

@AdamPollack "Personally tailored" is one of the red flags here--we typically want questions to appeal to more than just the person asking them.  Oswald's link contains three answers, one of which address the specific/tailored Number Theory aspect of the original post, but the other two are fairly generic.  Do those answers fail to address what you want to know?

I think this is unlikely, for the reasons outlined in the answers to this (slightly different) question: http://academia.stackexchange.com/questions/49595/is-it-common-for-an-undergraduate-thesis-in-pure-mathematics-to-prove-something

@zibadawatimmy thanks for the distinction. I missed that, but I see what you are referring to. I've read through some of the linked questions and it has definitely addressed what I wanted to know.

@TomChurch, Thank you for the link. Finding the right questions to read through has been very helpful, since I wasn't able to express exactly what I was looking for. Thanks again!

It's very reasonable to wonder how you, an absolute novice, could "help" experienced experts. Some people are fond of claiming that somehow "just trying hard" or "being smart" can make this possible in some way, but those are needless (and doubtful) claims that miss the mark about what the real question could be.
That is, many or most faculty are happy to mentor beginners and introduce them to the subject(s) the faculty know and like. It need not be the case that they "need help", and, if they did, sure, recruiting novices is not the best gamble. But that's not the point! The point is that experts may enjoy (and find stimulating) introducing beginners to their subject. So you help them by allowing them to do so.
It's not at all surprising that you have trouble reading their recent papers, and, again, that's essentially irrelevant. (The internet mythology about young people becoming world experts in a few weeks or months is invidious... In particular, no, you should not expect to "read those papers and then go talk to them about them.", contrary to much advice given on-line.)
An astute expert can find interesting "starter" projects for novices. It may happen that such a project produces something interesting to the expert. Or, it may be that the expert can so well foresee the outcome that the element of surprise evaporates. But that doesn't matter. Little kids don't have to immediately play sports (or whatever) with world-class professionals. But they can be coached by such professionals, if both parties are interested. I do think that's the correct analogy, though many other people on these sites are adamant otherwise.

Not only should you not expect to understand current research papers when just starting out, but you may already have tenure when you finally feel confident that you'll understand the introduction to a paper in your area of expertise more often than not.  It's not unusual for the introduction to be the most confusing part of a paper, even when well-written.  Introductions are full of sweeping statements, off-hand summaries of complex results, terms from other fields (a pure math paper may invoke a lot of physics terminology you weren't expecting), and references to a large number of papers.

Thanks for your comment. Combined with some of the links posted, this was the kind of advice I was hoping to get. I'm just trying to gauge how I could participate in research with my professors, and I think your answer has some good recommendations. I definitely get the sense that they would be interested in motivating me with "starter" projects and this is the initial experience I'm looking for.

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


text:
How to refer to experience in area X in a proposal when my work in area X is classified?
I am writing a postdoc proposal which will involve work in area X. Area X can be studied from a theoretical or applied perspective, and the proposal involves the latter. While my PhD has focused on theoretical aspects of area X, I also have experience in the applied aspects via an internship. The issue is that all the work resulting from the internship is classified, and cannot be legally shared. I cannot, for instance, cite a paper (though I did write an internally published paper on my work while an intern). How can I convincingly convey that I have experience with the applied side of area X?
I am legally able to share that I worked in applied area X during my internship, that I wrote a paper, and I may disclose the name of the organization I worked with. This information appears on my CV, but how should I best incorporate it into my proposal?
Or should I, without anything specific to say about my experience in applied area X, say nothing because saying anything would sound desperate?
Related: How to reference confidential data in reference list

Like Secret or Top Secret classified? Is the existence of the paper itself classified? Is the title itself classified?

@JonCuster Yes, that sort of classification. The existence of the paper is not classified; that is also on my CV. The title, however, is classified. Frankly, I do not even remember the exact title and have no way of finding out because my contacts at my internship could not share it with me if I asked.

Can you clarify the sponsor?

@yourfriendlyresearchadmin Do you mean to whom am I submitting the proposal? If so, the National Science Foundation.

Or should I, without anything specific to say about my experience in applied area X, say nothing because saying anything would sound desperate?

It is counterproductive to withhold truthful and relevant information about yourself out of fear that the information cannot be verified. You should share what information you are able to, and leave it to the people evaluating your proposal to think how to make use of that information. If they think the information is useless (I doubt very much they will), they will ignore it, and you will be no worse off than if you hadn’t mentioned it at all. There is no benefit to you preempting or second-guessing their judgment on this issue.

I am legally able to share that I worked in applied area X during my internship, that I wrote a paper, and I may disclose the name of the organization I worked with. This information appears on my CV, but how should I best incorporate it into my proposal?

Just mention it in the appropriate parts of the proposal, and explain the limitations preventing you from sharing more. It is not materially different than any other type of information you are including in your proposal.

yes, outstanding answer. anyone working your field will be likely to recognise the organisation and the situation as quite probable. If they do doubt you at all, they can ask for a little more detail in the interview.

Have you read the instructions? The PAPPG covers this:

D. SPECIAL PROCESSING INSTRUCTIONS

Proprietary or Privileged Information

Patentable ideas, trade secrets, privileged or confidential commercial
or financial information, disclosure of which may harm the proposer,
should be included in proposals only when such information is
necessary to convey an understanding of the proposed project. Such
information must be clearly marked in the proposal and be
appropriately labeled with a legend such as,
"The following is (proprietary or confidential) information that (name
of proposing organization) requests not be released to persons outside
the Government, except for purposes of review and evaluation." Such
information also may be included as a separate statement. If this
method is used, the statement must be submitted as a single-copy
document in the Proposal Preparation Module in FastLane or
Research.gov. (See also Chapter II.C1Chapter II.C.1 for further
information regarding submission of single-copy documents.)39
The box for "Proprietary or Privileged Information" must be checked on
the Cover Sheet when the proposal contains such information. While NSF
will make every effort to prevent unauthorized access to such
material, the Foundation is not responsible or in any way liable for
the release of such material.

Otherwise, assume any information you disclose is subject to FOIA.

Thanks for your answer, but my questions is not whether I should disclose classified information, but rather how to best convince the reader of my proposal of my experience, the details of which I cannot disclose? My question is not so much about rules as rhetoric.

I'm not sure I understand. These rules say here is how you disclose information that cannot be released to the public. Are you saying you cannot release the details to the government at all? At some point you have to decide to be direct and check the box as described or just state it's confidential and details are available on request. You don't have many options.

Yes, it seems I do not have options. The nature of my agreement with my internship organization is that without authorization from my internship organization (which is very unlikely), I am not able to disclose details to the NSF (or anyone else) under any circumstances, no matter what the NSF says in their instructions. So should I be vague hoping they understand I cannot be more specific, or just say nothing of my internship experience to avoid sounding like I am grasping at straws?

Moreover, the classified information is not "necessary to convey an understanding of the proposed project," merely to convey my personal experience in the subject of the proposed work (which work is in no way confidential). Therefore, I should not share details even by the NSF's own rules.

Yeah, this answer would be good if OP were merely dealing with trade secrets or other "privileged" information, but classified information is something different. Classified information simply cannot be shared outside of approved channels; there is absolutely no work-around.

I have had subs on my contracts and they just write something like details are top secret and available upon request. When such a situation comes in, in the event of an award, the Sponsor calls the sub directly and the prime awardee is bypassed. At some point you will either disclose or you don't. The only question after deciding to disclose is when and how (as I describe above).


text:
Emailing exams: is it okay by FERPA?
I am a graduate student at a US university. I work for a professor as a TA. Recently, we graded students' tests by scanning them, and marking them electronically. After submitting grades, the professor asked me to email the electronic copies of the tests back to the students. Not being one to do work by hand that a computer can do for me, I wrote up a little program to email the tests for me. It all worked pretty well. I mentioned my program to another professor (not the one I work for), suggesting that he could use my code if he wanted. But he said that he thought emailing tests may be insecure, and might be a FERPA violation. Is he right? I did make sure to use an SSL encryption when sending the tests, but I don't know how secure this really is.

My impression has been that the law is not really clear as to what kind of security measures are required, and as a result, each institution makes its own policies on issues like this, deciding how they want to balance convenience against potential liability. So you probably have to ask someone at your own institution.

What e-mail addresses did you mail the tests to? The students? Or the parents? Did you make sure those e-mail addresses belong to the students? Not the parents?

@scaahu Absolutely to the students. The emails I used came from directly from the students' accounts with the school. This is the same email by which they would receive all official university communications.

It is not a FERPA violation per se, but it might be a violation of university policy which is put in place to guarantee the privacy of student records. This is analogous to the law corresponding to the IRB requirement -- the US government doesn't say what the rule and procedure must be, just what the purpose is and that there must be rules and procedures. The main consideration is that student records can't be "shared" with unauthorized parties, the the university has an obligation to be sure that only authorized parties receive access to these records. My institution classifies all electronic communication with students as "student records", and requires all student records to be viewed and stored only on official university computers on campus, encrypted, and sent to an official campus email address. Technically, this means that if a student emails me a question, I can't reply until I'm on campus using an authorized university computer, and my response has to be encrypted.


text:
Can I get my degree revoked for misuse of citations?
I have been accused of not correctly attributing a person in my PhD dissertation that was finished several years ago. The person claimed he would bring the matter to the university I did my PhD at. I revised the text and the in-text references to this person's sources are there and in the bibliografy, but I realize that they could have been clearer references (same for cases of previous chapters that I noted in my re-reading). It was never my intention to plagiarize, though I know that is not important for these matters. Is is a case that could cost me my degree? I do not know how to react. Thank you.

Welcome to Academia.SE. Unfortunately, we won't be able to give you a personalized answer -- there are many "individual factors," and your university's policies, procedures, and personalities are hard to predict. But, we have distilled all our wisdom on this topic into a "canonical question" -- see the link above. Good luck.

I apologize for the previous repetiton. I had missed this! Thank you.

I doubt you have any problems here. The in-text reference are there, and even if they aren't, people make mistakes. A PhD dissertation is a huge document often with hundreds of references. Mistakes happen. Don't worry about it too much. Just apologise for any mistakes.


text:
Just realized I may have accidentally plagiarized some of my bachelor's thesis
I had been reading a news article recently about some politicians who had been accused of plagiarizing their master's or PhD theses, and I noticed something that really frightened me.
With some of them, what they did was copy, near-verbatim, passages from other articles or books which had citations in them, and they cited those same citations in the footnotes, without citing the secondary source. FWIW, those officials did so in humanities, law, and/or international relations. In contrast, my thesis was in a STEM field.
I was unaware that this is considered plagiarism, and realized that I had done something similar in my bachelor's honors thesis. I had looked at the thesis of a former student in the lab to get an idea of how a thesis was written. His work was closely related to mine, and as I was short on time, I ended up writing an introductory and methods section that were most likely, in some sections, extremely similar in wording and style. For the introduction, I tried to paraphrase what he wrote and cite the same sources he did (I did check to see if the sources were accurate) on background information relevant to both of our projects, but I'm sure that a side-by-side look would spot the similarity, as the sections were mostly definitions and descriptions of things we work with.
For the methods, as I had used some of the exact same protocols and procedures that he did, I just wrote down what I did but the wording most likely ended up being extremely similar to his, enough to notice, with no citation given for that part because the protocol was just given to me orally by the grad student when I was starting out. I thought this wasn't an issue because the methods section is difficult to phrase in different words if the experimental protocol was the same. I passed the defense and the thesis was approved - my PI didn't notice any similarities.
The parts of the thesis where I branched off in a different direction than that student I wrote without the aid of the previous thesis, and I cited sources as appropriate and reported my own work.
My former PI stores hard copies of his students' theses on a shelf in his lab, and there is another hard copy in the university library, but there are no electronic copies available. I don't have the thesis of that former student with me. What I'm terrified of is that a future undergrad in the same lab might use my and that person's thesis as guides to writing their thesis, notice the similarities, report me to my former PI and/or the honor council, and get my degree revoked for plagiarism. It's been a year since graduation and I'm about to head into grad school.
Do you think I am right to worry? If so, what should I do?

This is an appropriate thing to be concerned about and want to rectify; you don't need to fear dire consequences, especially if you take steps to address it. There are different kinds of plagiarism, and also different levels of awareness of what one is doing. Turnitin has an interesting diagram with catchy titles to distinguish them; yours sounds like a mix of "hybrid," "recycle," "aggregator," and "retweet." Probably the hardest overall concept to understand--and one that may not be fully comprehended by many undergraduates--is that when a key source shows you the way to other sources, you need to be careful that your paper isn't entirely dependent on that key source for its content and/or structure. You should also make sure to acknowledge if a quotation in your paper from a third source is there by way of that key source.
I tend to agree with Anonymous Mathematician's answer to a similar-ish question about plagiarism in a doctoral thesis. In particular, identifying the problem and issuing some sort of errata or revision, prior to anyone else coming across it, is likely your best path. Making a mistake as an undergraduate, and recognizing it and working to rectify it, is unlikely to pose problems for you if it later comes to light. (This is largely the tenor of the answers to a question by an undergrad about publishing in a journal, realizing later that the work contained cited but unquoted direct quotations.)
That said, it would be wise to seek counsel from an ombudsperson at your undergraduate school and your graduate school, as well as your undergrad advisor and your new advisor. You don't want anyone to be surprised by anything and jump to the wrong conclusions. Exactly how to handle the process of corrections might be delicate, but it is certainly the right path to take. The worst case scenario would be if you confessed this to your undergraduate institution to address it, and they were required to report this to your graduate school, which only read the words "academic integrity issue" and rescinded your admission. With proper communication and feeling things out with ombudspeople at both institutions (confidential advisors who can help you navigate the system), you should be able to avoid such a misunderstanding.
Minimally, you should probably clearly and concisely acknowledge your reliance on the other thesis, perhaps as an erratum sheet you could send to your undergrad advisor to stick into a copy of your thesis. It might say something like:

Much of the literature review and methods sections rely on the work of Prior Student's thesis, and I would like to properly acknowledge that debt.
I found sources A, B, C... (discussed on literature review pages X-X, Y-Y, and Z-Z, respectively) through Prior Student's work.
Prior student did similar experiments on __, and I relied on their phrasing for much of the content on pages X-X.

In another approach, you could produce a revised version that somehow does not rely on the previous student's work, and mention in a note that you produced the revision because you realized that you had inappropriately relied too closely on the other student's work. (For instance, find several more papers, read them and reread the sources you had before, and write a new literature review.) However, if you expend this effort without any guidance, you might not distinguish your new work enough, and/or you might be moving toward a different resolution than your advisor and undergraduate institution would find acceptable.
Good luck!

+1 for the "minimal" solution of drafting an erratum, or (if feasible) making a "v2" with the over-reliance removed. But, given that this is an undergraduate "honors thesis", I would suggest trying to resolve this by working with the professor who supervised the work before involving the ombudsman or anyone else; bringing other university offices into it may make this a bigger headache than it needs to be.


text:
Offering Authorship Prospects To Professors For MSc Thesis
I am conducting research for my MSc thesis and there is a paper that I have been putting a lot of work into trying to understand and incorporate into my thesis. Theoretically I understand what's going on, but mechanically carrying out the concept is stumping me. As such, the problem that I am faced with is that I have hit a wall in my intellectual ability to perform a particular computation within the paper; by this, I mean that I simply cannot reproduce the method the author used. If I had somebody I could talk to about this paper then perhaps I could figure it out, but for now, assume that my supervisor is unable to assist and the author of this paper lives far enough away to make travelling not an option.
My own research idea is dependent on being able to reproduce the results in the paper I am studying, and so if I cannot reproduce the results with my own data for myself, I cannot pursue my idea. So, what I was thinking of doing was reaching out to the author and asking if they would be willing to perform the computation for me in exchange for an authorship position on the paper if it can get published.
This is not ideal for me, because I would much rather just recreate the results and I feel that for an MSc thesis seeking external collaboration might be frowned upon, although I do not know for certain. However, I feel that I am at a point where this might be the best path forward to keep working on my original idea. If I cannot perform this computation on my own, would offering potential authorship to the author of the paper I am studying be a worthwhile path to pursue, given that I am doing this for my MSc?

Have you considered that the published result might be wrong?

Given what I know about the author and co-authors, I am trusting that the results are not wrong. The problem itself is purely the mechanics of integrating a very complicated integral which is itself a function of integrals. It's just mathematics that I have never had to wrestle with before, and while I can follow what the author is doing from a conceptual point of view, the actual computation is what I can't figure out how to do because I don't think I have the background to really carry out the computation numerically. Hopefully that is a bit more descriptive.

Since you are tentative about whether this would be acceptable, I suggest that you put that idea off for a while, at least. Talk to your advisor about the issue. It might be that co-authorship of any kind might not get you to your degree. You need to find out about that.
But the best option might be if you could work with someone with more math experience, even a professor, who could teach you the techniques you need. At a minimum they could offer advice about how the original paper was done so that you can reproduce the results. They might just be able to point you to a source for learning the needed technique.
This might be considered different than helping you with your own paper and might not result in co-authorship, depending on the questions you ask and the help you get. An acknowledgement would be appropriate, of course. But if co-authorship is ok at your institution, then a local one might be better than one with the original authors.


text:
Is it always essential to include "extensions of our work" in the discussion section of a paper?
I am an early career researcher and have written a couple of papers already in statistics. Usually, I include a line or two on "possible extensions of our work" in the Discussion/Conclusions section. I am finishing a paper, where I cannot see a non-trivial direction for the extensions of the proposed work. I could easily say use G distribution instead of F, or to consider applications in other areas, but this sounds rather generic and trivial to me.
So, my question is, is it valid not to include possible extensions in the conclusion of a paper?

Yes, it is certainly valid to not discuss possible extensions of your results in a paper.
In fact, often I advise coauthors against trying to discuss possible extensions. From my point of view, presenting possible extensions is only relevant enough to put into the paper, if it comes out intrinsically from discussing either the limitations or merits of the result, such as for example:

Regarding limitations of your results, if you can think of ways how they could be addressed / overcome, but these would be too costly or create other issues so that they are not reasonable to pursue for this paper, it would be good to still discuss these ways together with the limitations they could address. That can also serve to soften the impact of any limitations that you have.
If your paper solves problem A, but a similar or the same approach could also help in solving problem B, which should have been formulated or at least hinted at somewhere else, it is certainly good to discuss that within your contributions. This would also show.

Also, I would only present possible extension if they are relatively specific to your results, and could not have been designed without knowing the results that you present in the paper. If a researcher in your field could have come up with an "extension" even without knowing your results, and you think it is important in relation to your work, it may be better to discuss that in either the introduction or the discussion of related work.


text:
APA: Citing a text which references other works
I would like to pick up a claim made in Example (2012), which in itself references other academic writings. That is, Example (2012) writes something along the line of:

Inequality in France has increased since the 1980s (Source1, 1999; Source2, 2001; Source3; 2005).

In my writing, I would like to build an argument on this fact, that inequality in France has risen. How do I properly cite this claim, bearing in mind that I only have the book of Example (2012), and not any of the others. I know that secondary citations are usually denoted by as cited in, like this.

As inequality has been rising in France over the course of the past decades (Source1, 1999; Source2, 2001; Source3; 2005, as cited in Example, 2012).....

However, I feel that this citation style overstates the importance of the secondary sources to my argument. I would prefer something along the line of

As inequality has been rising in France over the course of the past decades (Example, 2012; referencing Source1, 1999; Source2, 2001; Source3; 2005).....

However, I have not found any such format in the APA guidelines.
Does anyone know how to handle this properly?

Neither "as cited in" nor your alternative is good.
The only way to handle it properly is to get the other sources and read them.
If you don't understand why, read "Academic Urban Legends" by Rekdal: https://journals.sagepub.com/doi/full/10.1177/0306312714535679

Yeah, the trouble is that the Sources are books without any indication of page number or chapter... But I do see your point.
If I go back to the primary sources, do I still have to cite (Example, 2012), as they pointed me in the direction of the primary sources?

Yes, it can be tedious. And you might find that all those sources just state the claim with no evidence except another citation (or several), and then you have to look those things up. Finding primary evidence can take time. You might even find that your sources don't lead to any at all! But when you find one piece of proper primary evidence, like some statistics about inequality, then I think you can stop and cite that. No, you don't have to cite Example (2012) in this case.


text:
If you made a minor error in publishing the experimental protocol of an experiment, what would happen?
If you were to publish a paper but you made an error in publishing the experimental protocol or parameters, what would happen to the paper? Let's say in this instance that the results of the experiments wouldn't be significantly affected. How would that process work? Would there have to be a retraction? A correction?

Was the experiment actually carried out correctly? Is it just a matter of misstatements in the paper?

The experiment was carried out at slightly different parameters than what was written, as a result of input error. Doing them with the parameters that were written got similar results.

Did the experiment involve anything random? Sampling, for example?

The experimental parameter that was affected was wavelength at which excitation and emission were measured. In both cases, they were 5 nm off from what was reported (due to misremembering the correct wavelengths during setup), and doing them at the reported wavelengths didn't affect the outcome of the experiments much at all.

Life as we know it may come to an end. Or not…

In most such situations there is no need for a correction. If random elements of any kind are involved then the effect of randomness might overcome small changes in parameters. You might be able to analyze that from your data.
If the system is relatively smooth then, again, small changes in inputs result in small output changes.
There are systems, however in which none of that is true. In any chaotic system (weather, for example) small changes can result in large effects.
Another factor to consider, however, is what real world effects might arise from getting it wrong. In some medical systems, say, it is important to be absolutely precise as lives may depend on results.
So, make a judgement call. If small changes result in small effects AND if there are no adverse health/societal impacts for being slightly wrong, then it can probably just slide.
You can also present your case to the publisher of your work and let them decide if a correction needs to be made.

And please use a log book or similar careful logging practices during experiments and their setup rather than relying on memory.

I see. In this case, the mistaken changes to the parameters were so minor that it had no significant effect on the outcome of the experiment. The reason why the mistake went unnoticed was because the results from each configuration (the ones from the correct configuration and the ones from the incorrect configuration) were indistinguishable from one another such that no alarms were raised.


text:
Student dissatisfied with exam grade: what to watch out for?
A student who has trained hard for my exam got a just-passing grade. They are dissatisfied with it, and have mailed me to ask to have a look at my corrections. Naturally, I agreed to this. In the mail, they are already calling into question my corrections and the exam content. Is there anything in particular I can do at this point to minimize the chances of a dragged-out discussion or procedure with the exam committee?
Crucial info:

The course I gave was extracurricular, and planned to be pass/fail based on participation. I only added the exam after this student asked for it, because they needed a grade for some administrative reason. The exam was taken by a very small number of other students (inadequate comparison material).
At that point, I asked the student if they aimed for a particular grade, and the answer was 'no'.
The student got all knowledge-based questions right, and flunked almost all applied knowledge questions.
As the course was extracurricular and covered an advanced topic, I made sure to cover the basics, but on top of that I covered a lot of content quickly, allowing advanced students to learn additional things if they wanted to.
I suspect this student simply missed the bulk of that information, partly due to a language barrier.
During correction, I already scrapped one question from the exam that no-one got right and that strongly seemed like I had mentioned it too passingly during the course.
After calculating the grade based on a linear transformation of the point score, I felt that the best grade (which was moderate) did not give credit to that person's understanding; besides, the student discussed here would have received a fail grade. I added two point-increments to the final grade, fixing both of these issues.

In my homeland we have two types of course evaluations: Pass/Fail and Exams. One cannot simply change one for another on-the-fly no matter what "administrative reason". All students shall have the very same options and demands to pass the course.

Point #4 concerns me. Did the exam contain any of these "additional things" that "advanced students" could learn "if they wanted to"? If so, that seems like a recipe for trouble.

The discussion on he/she vs. they has been moved to chat.

Followup questions that might help answer the question better: Did the majority of students pass? Where on the bell curve did this student fall? (And there wasn't a bell curve, do you know why it wasn't, and was that a contributing factor for this student?)

What is the "administrative reason"? The only possible reason would be something about GPA/average of votes. But, AFAIK, universities don't take into account pass/fail exams so maybe the student is simply wrong in thinking she need a grade (or maybe she is trying to cheat by having one more grade for some reason) or the administration is.

@J.R. That is my lesson from this episode. The exam was more or less half basics, half advanced. It was made-to-measure to the actual content post-hoc. But rather than exclude the advanced part from the exam (which would not do justice to insightful students) I will simply never again allow an exam for a course that wasn't meant to have one.

@corsiKa those are indeed good questions, though in my specific case, statistics on the scores are moot as per my point #1.

@Crowley Indeed. My university's regulations say that I may add an optional exam, which has the potential to add a grade to the course result, but not change the pass/fail outcome based on participation I already set.

Whatever you do, make a copy of the exam and never let the student touch the original.

By asking for an exam, the student asked you for a fair, honest, informed evaluation of their mastery of the course material.
If you believe that the exam grade fairly and accurately reflects the student’s mastery of the course material, say that, and explain why.  Be respectful and honest.  Stick to your guns.
In particular, you should have some record of your announcements of both the contents of the exam (“How was I supposed to know this?”) and your expectations for certain grades (“Why did I get this grade?”)—the course syllabus, or a handout, or email to the students.  You should have sources/proofs for the correct answer for each question (“Why is this wrong?”), rubrics for awarding partial credit for partially correct or suboptimal answers (“Why did I get so few points?”), and well-reasoned rules for converting raw exam scores to reported grades.
If you do not believe that the exam grade fairly and accurately reflects the student’s mastery of the material, then you need to reevaluate the exam for all students. You’ve already done this by throwing out one question and curving the scores.

The OP said that the student wanted an extra exam for "an administrative reason" not necessarily to show mastery of the course...

Asking for an exam should, by definition, amount to a fair, honest, informed evaluation of mastery. Nothing else should ever qualify. It could be the student has motives, but that doesn't change the meaning of the request.

@SolarMike and that's the real problem here.  A student wants the paradigm of the course changed to meet some unknown need.  The teacher should never have agreed to provide either an exam or a grade.

@CarlWitthoft that is so right...

As someone who has had a few discussions about grades in exams, ranging from
me leaving the room after five minutes because they gave me more points than I would have given myself to
sitting there for over an hour and going from 59/80 to 70/80 (no typo) with one of the correctors joking he must have been drunk when correcting that exam when I called him the third or forth time for something he obviously missed (wrong multiple choice corrections, correct calculations marked wrong, calculations not seen and marked as not done).
There are two things a student (well, me anyways back then) wants. A sheet with solutions (and the rubric telling which parts of the answers gave which points) to compare theirs with (or you explaining every damn thing in depth, because how else am I supposed to judge that correction in a few minutes time?) and factually correct arguments. If you're wrong, admit it, and if the student is wrong, tell him/her why. I've had people telling me they can't give me those points because they didn't give them to others. That's no argument ... Don't do that. The answer (or partial answer) is right or wrong. It isn't “right, but ...“
You'll get students that don't care about that and just want points. Firmly tell them they aren't on a bazar. I'm sorry for those. But don't treat all students like that. I once had to ask three times for an explanation why my answer was wrong because the answer was “sorry, I can't give you points for that.“ Well yes. That wasn't the question.
It boils down to one thing. Be as fair and respectful as you want to be treated until treated otherwise. Like one should be always.

Helpful answer.  I agree with most of it. But: "people telling me they can't give me those points because they didn't give them to others. That's no argument " - that is a significant argument, and one that is important (even if it does sound bad).  I agree with your broader point that it is important to communicate the reasons for the rubric.  And hopefully there are valid reasons behind the rubric.  At the same time, once a rubric is chosen, it's important to be consistent across students.  Especially in subjective cases where judgement is needed, consistency is very important.

@D.W. it may be a significant argument, but that does not make it a correct one.  The presence of errors in one evaluation does not excuse the existence of errors in another.  Presumably the other students, if they cared, could also come and have their exams corrected properly.

@StackTracer, I understand your point of view, and if it's a clearcut error, then I agree with you.  But sometimes it's not a matter of clear error.  Sometimes it's a judgement call about how much partial credit a partially-incorrect answer should receive.  Should it receive 2/5 points or 3/5 points?  In that case, "I must be consistent with the rubric, and with the score I have given other students" is a powerful consideration, assuming the rubric was at all reasonable.  (continued)

It's still true that when communicating with the student you should give the reason why (you got 2/5 because you fall under this category of the rubric; the reason we only give 2/5 for that type of answer is because it doesn't consider factor X).  So as a matter of communication it's better to focus on that substantive reason.  I don't discount any of that.  But if the student says "I still feel like I demonstrated some knowledge and 3/5 would better reflect my knowledge", at that point I think references to being consistent with the way other students were graded becomes a powerful argument.

@D.W. Generally speaking, rubrics are an attempt to shoehorn a subjective evaluation into an objective metric.  I generally will give students that upgrade to 3/5 (assuming they have a decent level of coherent reasoning). Why? Because by coming back to challenge this decision they're demonstrating their knowledge further, but also (more importantly in my opinion) they're demonstrating their interest in the subject, and I'm not sure I could come up with a better way to turn a motivated, interested person away than falling back on "well, rules are rules".

Because by coming back to challenge this decision they're demonstrating their knowledge further — [citation needed] — I could come up with a better way to turn a motivated, interested person away than falling back on "well, rules are rules" — Maybe so, but I am perfectly comfortable turning away motivated, interested sociopaths. Asking me to ignore a reasonable and consistently applied rubric and give you more points is asking me to treat you differently from anyone else. No.

@D.W. in that special case, the question was “explain algorithm x in a way that it answers the following questions 1-7“. Others explicitly answered the questions. I didn't. I didn't get points for them. Reason: others explicitly answered them.

@D.W.: That's not an argument, that's just an explanation of why the grader/teacher might need to correct many people's grades. Which is more annoying, but no less necessary, if a grading mistake was made. And if a matter is not clear-cut, then the famous sentence applies: "If there is a doubt, then there is no doubt". Benefit of the doubt goes to the examinee.

It can be helpful to have a policy for how to submit regrade requests.  Here are some elements that can be helpful to include in that policy:

Specify the format for regrade requests. It helps to specify that regrade requests must be submitted in writing, and must identify which problem(s) they believe was incorrectly graded and provide a justification for each problem they believe was incorrectly graded.  Similarly, you should provide a response to their request in writing.  It helps to provide an explanation or justification with my response.
Specify the deadline for regrade requests. You should set a deadline.  You might require that regrade requests be submitted within one week after the material was returned to them (or some other reasonable amount of time).  This is important so you don't get people at the end of the semester submitting a pile of regrade requests for assignments they got back months ago, as a last-ditch effort to improve their course grade.
Set expectations for how regrade requests will be evaluated. It may help to clarify up front that you will only regrade problems when our grading rubric was incorrectly applied; it's important to be consistent across students, so you can't accept requests to change the rubric or arguments that the rubric was unfair. On the other hand, if they found a correct solution that the course staff didn't anticipate on the rubric, and they didn't get full credit, please submit a regrade request so they can receive credit (but I recommend only following this in case of fully correct answers, not for partial credit for answers you didn't anticipate).  It may  also be helpful to state that in borderline judgement cases you will go with the original grade unless it was clearly wrong.  Make your rubric and sample solutions visible to students.
Encourage students to check sample solutions before filing a regrade request. It's helpful to make sample solutions to the exam available to students.  Include comments about common errors/misconceptions here and there in the solutions, to help them learn.  When announcing the regrade policy, encourage students to read the sample solutions before filing a regrade request, as their approach might be discussed there.
Encourage regrade requests. I suggest you tell students that you're human and you make mistakes, and you want students to get credit for their work so if they suspect an error they should let you know so you can correct it.  I suggest you tell them, please don't hesitate to submit a regrade request if you think the course staff made a mistake and we'll be glad to look into it.  I don't like policies that try to penalize or discourage regrade requests (e.g., by a vague threat to regrade to their entire exam).

I also encourage you to set a policy with your teaching assistants and course staff, to tell them not to evaluate regrade requests in person, even informally.  The scenario you want to avoid is where a student goes to a teaching assistant, shows them their answer, and the TA says "looks right to me, you should submit a regrade requests", and then the student submits a regrade request and it turns out they don't deserve credit.  Then the student feels screwed, since they're getting mixed messages -- one TA said they deserve credit, but you aren't giving them credit.  There are a number of reasons to discourage course staff from giving in-person off-the-cuff assessment like that.  First, there isn't always time in person to check the details.  Second, if the TA wasn't the one who graded that problem on the exam, they might not be familiar with all the weird corner cases or the policy used by the person who graded it.  Third, we absolutely want to avoid cases where the off-the-cuff evaluation said "you deserve credit" but we actually can't grant their regrade request.

If you don't want any discussion then don't allow one. It is simple as that, and here is how this works:
Tell the student that any complaint they have about the corrections or awarded points they have to write down on a piece of paper. Any questions on the content ("How to solve...?", "Why is this not right...?") can be asked in person. If they start with a question of the latter class and they try to get you into a discussion about the grading, remind them or simply point to the piece of paper and the pen.

And then what do you do with the written complaint?  This answer seems incomplete without that.

Of course you evaluate the complaint totally fair and change the grade if and only if the initial grading was wrong.

In addition to the other answers here:
Your point 3): If somebody flunks nearly all applied knowledge Questions, it is perfectly in the range of expected outcomes to "just pass", and it certainly does not point out an unfair priority on your behalf.
Your point 5): Your evaluation should not take that into account. The student agreed to taking this course in this language. And if somebody later hires him or takes him into an academic project, this is not going to matter.

Two points:

Find out whether they actually need a higher grade for some reason. If they do, can you change the grade back to pass/fail or let them retake the class to solve the issue? If not, is there someone else (e.g. someone in charge of the scholarship office if their scholarship is in threat, some sort of academic advisor if their program standing is in threat) who you can point them to instead?
It sounds a lot like your student doesn't understand the importance of applied knowledge or doesn't understand how to apply knowledge. You say that they studied hard, that they did great on the knowledge questions but terrible on the applied questions, and that they are from a different linguistic background. It's likely that their cultural or individual educational background caused them to study wrong so they didn't learn how to apply their knowledge. Probably the best thing you could do for them as a teacher is talk to them about that so they understand the problem and help them brainstorm ideas to improve their ability on applied problems in general. Doing so will likely get them off your back if they don't actually need a higher grade in that class, since you'll be empowering them to turn the poor grade into a positive learning experience.