Visualising connections between scientific papers So i just began to write my literature review and have a big bunch of research papers saved in a folder.

Is there a tool that would help me visualize the references between those papers saved in my folder?

I.e. for example paper A mentioned paper B in its bibliography, and B referenced C, C referenced D and E, A referenced E.

Not sure if there is a good way to visualize the connection between the references that I am aware of. However, a good way to manage and organize references is using the free tool called Zotero (https://www.zotero.org/) where you can create tags, directories and subdirectories. So, may be using these you can group similar references into one category. It also has plugins for all the popular browsers and also a standalone version, so you can pretty quickly import references and build your library and it also supports all the popular formats for bibliography. There is also an online account that you can create to manage your library over the cloud.


Authorship Dispute: Soft threats from funders to cancel project unless they are listed as coauthors A lot of backstory but I will try to be brief. I am employee of USA university but work abroad at a research nonprofit serving industry. (industry meaning an industry in general; many companies) My assigned handlers at the research nonprofit have power to ban me from the research non-profit facility, which would lead to unemployment and loss of residency. Access to the research nonprofit facility is a type of funding because academics don't normally get to work on tools this expensive. The (non-scientist) handlers don't help train me on equipment, get access to the research nonprofit facility and its resources, don't plan experiments, don't collect or analyze data, etc. When I was starting out and asked the handlers for help they indicated I was external and any issues I had with access or training were my own problem, and that asking the handlers for help was inconveniencing the handlers from their own work activities.

Generally the handlers are mean to me and take away opportunities to present my data to the industry sponsors which are afforded to my peers at research nonprofit who are internal. The handlers invoke the contract which gives the handlers all discretion in this area. My USA bosses threaten me with the handlers banning me from the research nonprofit facility if I do not make slides about my data and let the handlers present it. When the handlers present my data in situations where they don't think I will be able to see, the handlers just put their own name next to it, not mine or any of the USA people/institutions. My friendly colleagues at research nonprofit who do see such presentations then show me what the handlers are doing. I kept my head down and worked independently of them for a year and a half to get data in this tough situation. Now that my contract is up and the handlers and USA bosses can't hold employment/residency as leverage anymore I would like to publish my data ethically and independent of the handlers that do not satisfy any criteria for authorship I am aware of.

Including the handlers as coauthors would also be against the Publication Policy for the research nonprofit and EU university that handles my Visa. However USA universities I am aware of do not have a written Publication Policy and research nonprofit would likely defer to the USA universities in a formal dispute. USA bosses say I need to put handlers as coauthors because not doing so would threaten the project. Since the handlers presented the slides I authored to industry USA bosses say that counts as coauthorship of any publication resulting from my time here. Also the handlers are managers of some of my peers who did contribute to my work. What I see as threats of being banned from the facility if I do not list them as coauthors USA bosses say is actually a type of direct support of me that I should be rewarding them with coauthorship.

Sorry, I feel that was already too long. Any advice on how to handle this? Just don't write the paper? Create a messy dispute? Acquiesce? I already have 30 or so papers, so while I would like to show productivity from this stint it won't make or break my next career move.

Moo You need to get a new job, and you need to submit this work for publication the second that these people no longer have any power over you. It sounds like they have copies of all of your things, which unfortunately means that if you just leave and don’t do anything you could wind up with them publishing your paper(s).

If they don’t have the ability to publish your work, you have more flexibility. I have no idea what your professional situation is like or if your work is time-sensitive, but you do have the serious option of delaying publication until you’re further away from them. There are pros and cons to each option, it’s pretty context dependent, but if you can take the hit for not publishing, letting the paper languish they might drop it. On the other hand racing and publishing it without them might make them give up. It depends on the psychology of the handlers, but if you can guess the lengths they’re willing to go, you might able to get out of the situation without having an authorial dispute. Both choices could also lead to further conflict: either ten hounding you about it indefinitely when you don’t publish the paper or them contacting the journal and trying to formally dispute the paper.

Your main goal for an authorship dispute should be to get as many walls between you and the handlers as you can. Straight up don’t talk to them as much as you can. They’re already in violation of their own policies and of the EU University policies (it sounds like there’s a partnership between the non-profit and the EU University), which is a great start. Contact the ethics office at the EU University and explain the situation, including providing any documentation that you have of what work they did or did not do. From then on, you can forward any angry emails to the person in the ethics office working with you. If the non-profit has an ethics office, then you can use them for this purpose too. You should also talk to the ethics office at your university and feel out how receptive they would be to helping you out. This kind of filibustering is incredibly effective in all kinds of disputes.

However, the best wall you can put between you and these people is the journal itself. Submit your paper(s) to journals that have clearly defined authorship definitions, or even better require submissions to document authorial contributions. At the end of the day the journal is the final arbiter of who gets on the paper and who doesn’t.

Another option would be to fake conceding. Split the work up into multiple papers and divided it such that the stuff they’re claiming they touched is all in one paper and the core concepts are all in the other. It’s easy enough for the joint paper to languish in revisions while your other paper gets published. How effective this is can wildly change depending on the exact circumstances though.


Postdoc health insurance for dependents in US? I am looking towards a postdoc position at a US institution. Do university employers typically contribute to/pay for health insurance coverage for dependents of the employed (i.e. my wife and child)? As a PhD student, my health insurance was covered, but we had to pay $2000 up front each year for my wife's health insurance...

Yes, US universities generally offer health insurance to spouses and children of full-time employees, especially academic employees.  You'll likely have to pay for it (part or all of the policy's cost), but normally the premiums would be deducted from each paycheck, not paid in advance.

Most universities have public websites for their human resources office, where you can read about employee benefits.


Need a good, inexpensive app to catalogue journal articles and books Like the title says, I'm looking for an inexpensive app or program that can catalogue both journal articles and books. I need something that has or can take input from an ISBN/QR/barcode scanner, and can also do in-line article annotation like Mendeley.

Background: I work at a very small consulting firm. We do IT, custom software, creative services (design and UXD) and user research (theory, strategy and testing). We're just starting to put together a research library, and we quite frankly don't have the money for high-powered library software.

I know I'm probably asking for a magical unicorn here, and if what I want doesn't exist, please tell me. I figured research professionals would have had the most need for something like this; any help you could throw my way would be much appreciated.

-Z

I recomment to meet some librarians and talk with them about your requirements in more detail. There are a lot of software solutions that could fit.

I assume from what you wrote that Invenio could fulfill your requirements. It's an Open Source Software for publications and can be used for repositories and as an integrated library system. Invenio is developed by CERN as a framework and everyone can create its own overlay. I know at least one library using it with RFID but none with bar codes so far. It allows to catalogue all types of publications.


Should I publish as a master’s student? I am a master’s student and have done some original research work which may not be that great.

I have asked my professor who works in that area where can I publish my work or is it at all publishable.
But he seems to be not so concerned about my work nor does he say whether I should publish it or not.
He says I might try it, but he seems more interested with his doctoral students.

What should I do?
Should I try to publish it in some journal?
If yes, how can I choose a journal?
Are there any journals which publish small works of master’s students?

The practice of preparing a piece of work for publication is, itself, worth the effort. I suggest that you write up your work as best you can. Once you have a really solid draft, ask your professor, again, for advice on it.

However, you can still submit it to an appropriate venue, independent of the support of your professor, and that experience is also worth having. If you are lacking in any way, the editors and reviewers of the paper will give you additional advice that is independent of what you can get locally. This can help you evaluate a lot of things about both your work and your approach to it.

If you want a career in academia, then publishing early and often is definitely a plus. The review you get helps you improve for the next time.

But make sure you have also done a literature review to avoid embarrassment of submitting something already known. That is another valuable skill, of course. (literature review, not embarrassment).


Does publishing a manuscript in a respectable journal increase chances of getting a scholarship? I am a second year physics undergraduate in a not so famous University. However, I have constantly received top marks in my class and I have just published a paper of mine in one of the highest ranking journals in my field, with reviewers expressing extreme interest in my work and I am working on a second paper. My question is will this help me get a masters scholarship in a western university?

Definitely!  Why 'Masters'? If what you said is true, then aim for a PhD.  I am sure any universities will offer you a scholarship when you wave your marks and paper at them.

Note: every university has a fixed number of scholarships.  So if one doesn't give you a scholarship, don't be too discouraged. It just means there are students with a better CV than yours.  However, there are many universities and only a very small percentage will have that kind of CV.


Is it better to do an MBA with some work experience? I wish to pursue my MBA in a premier business school. Is it better to go straight from my graduation (B.Tech in CS) or get some work experience and then go on with MBA?

Usually, MBA is something that you do when you have significant work experience. There is a good reason for that. If you go straight from your graduation into the program, you will learn a few thing on the theoretical side of business administration. But if you already have encountered troubles in management, you will learn a lot from the numerous case studies (because most of the learning in a MBA is through case studies) and exchanges with other "students".
Moreover, the main advantage of a MBA, besides the few things you learn, is the network that you will acquire, and only a few fellow students will be ready to network with somebody without experience.


What specific techniques can help someone facing mental health problems (depression, anxiety, ADHD) have a productive academic career? Question originally found here

In the past few months, I have been diagnosed for depression, anxiety, and ADHD. While learning this has been helpful, treatment made my already poor performance worse. Jumping around medications as well as the mental and emotional exhaustion that can come from counseling sessions made my academic pursuits almost impossible.

After medication and therapy, it seems that the only advice I can find to treat my conditions is more self-discipline. I don't disagree and find that it can be extremely helpful, but in this (for lack of a better term) recovery process, self-discipline is made harder. Does anyone who have had similar problems throughout their academic career have experience with "coping" mechanisms that go beyond "make a to-do list"? My goal is to one day enter a graduate program, but most steps I have found in researching both ADHD and depression/anxiety have been more suited for those entering non-academic careers or the parents of high school and grade school students.

First, please know that you are not alone and that it is possible to pursue a graduate education even with mental health issues. Several studies have actually indicated very high rates (as much as 40-60%) of anxiety and depression among graduate students (Arnold, 2014; Bernstein, 2015; Wyatt & Oswalt, 2013). So, there are students who have mental health issues who are still pursuing a higher degree. That said, just because it is common doesn't mean it is accepted. Stigma is common in academia, as it is in the rest of society (Pescosolido, 2013), and students may fear being stigmatized if they discuss or reveal their condition. Also, mental health issues, like any physical illness, bring additional challenges that must be managed. Fortunately, there are several things you can do to identify the self-management approaches that may help you succeed.

(As personal context, I have a neurological condition and have experienced periods of depression. I am successfully engaged in a doctoral program).

Take care of yourself

You rightly noted that some of your cognitive difficulties may be due to your mental health symptoms. Depression, anxiety, and ADHD have all been shown to compromise executive function, such as attention, concentration, memory, and problem solving (Biederman et al., 2006; Castaneda, Tuulio-Henriksson, Marttunen, Suvisaari, & Lönnqvist, 2008). As you continue with treatment, you may find that some of these difficulties begin to resolve. Whether you pursue graduate school or work,  prioritizing your own health and wellness is key (Myers, 2012). Some graduate programs are notorious for suggesting students engage in “self-care” but have such grueling schedules that this is difficult. Guard your well-being ruthlessly. If your physical and mental well-being suffer, so will your performance in other areas of life. Specific suggestions:

Be open with your mental health providers about your academic and
career intentions. Discuss treatment options in the context of being
able to effectively function in a graduate school environment. If you
find certain medications are causing side effects that impact your
academic functioning, bring it up and address it. Determine whether
there is a risk of developing a tolerance to your medications so that
they would become ineffective. If that’s the case, work to identify
two different medication regimens, so when you develop a tolerance to
one in the middle of the school year, you can seamlessly switch to
the other. I have found many professionals are sympathetic to
students who express interest in higher education and was able to
effectively partner with my providers.
Identify a routine that contributes to your well-being and stick to
it. For example, if you know that an irregular sleep schedule
contributes to your anxiety, make your sleep schedule a priority. If
you know your depression worsens when you don’t get enough light, and
realize you’ll be working in a dark, interior office, ask your
provider about light-box options.
Consider tracking your schedule (sleep/waking times, eating times and
amounts, etc) and symptoms on an ongoing basis, or in periods when
your symptoms seem to worsen. This can help pinpoint instances where
your routine has become disrupted.

Operationalize your academic challenges, then identify possible solutions

First write down a detailed, specific list of the ways in which you are struggling academically. I posted several follow-up comments to your initial question, because it wasn't clear to me how your studies were being impacted by your symptoms. Determine if there are specific activities or tasks that seem to have become harder in recent months. Once you have list of specific examples, it will be easier to identify specific solutions. Some examples include:

Problem: Low energy/motivation. Possible Solution: Create a concrete schedule, identifying when you will complete brief, manageable assignments. Unlike a to-do list that is open ended, this involves scheduling writing your methods section for your biology paper at 6pm on Tuesday. Rather than dread completing a task at some point, you’ll know exactly when you need to knock that out.
Problem:  Poor concentration makes it hard to focus on long assignments. Possible Solution: Break tasks into smaller components (e.g., breaking a paper into individual sections), and take breaks in between. Remove other distractions (cell phone, email, TV) from the area where you are working. If you can’t resist temptation, go to the library and leave your phone at home.
Problem:  Poor attention makes it hard to take notes during lecture. Possible Solution: Audio-record lectures so you can listen to them later at your own speed. Join a study group where you can compare your notes and understanding with other students.
Problem: Difficulties with memory impact school work. Possible Solution: Identify new ways to study, such as taking more extensive notes, re-writing your notes (this is more effective than re-reading them), or using mnemonic devices.

Your therapist should be able to help you think through many of these issues. Additionally, your school may have resources for adapting to learning difficulties.

Identify external supports

In addition to the internal coping skills you are developing personally and academically, it is important to identify external supports. Social support is crucial to successfully managing ongoing mental and physical health conditions (Gallant, 2003; Kolbe, 2002). You’ve mentioned some feelings of embarrassment and worry about how you will be perceived due to your diagnosis. Disclosure of a mental health diagnosis is a delicate subject, primarily because there is still a great deal of stigma towards mental illness. Your decision to disclose will likely depend on whether you trust that the person you are speaking with will be accepting and that the disclosure will not result in negative consequences. In some cases, you might decide if feels safer not to disclose; this is your choice.

Possible sources of social support include:

Family and friends
Your therapist and/or medication prescriber
Professors, colleagues, classmates – You may find you are comfortable
discussing issues with trusted classmates, but not with your
supervisors. Also, keep in mind that schools and employers cannot
legally ask about mental health conditions in interviews and you are
not required to mention it. However, once you are hired, you can
request certain accommodations (see next point).
ADA officer – If you live in the United States, mental health
conditions are protected under the Americans with Disabilities Act,
meaning that employers and schools must make “reasonable
accommodations” to allow you to function within that environment
(Leibert, 2003). Examples of accommodations include longer testing
periods or moving through the program at a slower pace. Most schools
have an ADA officer or office that oversees students who want to
receive accommodations. Even if you choose not to disclose your
condition to your program, you can use the school’s ADA officer as a
source of support (Willyard, 2012).
Some academics and graduate students have been open about their own
mental health conditions and the impact it has had on their careers
(Keely, 2013; Kelsky, 2013a and 2013b; Shine, 2013). These blogs can
provide additional examples of managing mental health conditions in
academia.

There are two brief caveats. First, if you choose to disclose you might need to educate people on your conditions. They may not initially understand how it impacts you. You can choose how detailed you want to be; sometimes a general explanation is sufficient. Second, when illnesses are “invisible,” and the symptoms are not immediately apparent to those around us, even people who know you have a certain condition can “forget” about the impact it has on your life on a daily basis. You may need to remind them from time to time, and you may also need to remind yourself! This leads to my last point…

Remember to give yourself credit for managing both academic and personal challenges.

Managing a long-term health condition requires a constant amount of mental and physical energy (e.g., ensuring you get enough sleep, remembering to take medication each day, coping with ongoing side effects). Keep this in mind when you are tempted to compare your own performance, achievements, and routines to other students. Other students may not be facing the same difficulties, and may approach their academic endeavors differently. I’m not suggesting your illness will be an excuse to perform less well than others; rather, remember that in some ways you might be starting at a disadvantage, which makes your accomplishments all the more hard-earned.

References

Arnold, Carrie. (2014, February 4). Paying graduate school's mental
toll. [Web log post]. Retrieved from: http://sciencecareers.sciencemag.org/career_magazine/previous_issues/articles/2014_02_04/caredit.a1400031
Bernstein, R. (2015, May 13). Depression afflicts almost half of STEM
students at UC Berkeley. [Web log post]. Retrieved from: http://sciencecareers.sciencemag.org/career_magazine/previous_issues/articles/2015_05_13/caredit.a1500125
Biederman, J., Petty, C., Fried, R., Fontanella, J., Doyle, A. E.,
Seidman, L. J., & Faraone, S. V. (2006). Impact of psychometrically
defined deficits of executive functioning in adults with attention
deficit hyperactivity disorder.The American Journal of Psychiatry,
163(10), 1730-1738.
Castaneda, A. E., Tuulio-Henriksson, A., Marttunen, M., Suvisaari,
J., & Lönnqvist, J. (2008). A review on cognitive impairments in
depressive and anxiety disorders with a focus on young adults.
Journal of Affective Disorders, 106(1), 1-27.
Gallant, M. P. (2003). The influence of social support on chronic
illness self-management: A review and directions for research. Health
Education & Behavior, 30(2), 170–195.
Keely. (2013, February 11). How to keep moving forward, even when
your brain hates you. [Web log post}. Retrieved from:
http://www.littledose.keelium.com/2013/02/11/how-to-keep-moving-forward-even-when-your-brain-hates-you/
Kelseky, Karen. (2013a, February 13). Academia and Mental Illness: A
Preliminary List of Resources. [Web log post]. Retrieved from:
http://theprofessorisin.com/2013/02/13/academia-and-mental-illness-a-list-of-resources/
Kelseky, Karen. (2013b, March 13). Managing Mental Illness in
Graduate School: Some Recommendations (A Guest Post). [Web log post].
Retrieved from: http://theprofessorisin.com/2013/03/13/3546/
Kolbe, J. (2002). The influence of socioeconomic and psychological
factors on patient adherence to self-management strategies. Disease
Management & Health Outcomes, 10(9), 551–570.
Leibert, D. T. (2003). The mentally ill and access to higher
education: a review of trends, implications, and future possibilities
for the americans with disabilities act and he rehabilitation act.
International Journal of Psychosocial Rehabilitation, 7.
Myers, S. B., Sweeney, A. C., Popick, V., Wesley, K., Bordfeld, A., &
Fingerhut, R. (2012). Self-care practices and perceived stress levels
among psychology graduate students. Training and Education in
Professional Psychology, 6(1), 55.
Pescosolido, Bernice A. (2013).  "The public stigma of mental illness
What do we think; What do we know; What can we prove?." Journal of Health and Social Behavior 54(1), 1-21.
Shine, Jacqui. (2013, December 18). On Depression, and the Toll
Academia Exacts. [Web log post]. Retrieved from:
https://chroniclevitae.com/news/228-on-depression-and-the-toll-academia-exacts
Willyard, Cassandra. (2012). Need to heal thyself? gradPsych, January. Retrieved from: https://www.apa.org/gradpsych/2012/01/heal.aspx
Wyatt, T., & Oswalt, S. B. (2013). Comparing mental health issues
among undergraduate and graduate students. American Journal of Health
Education, 44(2), 96-107.


At which level (D or E) should I apply for an advertised faculty position in Australia? I am putting together an application for an academic position that has been advertised as either level D or E at an Australian university (equivalent to full professor or chair professor in the US). The selection criteria are slightly different, depending on the level at which I apply, and I need to specify which level I am applying for in my application. I would happily accept the role if offered at level D, but would also be a credible candidate at level E.

My publication record and h-index are comfortably on par with existing level E professors in the department, my grants and funding record is good, and I would also bring the industry experience and leadership skills that they are looking for. On the other hand, I am not a shoe-in for the role, even at level D: my research interests are only just within scope for the department and I have limited teaching experience. It's a ("Group of Eight") research-focused university, so teaching is likely to be secondary to research, but it is still a factor.

I am guessing that they would not consider me at level D if I apply at level E, or vice-versa. Australia has less of a culture of salary negotiation than the US. I have thought about addressing both sets of selection criteria and leaving it up to them, but worry that might simply be annoying.

What is your advice?

It is my understanding that when a position is advertised so broadly, i.e. D or E, they are likely looking for someone really big. That being said, I think they are likely looking for someone at the level E, but would consider a strong candidate at level D.

If it were me, I would evaluate my qualifications and fit with both D and E positions honestly, and then put all my effort into whichever feels like the best fit.

If the only motivation to try for E is salary, and you probably fit better for D, then you are likely risking both.


Is it okay to include a very long appendix (for MS thesis)? I am currently doing my MS thesis and I have to include an appendix to describe a mathematical subject. However, I added extra details in that appendix and it is now too long.

My Prof. suggests I better not include it "at all", or if necessary just make it shorter (though he admits that it is very well written and referenced).

Is it unusual to include a very long appendix in a thesis?

My thesis is now 150 Pages; 20 pages are for that appendix.

This does not sound unusual to me. Just ask yourself, is there a possibility that the reader would need this?

I have seen theses and dissertations with no appendices and some with over 50 pages of appendices. In my field, these are often filled with user study materials, source code, or raw data which can easily eat up many pages.

I don't see any harm done with being conservative and including everything. In this case, I have seen people list two versions of their thesis online, one with and one without the appendices.


What are "post-deadline paper submissions"? I'm still in the beginnings of my life as a graduate student researcher. My advisor is pushing me to submit my work to upcoming conferences. Now, I'm a complete novice to these procedures, so I began to sift through various conference websites to learn a bit more. I noticed that some conferences have post-deadline submissions for research papers. What does that exactly mean?

Do post-deadline papers get vetted differently, or do they basically receive an extended deadline?

(Physics, if it matters.)

Edit:

Example: http://www.ofcconference.org/en-us/home/submit-papers/

You can think of post-deadline submissions as reserving seats on overbooked flights: if someone doesn't show up, you get the place. But in case of conferences, not that automatically.

Some twenty years ago, when conference submissions were handled through emails, post-deadline submissions were not that uncommon, at least in my field. You would have sent an email apologizing for not having been able to respect the deadline, and hoped for the best. If the technical committee found your work valuable and the organizers could find a free slot, either oral or poster, your paper would have been accepted and your submission would have been added to the book of abstracts as a spare sheet with the headline "post-deadline submission". I recall conferences with around 5-6 post-deadline submissions.

With the advent of submissions managed through websites, it seems to me that post-deadline submissions have been progressively less accepted.

  Do post-deadline papers get vetted differently, or do they basically receive an extended deadline?

How post-deadline submissions are handled really depends on the conference organizers, and how much post deadline the submission is. In some cases, they could be reviewed directly by the chairs of the technical committee rather than by the designated reviewers.


Should I disclose my mental illness and medication in a PhD position interview? While I was doing my PhD in my previous position I was diagnosed with a mental illness. I started medication however as a result I could not concentrate very well and it made me quit my previous position. I continued my medication and recently have reduced it. Now I think I am able to concentrate again.

Soon I will have an interview for a new PhD position. I was wondering if I should bring up the matter. On one hand, I think I should be honest to my future supervisor. On the other hand, I don't want to lose the chance by scaring them.

Would you please help me with your opinions?

If I shouldn't bring it up myself, what if they asked me about my previous position? Should I tell everything then?

There is no requirement to disclose and given the current climate around mental health, I would not suggest disclosing.

I would say that you had health problems that resulted in your having to leave your former school, but that these issues are under control and you are confident you will succeed at your new program.

I would be sure you tell your letter writers to also use the vague rubric of "health problems" as some may inadvertently disclose without thinking about how you want to be framed.


Do advisors typically fund travel for PhD students in non-conference settings (e.g., university seminars, industry meetings, etc.)? Do advisors typically fund PhD students for travel to events other than academic conferences? Examples include:

Seminars at other universities so the student can promote their
research
A Technical Program Committee (TPC) meeting
An industry conference where the student hasn't published anything but is there to promote their work in a talk or demo

These events are not directly related to the bottom line of publishing papers, but are helpful for the overall career of the students.

All work related travel that has been assigned to you by your advisor should be funded. That's a general rule (also outside academia, at least in Germany).

You may also ask your advisor if they'll refund travel costs for the things you mentioned. In this case your advisor may ask you to check for other funding resources (travel grants for conferences, possible refunding by the university that invited you…). More concretely for your examples:

Seminars at other universities: If you are invited to give a talk but the other university is not funding you, then I'd hope yes but no for just attending that seminar.
A Technical Program Committee (TPC) meeting: If you are a member of the TPC then yes (however, for the TPCs I know, the member usually have their own funding).
An industry conference where the student hasn't published anything but is there to promote their work in a talk or demo: If you have a talk or official demo at the conference then I'd say yes, if you only want to go there networking then generally no (unless there are some funds that are going to expire).


Citing multiple images scraped from website I scraped a few thousand images from an open source online collection (https://www.metmuseum.org/art/collection --> Open Access Artworks) for a coding project. I want to cite the selected works from the collection with one Harvard style citation for my code report's bibliography. None of them show up in the report itself, they're just research materials. Does anyone have a suggestion for this?

In this case it turns out that the Metropolitan Museum has made available a large number of public-domain works under the Creative Commons Zero license. Legally, I think this means you don't need to cite anything, but you'll probably still want to, both in order to be a good scholar and to encourage the museum to keep expanding their digital collection.

Individually citing thousands of individual images is obviously excessive, especially when they don't show up in the paper. Instead, I would suggest citing one or more of the datasets they have made available on GitHub. You might not have used these directly, but if they include all the images you've used this makes for an inclusive reference. Also, they write

  Attribution

  Please consider attributing or citing The Metropolitan Museum of Art's CC0 select datasets, especially with respect to research or publication. Attribution supports efforts to release other datasets in the future. It also reduces the amount of "orphaned data," helping to retain source links.

For reproducibility reasons, you might also want to include a list of all the pictures (or their accession codes) in some kind of electronic Supplemental Material.

For completeness, if you want to cite an individual image, their FAQ states

  How should I cite and credit a CC0 image that I've downloaded from The Met's website?

  CC0 (Creative Commons Zero) does not require any attribution or credit, but as an educational institution, the Museum hopes that you will include a citation. All the information necessary for proper citation of a CC0 image is available on the Collection page for that object.

  A sample object credit line format is as follows: "The Metropolitan Museum of Art, New York," followed by the specific information identified as the "Credit Line" on the Collection page for each work of art. The citation could also include the URL www.metmuseum.org.


Is "get passing grades and follow voraciously your curiosity on the side" a good strategy for graduate school? I will be starting my PhD in Math this fall. I have diverse interests including philosophy, history and economics, but I concluded that a PhD in Math would be most useful in the real world. I wanted to hear people's thoughts on Nassim Taleb's strategy for graduate school, which can be summarized as follows: "get passing grades and follow voraciously your curiosity on the side." Here is the full quote:

From Antifragile:

  My idea was to be rigorous in the open market. This made me focus on what an intelligent antistudent needed to be: an autodidact—or a person of knowledge compared to the students called “swallowers” in Lebanese dialect, those who “swallow school material” and whose knowledge is only derived from the curriculum. The edge, I realized, isn’t in the package of what was on the official program of the baccalaureate, which everyone knew with small variations multiplying into large discrepancies in grades, but exactly what lay outside it…

  Again, I wasn’t exactly an autodidact, since I did get degrees; I was rather a barbell autodidact as I studied the exact minimum necessary to pass any exam, overshooting accidentally once in a while, and only getting in trouble a few times by undershooting. But I read voraciously, wholesale, initially in the humanities, later in mathematics and science, and now in history—outside a curriculum, away from the gym machine so to speak. I figured out that whatever I selected myself I could read with more depth and more breadth—there was a match to my curiosity. And I could take advantage of what people later pathologized as Attention Deficit Hyperactive Disorder (ADHD) by using natural stimulation as a main driver to scholarship. The enterprise needed to be totally effortless in order to be worthwhile. The minute I was bored with a book or a subject I moved to another one, instead of giving up on reading altogether—when you are limited to the school material and you get bored, you have a tendency to give up and do nothing or play hooky out of discouragement. The trick is to be bored with a specific book, rather than with the act of reading. So the number of pages absorbed could grow faster than otherwise. And you find gold, so to speak, effortlessly, just as in rational but undirected trial-and-error-based research. It is exactly like options, trial and error, not getting stuck, bifurcating when necessary but keeping a sense of broad freedom and opportunism. Trial and error is freedom.

  (I confess I still use that method at the time of this writing. Avoidance of boredom is the only worthy mode of action. Life otherwise is not worth living.)

The passage you have shared refers specifically to a baccalaureate degree:

  The edge, I realized, isn’t in the package of what was on the official program of the baccalaureate... but exactly what lay outside it.

In a PhD, coursework takes a backseat to research. In research, there is no such thing as "get passing grades"; there is no meaningful threshold at which your research is considered acceptable, only a continuum of poor to exceptional. At the end of your PhD, your prospects on the job market (especially the academic job market) and the impact you have made with your work depend on how close you are to the "exceptional" end of that range, not just having achieved some minimum requirements and earned a piece of paper that says you have a degree.

Furthermore, PhD-level research requires a level of depth and focus that is not typically present at the undergraduate level.

That's not to say you can't have broad interests, and you can even leverage your broader interests to improve the quality of the work you do in your primary field. But a strategy of planning to undertake a PhD and put minimum effort into your PhD research while doing other things on the side is not a winning strategy for most people. Instead, you should try to use your curiosity for your PhD research. (Also see: Can I slack off and get a PhD?)

In fact, later in that same chapter, Taleb describes how his curiosity and drive to understand probability led him to specialize in that and focus on that to the exclusion of everything else:

  When, at Wharton, I discovered that I wanted to specialize in a profession linked to probability and rare events, a probability and randomness obsession took control of my mind. I also smelled some flaws with statistical stuff that the professor could not explain, brushing them away—it was what the professor was brushing away that had to be the meat. I realized that there was a fraud somewhere, that “six sigma” events
  (measures of very rare events) were grossly miscomputed and we had no basis for their computation, but I could not articulate my realization clearly, and was getting humiliated by people who started smoking me with complicated math. I saw the limits of probability in front of me, clear as crystal, but could not find the words to express the point. So I went to the bookstore and ordered (there was no Web at the time) almost
  every book with “probability” or “stochastic” in its title. I read nothing else for a couple of years, no course material, no newspaper, no literature, nothing. I read them in bed, jumping from one book to the next when stuck with something I did not get immediately or felt ever so slightly bored. And I kept ordering those books. I was hungry to go deeper into the problem of small probabilities. It was effortless. That was
  my best investment—risk turned out to be the topic I know the best. Five years later I was set for life and now I am making a research career out of various aspects of small probability events.


Proper ways to contact US academics from outside academia? Forgive the question for being silly, but I do not live in the US and work in a different field.

I am developing an application I believe would be a wonderful (free) asset to the study and comprehension of a particular subject (history, which I suppose brings with it philosophy, sociology, and many others really) for students and docents alike.

I would thus like to gather the opinions of any number of actual professionals (maybe pique their interest and earn their cohoperation), who may be kind enough to waste a few minutes, on the concept, which is handily laid out in brief at the project's URL.

A quick look at a few universities' websites made it clear that is not the way, unless I wish to enroll.
I briefly considered contacting PhDs through LinkedIn, but it feels wrong.

So the question is:
what are the proper (sensible, respectful, appropriate, expected) ways and channels, if any, for a complete professional stranger, to contact a US Professor and hold some expectation that they may react after some fashion (or at least a suspect they may have actually received the message) ?

Why the US ?
Because it seems like a good starting point. There are so many people and learning institutions in the US. And American history is quite unique. And the geography is vast, it fits well with the concept. Plus, english.

The Answers all raise very helpful points, I wish I could pick at least 3. It being a question about new tech, students may be the ones to pursue. Thanks all.

I am developing an application I believe would be a wonderful (free)
  asset to the study and comprehension of a particular subject for
  students and docents alike.

Consider presenting it at an academic conference. In my field, there are usually industry booths at the conferences. But there is also often the opportunity to present innovative software with a poster, or sometimes even as a talk.

Don't expect any responses to unsolicited emails marketing your software. These will usually be regarded as spam.


Current Masters student, need advisor for PhD (no public announcements in the department)? I am a masters student at a top-rated US university in electrical engineering. I have been working under a professor who joined the department last semester. He is quite happy with my progress, but can't offer me a PhD as he doesn't have enough money. He has agreed, though, to help me get a PhD by recommending me to other professors.

The task of finding a professor, however, is on me. The issue arises here, as in my department professors don't actively search for students. It works mostly like a referral system, where the professors take up recommended students. Thus most of the openings get filled up before they make a public announcement. One way to solve this is to write mails to several professors to ask for openings. What I am looking for is this: is there a better strategy?

Rather than emailing lots of faculty asking for openings, I would recommend emailing a few faculty who seem most interesting to you asking for a discussion about the possibilities of joining their department.  The reason is that rather than just polling for openings, you want to get connected to the referral network (which your current professor appears unwilling or unable to do for you).  I would thus recommend approaching the discussion not as:

  Hi, can you hire me?

but instead as:

  Hi, I'd like to figure out whether my research interests and personality are a good match with you or others in the department.  If they are, can you hire me or else can you point me to somebody else who is likely to be interested in doing so?

This way, instead of asking a simple yes/no question, you are engaging the person in a way that may also lead you to good connections that you wouldn't have even thought of asking about.  By following the leads from such conversations, I think you are significantly more likely to find a good match than just by sending out polling emails.


What to expect when pursuing a second doctorate in an unrelated field Long story short: I got a PhD a few years ago (let's say, in numerical methods for nonlinear PDEs).  I've since gotten experience with a couple post-docs and a variety of collaborators, but I'm not really satisfied with what I'm doing.  I feel out of place.

Earlier in life, I made a tough decision between science and humanities-- my other passion has always been, let's say, east Asian languages.  If my bachelors program had had better language courses or options for "hybrid" fields like computational linguistics, I probably would have gone that route, instead of fully focusing on math.

I've sought out collaborations that might help me bridge the gap between math and languages; I've also looked at postdocs to help make the transition.  I've reached out to leaders at research groups who do stuff I'm really interested in.  The common denominator is: I'd need a PhD in some kind of linguistics to research seriously what I want. So...

What key things should I take into consideration when pursuing a doctorate, given that I have a doctorate in an unrelated field?

Please consider the question within the following context: I'm not asking whether having two PhDs is good or bad (I frankly don't care), how to needlessly pad my name with titles, or how to get two PhDs simultaneously. (That is all to say: this post doesn't answer my question.)  I'm asking about what to expect when changing careers, specifically, if the source career is in one academic field and the target career is in another, unrelated field.  Assume I've 100% decided to leave my current field and pursue this second doctorate, for the purpose of changing careers. Assume also that I already have substantial content knowledge in the target field, as I have a bachelors degree in it already, and it's been an avid hobby for most of my life.

Some sub-questions that don't need to be specifically answered, but I think help narrow the question: in what way could my current PhD be a hindrance in getting into a new program?  Will my supervisors and colleagues see my past PhD as an asset, or as weird-looking mole they will try to politely ignore?  What are other questions should I ask myself to prepare for such a non-traditional career path?

Note: I've edited this question multiple times in a vain attempt to get the duplicate label removed. If you agree, please vote.

In my experience, nonstandard paths like what you propose are initially viewed with surprise, and with varying degrees of suspicion. That includes admission committees, potential supervisors, fellow students, etc. However, that comes from uncertainty and unfamiliarity and can be shaped by the narrative you supply, and how you follow through.

Basically, people will probably have 3 archetypes in mind when you first contact them. The most positive one is that you are some sort of polymath genius. The most negative one is that you are a serial fail-to-deploy-in-life perpetual student, a model everyone in academia has encountered. And the 3rd is that you want to do research in some unexpected interesting intersection of your old and new field (which you've said is not the case). You therefore need to replace that narrative with a truer, credible, if possibly slightly airbrushed one, something like: you've always been interested in both X and Y, initially pursued interesting topics in X leading to a Ph.D. and start of a promising career, but are increasingly passionate about Y and want to refocus on that. I would be open that you don't expect to directly harness your expertise in X, but that you do expect that your background will help you be a very effective student in Y.

And then you need to back that up with your actions! Your Ph.D. is a credential indicating you have demonstrated the ability to advance the state of the art of knowledge in some field, and that you have learned sufficient academic "tradecraft" to be an independent researcher, at least from a competence point of view. (Footnote: The at-best only partial independence of a post-doc, and indeed the whole post-doc position, is more a reflection of funding realities than of a junior academic's presumed research abilities). So if someone with a Ph.D. and post-docs would approach me, I would expect them to be able to motor through the usual initial stages of a Ph.D. much more quickly than a "new" graduate student. I would expect that they will have done a fair amount of foundational reading in the field already -- that's something that hardly needs an advisor, though an advisor will be helpful in helping identify important strands that may be nonobvious from the outside. And I would expect them to arrive with some well-developed thoughts on potential research topic, though of course we might well adjust it together.

If you were to come with this type of pre-preparation, I'd consider you a lower-risk admit -- as a committee member or prospective advisor -- than someone whose basic skilset is unproven. Conversely, if you were to arrive, with the background you describe, with the typical keen-but-blank-slate mindset a fresh-out-of-undergrad student usually brings, then I would be more worried you belong to the serial-failure-to-deploy archetype instead.

Second, I would suggest you be very open about discussing your financial expectations. Do you need/expect funding (and is it usual in your target field)? Or can you fund yourself by continuing to work in your current field part-time? Or do you have enough saved up from a well-paid science/tech job (and academics in the humanities/social sciences tend to assume all science/tech jobs are well paid....) that you will be self-supporting? All of those are acceptable, just avoid unpleasant surprises from failing to bring up the topic.

Good luck!


Is it ok to mention assistance in grant writing on your CV? On behalf of my advisor, I recently wrote a grant to obtain some specialized and expensive hardware. Is it ok to mention this on my CV, even though the grant is in my advisor's name and if yes, what would be a good way to word it ?

You can list on your CV whatever you think is useful information for the reader. In your case, whether something is useful depends on what your position in life is. If you're a full professor with a long history of funded research, what you describe is likely not useful to list on a CV. If you're a graduate student with an otherwise relatively short CV, then that's a different story. I would suggest wording such as

  Co-authored the proposal for grant XY-1234-5678 (PI: Professor Z).

Now, whether an entry such as this has any impact is a different issue, but it is certainly not going to hurt.


Repetitively citing studies in a literature review I am writing my first literature review (not using a systematic methodology) and I am trying to put some thought into the underlying structure of the literature review. I have considered these two structures:

Structure 1

  Study A does this...
  Study B does that...
  Study C does this...
  My study does this...

Structure 2

In this structure, (at least early on in the review) I write about how the papers that I have gathered vary based on their collective characteristics as parts of a greater whole, e.g. general modelling approach, spatial and temporal scale, problem framing:

  These studies differ based on their general modelling approach.
  These studies differ in their spatiotemporal scale.
  These studies differ in their framing of the problem.
  My study is similar in characteristic XYZ, but differs in characteristic ABC, and advances the field through characteristic EFG.

I personally think that Structure 2 is more interesting in terms of content layout and synthesis of the material relative to Structure 1, but at each point of discussion it requires me to talk about mostly the same papers, just in different contexts.
So I am concerned that repetition in Structure 2 could be a problem as compared to Structure 1.

Are my concerns justified and are there any further arguments for one of the structures?

You should definitely go with Structure 2. It is far more helpful to you (that is, it forces you to engage more deeply with the literature) and your readers (that is, it gives them a more useful review of the literature).

The article that is probably the most seminal in my field (information systems) on literature-review methodology is mostly famous because they clearly addressed precisely this distinction. Webster and Watson (2002) argued that author-centric literature reviews (your Structure 1) are not very useful. They are simply an extended bibliography. (When you think of it, all that does is little more than summarize the abstracts of each article, which are already summaries of the articles.) They argued instead for what they called a concept-centric approach to reviewing the literature.

The concept-centric approach is not quite the same as what you describe in Structure 2: what you describe, I would call a topic-centric approach. Webster and Watson’s concept-centric approach identifies the theoretical concepts in each article and then presents them as the structure of the review. Your Structure 2 identifies common topics in each article. While not as useful for developing theory as the concept-centric approach (and maybe developing theory is not your goal at all), it is far more useful than the author-centric (or more accurately, article-centric) approach of your Structure 1.

Reference

Webster, Jane, and Richard T. Watson. Analyzing the past to prepare for the future: Writing a literature review. MIS quarterly (2002): xiii-xxiii.


My professor never answered my email. What should I do? I'm having trouble submitting an assignment into turnit in and my professor never replied back to my email. The assignment had 3 different parts to it and I was only able to submit one of the parts because I tried to submit them separately instead of together. I asked my professor if I could just email him the other 2 parts of the assignment and he never answered back. I emailed him 4 days ago.

You can 1) send a reminder, 2) stop by his office in person and ask, or 3) ask him after a lecture.

If it's urgent I'd do #2, otherwise it's up to you.


Should I contact the EIC for additional information regarding his decision on my paper? I just received the feedback from the Editor-In-Chief that my paper has been rejected for publication in this high-ranking journal.

  There are several concerns raised by one of the reviewers. Therefore, it would not be possible to accept this paper for publication.

Based on the reviewers' comments, two of them seem to be in favor, as they raise no "substantial" concerns (they raise 5 and 4 points, respectively), i.e. their findings are mostly of a cosmetic nature (rephrase that, elaborate this, color the figures differently, correct a spelling mistake), and their recapitulation of the work is more precise than that of the third reviewer.

Now the third reviewer raises 6 points of concern. 4 of them are very valid remarks, however, they are not fundamental problems, at least, I don't perceive them as such, because they are easily amended (by at most 2 sentences each) and present no conceptual fallacies, i.e. as I see it, the particular parts are not clear to the reader and need additional explanations and more appropriate emphasis. The fifth concern addresses the structure of the paper, the reviewer proposes another ordering of the sections. The final point states the need for a discussion, which I indeed drafted, but chose not to include in the paper. It is not irrelevant, but it is not crucial for the problem, solution or background and could possibly distract the reader from the focus of the paper. In addition to space constrictions, this discussion was left out before submission.

Between submission and the decision, there was a change of the Editor-In-Chief at the journal. This might be the reason the review took longer than usual (10 instead of 6 weeks). Perhaps that could even influence the accepting policies...

After the first review, I'm used to getting rather harsh comments, either rejecting the paper or proposing another review cycle, it doesn't matter. The important part is usually that I get meaningful feedback about my paper and improve it. In this case, however, the reviewers' comments resemble something I would expect after the second or third review cycle, i.e. something that I can alleviate in a morning.

The problem is that I don't understand the reason for rejection. Even when I address all the reviewers' suggestions, I would still feel that nothing crucial has changed. Furthermore, when rejected, I can't submit the same paper to the same journal. I obviously intend to submit the paper to another journal. However, before doing so, I consider emailing the Editor-In-Chief and asking for more information regarding his decision. As things are now, the reviewers' comments state neither fundamental fallacies which imply that the paper is of low scientific value nor point how I could realistically improve on it. Is this a good idea?

I have never been an EIC but I have spoke to some, I have been a reviewer of many papers, and I have had the similar experiences as you described.

It is probably useless to further inquire about your paper. The EIC decision could have been based on the private communication channels of the review process. The reviewer might have been lukewarm about your paper - maybe it was not a case of a substantial error but that the result was uninteresting. It could also be the case that the new EIC did not have the time for a careful consideration of your paper, of balancing the different reviews and based her decision on the less positive one. EIC are usually very overloaded and some of them explicitly use the rule of deciding based on the most negative review. If it is any of these two cases, you will not receive any further information from the EIC regarding your paper.

My personal experience is that I was only able to change a EIC decision once, when the negative review was reasonably detailed and I could show that some of the  main points made by the reviewer were 100% opposite of what was already written in the paper. The other occasions where I asked for more info or criticized what I thought was a wrong interpretation of the paper, I would receive a polite answer that the decision was made.

Now, I wait a week until the frustration and the anger of how "dumb is this reviewer" subsides, make the the changes I think are reasonable and send to the another journal.


How should I cite a tool or a library in my article? When using an online library, tool, framework or something similar, what is the proper way to reference it in an article?

(I work in Computer Science). For example, I want to say that many popular implementations of the method presented in [article reference] use a slightly modified version of the main formula. I mention some examples for the implementation (e.g. OpenCV, VLFeat).

When thinking of a way to reference this, I have several dilemmas:

I could put a small explanation in a footnote or add it to the list of references
I could use the link to the main webpage or to an online manual
do I reference it at all?

This question about how to reference Python is somewhat similar. The difference is that the tools I want to reference are fairly well known in my community (unlike Python for biologists).
In short, I am looking for a good way to acknowledge tools, frameworks or libraries not associated to any article in my writing.

A good citation has the following properties:

Gives credit where it is due for an (idea, tool, dataset, etc.) that is not your own.
Directs the reader of your paper where to look, if he/she wants to verify that your claims about the (idea, tool, dataset, etc.) are correct.

Any of the following can be used to cite a tool, as long as the above properties are satisfied:

If the authors of a tool explain how they would like it to be cited, follow those recommendations.
If there is a paper or tech report about the tool, cite that, because that is what the authors would probably want (if they didn't specify).
If there is no paper or TR, cite the website of the tool.

Of course, in most cases, you're not the first person to cite the tool - go search Google Scholar for the name of the tool, and find out how others cited it.


Where to add citation when having several paragraphs from the same source(s)? So, if I have three paragraphs, inspired and even having copied sections from the same source, do I add citation at the end of each paragraph or at the end of the third or where else?

When you have such a substantial chunk of information attributable to one source it can be useful to start the text by simply declaring the source. This can be done in the following way (exact formulation can of course be changed; I chose Harvard style referencing as an example):

  The following [x] paragraphs follow Name (yyyy) unless stated otherwise.

The formulation can be changed to better blend in with the text by adding details about what the information is about  or why this source is good or should be repeated, or both. The "unless stated otherwise" can be omitted if you have no need to add other references in these paragraphs; I added it for completeness.


How to find the right balance between a challenging and an enjoyable mathematics exercise session? Next semester, I will be leading exercise sessions in a first year course of mathematics. More precisely, the course is Linear Algebra and the audience consists of young, first year undergraduate mathematics-students. The course is taught at a university in continental Europe. Judging from my personal experience, I know that most first year students of mathematics have plenty of troubles with the new, abstract material that is taught at a university. Hence, it would be good to make the student's experience in my exercise sessions as "easy" and enjoyable as possible.

However, I am not a fan of just doing simple, easy and short exercises. My opinion is that you do not make things easier for the students, if you omitt doing the hard exercises and just do the easy ones. Of course, this does not mean that everything I want to do is hard, but every now and then, something difficult will have to be discussed in the exercise sessions. Often, the hardest exercises are the most enlightening ones.

Moreover, my experience tells me that most students have wrong expectations of an exercise class: they expect to understand everything without (only a tiny bit) personal contribution and blame the instructor (which would be me in that case), if they do not understand everything. This has happened more than once to me and if I tell them that they have to work, I am considered to be the 'strict teacher', whose subject is the most important one and who does not understand that the new material is hard. I would be totally fine with that image, but this demotivates students and let them feel safe because they have someone to blame (Once, I heard the sentence "I would have understood the new material, but the exercise class was too bad and on a too high level" - in my opinion, I discussed everything in detail and pointed out which things are the most important ones and focussing on these).

In short, I find myself in the following vicious circle (it seems like you can achieve two of the three things below at a time, but not all three together):

Maximizing the students' enjoyment level (i.e., they should understand as much as possible and just have a good time during my exercise class)
Doing an exercise class which is on a reasonable (not too high, but also not too low) level
Keep the students motivated and tell them quite clearly, that they have to work to understand the new material

Or - in very short - the question is: Which aspects constitute a good exercise class (in mathematics) and which of these aspects are the most important ones?

As a grad student now who took undergrad linear algebra with a professor I really liked, I will attempt to generalize what I saw that worked.

The best way for students to learn something that is as potentially abstract as linear algebra is to relate it to something concrete. My professor always liked to point out that once you leave R2 and R3, everyone visualizes geometry differently. As a result, he often tried to keep his visual explanations in that space.

However, for higher dimensional vectors, you can still relate the material to multi-dimensional concepts without drawing a picture. A great example (and pretty interesting exercise) is Markov chains. When we went over eigenvalues and eigenvectors, we motivated all of the math by walking through Markov chains. He used Markov chain gambling schemes (e.g. holding a bet steady when you win, doubling when you lose) to illustrate eigen-decomposition in a practical way. In that way you can help students develop intuition by talking about something that makes sense outside of the math-sphere.

In terms of practical exercises, I've found that progressive problems tend  to work best. That is, where each problem is working towards one ultimate problem solution. Generally, each step is a little more complex as well. For example, maybe the first step is finding the Eigenvalues and Eigenvectors, the second is diagonalization, the third is something tangential like inverting the matrix, and the last is applying what you've calculated to some practical problem like a Markov Chain.

In other words, ease students into the harder material by showing them the simpler ways to do it first. Once you can intuitively understand the general concept at basic level, it's easier to move on to more advanced views of the same and similar concepts. Plus, when students see complex material from the viewpoint of something simpler to understand (like maximizing gambling winnings), it provides a reference point for them to start from.


Which software converts academic publications from PDF to Word without mangling complex formatting? I'm asking about this in StackExchange Academia rather than a software-recommendation site because I have conversion problems specific to the layout of academic publications. I'm helping a student who has problems with their eyesight. They find it hard to read academic papers and books on screen, when distributed as PDF. They prefer to have these converted to Word, then read that on screen. This helps them because they can change the font of any part that's hard to read, as well as highlighting section headings and other cues to help them navigate. There are many PDF-to-Word converters, but all the ones I've tried (see below) have defects. Can anyone recommend something better than those I've listed? The converter must not mangle tables, diagrams, footnotes, formulae, subscripts and superscripts, or other complicated content typical of academic publications.
The student does not like to read printed text, and only has an A4 printer, so blowing up the text and printing that isn't feasible. The pandemic introduces its own constraints, since they don't want to venture from their flat to use University computers. So they're restricted to what I think is a 22-inch screen, Windows 10, and their A4 printer. I only mention these because commenters suggested them. The student is comfortable reading Word files, and I want to help them do that, rather than force them to do something outside their preferences.
Getting back to PDF-to-Word converters, so far, we have tried:

Kofax Power PDF, but it's very erratic, though. For example, when I converted an archaeological report which I had to ask Power PDF to OCR, it "thought" it had found characters in the thin lines indicating boundaries in a diagram of the archaeological site. Power PDF also mangles structural chemical formulae, even when told not to OCR. Footnotes and tables cause even more problems, as do in-line chemical formulae, and subscripts and superscripts.

SmallPDF. This claims to be "the platform that makes it super easy to convert and edit all your PDF files". It is not. It converts some so they work better than those done by Power PDF, but crashes on others.

PDF24. This probably does a better job than either Power PDF or SmallPDF, when it works. But on some PDFs that need OCR'ing, it just emits the original page-images. This may well be a bug, and I've reported it, but I've not had any reply.

Does anyone have any recommendations?

UPDATE: The question has gone through 10+ revisions since I wrote this answer. I haven't checked to see whether it is still relevant. I'll try to respond to comments.
I'll start by disclaiming: My initial solutions do not follow the prescribed pdf to doc conversion (whilst my last solution does, albeit, it's probably a bad solution), and I haven't tested them, which violates the OP's constraints. I disregard these constraints because I don't think they are particularly relevant.
It isn't clear whether on-screen, digital reading or printed, physical reading is preferred, nor how much adjustment in text size is desired, clarification may allow more focus.
The trivial, obvious solutions, which have surely been tried, are: Large screen plus zoom and printing to a larger paper size, e.g., A3 or A2 (the former being more commonly available), rather than A4. Annotations and highlighting can be applied to pdfs with numerous tools.
For various other enhancements, numerous tools exist on Linux, which can be scripted to suit needs. For instance, a page could be split into smaller parts and manipulated in various ways, e.g., split a portrait page into top- and bottom-parts, and blow up each part onto a horizontal page (optionally of larger size). All operations can be automated. This approach cannot fail particularly badly for academic papers. At worst, perhaps the split is applied in the wrong place, but, the two parts can be displayed simultaneously, aligned at the lower/upper edge, or by folding the top edge of a printed page.
Linux tools can also be used to convert to word processor format, for instance, pdf2ps and ps2txt can be combined to convert pdf to plaintext, which any word processor can open. (This is my worst solution. I doubt tables, footnotes, formulae, etc. will be handled particularly well.)
Converting to a word processor format seems like a misdirection. That's why my last solution probably won't work. Extracting another format from a pdf seemingly goes against the design goal of the pdf format, namely, to present documents in a [software independent] manner...encapsulat[ing, in each file,] a complete description of a fixed-layout flat document, including the text, fonts, vector graphics, raster images and other information needed to display it (source: Wikipedia).
My apologies if I'm way off mark here. I'm unsure of your precise requirements.


Rights of funding data in research I have used data of my colleague with her permission in my article while that data was funded by an external organization for her other project. Although my research is not funded by that organization, I made use of some data.

Is it okay to acknowledge my colleague and the other organization in my article, or do I have to provide funding details to answer the question 'Did the research in this article receive funding?'.

Thanks

I would write:

The research in this article did not receive third party funding. The research is (partially) based on data gathered within the project xyz which was funded by abc. We would like to thank uvw for the data acquisition and support.


What should I do about a bad professor? My professor has not and will not hand out a syllabus (I have asked as well as others). I have a very vague idea about how grades will be calculated and no idea what the class schedule looks like (I don't believe the prof knows until the day before, either). He has also said that he has no office hours and will not answer email. I have no idea how to handle this because I have to have this course this semester and cannot drop it, but I also cannot that I will make a bad grade because of lack of preparedness on the prof's part.

Any suggestions?

I suggest going to the department secretary. In every department I have been involved with, this is the person who handles the mechanics of things like getting profs to submit a syllabus, grading scheme, calendar, and so on. Simply ask

  Do you have the [missing item] for [course] by [prof]?

If you thus receive what you want, mission accomplished. If the answer is "no, I understand [prof] was going to hand them out in class" or just "no" you can go on to

  We didn't get them in class and I have emailed and asked for them but no reply.

Typically at this point the secretary will swing into action. I've seen profs called while students are standing there, I've seen heads visited, emails sent, all kinds of things. This is what this person does and the ones I know all do it very well indeed.

If the secretary just kind of stares at you in a "sucks to be you" way, you could try

  Is this something I can raise with [head] because I have no idea what the class schedule looks like and only a very vague idea about how grades will be calculated.

You will now get a yes or a no, if it's yes the secretary will set you up an appointment, if it's no then you need to ask why, take notes, say thank you and leave. After you leave the office check to see if you have an Ombud or someone in Student Services who can help you. But I actually doubt it will come to that.


Why do major international universities still have courses in languages other than English? As an example ETH Zurich, which is arguably one of the best universities in Europe, still educates Bachelor's students in German:

  Please note: the Bachelor’s degree programmes begin in German. In the second and third years of the programmes, some of the courses may take place in English.

This doesn't make sense to me as it's obvious that the vast majority of technical literature and textbooks are published in English. And pretty much every major scientific journal only accepts works in the English language. This also decreases the amount of competition between the applicants as German speakers hold an advantage over others (not to say native English speakers don't hold the same advantage back at home, but English is by far more common).

So why didn't every single major university switch to English already?

EDIT: I am mainly referring to programs in the STEM field, such as engineering

ETH and all other universities in Switzerland are funded by the government and offer college education for minimal tuition. While foreign students are welcome to attend, the primary purpose (at least at the undergraduate level) is to provide education to the locals. Nonetheless, that doesn't seem to be a limiting factor, especially at the graduate/research level since ETH has been recently ranked one of the most international institutions by Times Higher Education.

There is a wealth of excellent textbooks in German, and many fields still have original research published in German.
Also, the majority of students don't pursue academic or research careers and thus might very well spend their entire career speaking almost only German.

Plus there are practical considerations too: asking non-natively English speakers to teach in English is most certainly going to decrease the average teaching quality. Now if it's to give lectures to a class that is almost entirely German speaking, it borderlines the absurd.

The question seems to be more: why would some universities switch their teaching language to English?


Do any math PhD advisors work on a problem with their student? I am wondering if anyone’s math PhD advisor worked side by side with you on your thesis problem? In other words, instead of meetings consisting of updates of where you are at in your research and just talking about ideas, the meetings consisted of working at the board together on the problem at hand.

If done over the entire course of the PhD, this is a very bad idea for any student interested in a research career.

Of course, it is reasonable for an advisor to work more closely with a student to get him or her started on a project.  It's also reasonable for an advisor to contribute some (but not all) of the key ideas.

If a thesis advisor cannot say in their recommendation letter that a student solved their thesis problem (or some other problem) with not too much help from the advisor, the student is not likely to be hired for a research-oriented postdoc.

Different professors have different standards for co-authorship with their advisees, but generally it is expected that at least one of the papers a mathematics student publishes from their PhD work will not have the advisor as an author.  (It is generally known in the community which professors are more likely to put their names on papers with their advisees.)

To actually answer your question:

Most advisors understand this reality and a good advisor will be reluctant to get too involved in their students' projects, but when they have a student whom they don't see as capable of a research career, they will frequently step up to get the thesis done so that the student can move on to a non-research job in industry or a teaching-oriented job.


Postdoc: established project vs your own I am considering the pros and cons of two types of postdoc positions I have come cross:

The most common is 1-3 years of work on an established project for which a supervisor PI typically won a grant.
Some departments ask for a 'research plan' and the postdoc who wins the position works alone or with a local supervisor on the project he/she proposed.

The pros of 1 are clear:

In my field, these jobs are usually offered in stronger departments (though not always).
Likely more publishing output with a team and/or invested supervisor.
Contacts.

I was wondering about the pros of 2 and how it is perceived because the independent work is attractive to me.

Your second option many not even have a "supervisor" as such. It might just be an opportunity for an aspiring academic to work with a small research group on questions of mutual interest. This might be especially true in mathematics, for example. It is a way to get some experience, possibly even including teaching a bit.
I've been in a department where a post doc was hired specifically to work with a junior faculty member to boost their mutual CVs and experience.
Another situation involved a person who had an interesting (to some of the other faculty) research program so they hired him to work with the others, bringing new ideas into a research group. It was mutually beneficial as was my other example. In this case the long term intention was to offer the postdoc a permanent position later if possible.
There are hardly any disadvantages as long as the postdoc works well with others as a colleague and both gives and accepts help.


What can a publisher offer to its best reviewers? As a publisher, every now and then I saw reviews which are so good, I thought I should thank the reviewer with something more than "thanks". What can a publisher offer that will actually be useful?

Ideas:

Cash. This is probably not happening. Cash is too liquid, too precious a resource to offer. The only conceivable way top management might be persuaded is to have a small pool of best reviewer prizes (say 5 prizes/year @ $500 each), company wide. That makes it hard to reward all good reviewers, since there're tens of thousands of reviewers a year. I also suspect that if top management were to entertain such an idea, they'd prefer to have a best paper award.
Best reviewer certificate. I don't see this as very useful though, since it's just a computer graphic. Plus they're easily hacked - I changed one of these to put my name on it instead of the reviewers', which might be enough to deceive a casual observer.
A free book from the publisher's collection. This is more doable but is not cheap (since it also requires postage), so I won't be able to do send many of these - maybe one / year.
Cheaper open access. This is doable: there's a discretionary range with open access article processing charges (to e.g. offer bulk discounts and to waive them for authors from developing countries). However many reviewers never publish in the journal they review for, and even if they do they might not want to publish open access. I am not sure how useful this is.
A personal subscription to ___ journal. Not sure how useful this either since the reviewer probably already has access to the journal via his or her institution, and if not, there are (usually) other ways to access a needed paper.
Something else?

Edit: Thanks for all the answers.

Make best reviewer awards public: this should be easily done. My only concern is that this can break reviewer anonymity for small journals. Still, a central list of all the best reviewers who have reviewed for the publisher should be doable, with the only drawback being someone will have to compare reviewers from different journals (or there'll have to be set numbers of best reviewers for each journal, which would favour small ones at the expense of larger ones).
Give reviewer feedback: unfortunately only the editorial board can do this. The publisher can suggest, but cannot force the editorial board to do it.
Appoint as editors: it's potentially doable, but needs the approval of the rest of the editorial board.
Free store credit: this is doable, maybe even better than providing free books from the perspective of the publisher. After all, the publisher would not have to pay postage charges, and it's a revenue-generating activity. Making it transferable would be a nice touch!
Free mugs/T-shirts etc: considering publishers make books and journals (instead of mugs and t-shirts), I am not sure this is a good idea.
Reception at conference: the problem with this is the cost. First one would have to rent the necessary space (expensive) followed by send staff there (also expensive). It would be pretty hard to get some kind of personalized welcome; the staff that attend will probably not be those handling the journal for example, and there might be reviewers for multiple different journals at the same reception. I can float the idea, but not hopeful.

Again, thanks for ideas.

There are a number of quite reputable journals that actually do give public "outstanding reviewer" awards, and their value (while not large) is non-trivial.

If the journal announces their awards publicly online, as these tend to do, then there's no worry about faking a certificate or such. It's probably not going to win anybody a job, but it's another line on the "service" or "awards" portion of a person's CV, and it will be noticed in their community.


Is it reasonable to write the major part of my statement of purpose on machine learning for masters in data science? I am an aspirant for masters in data science and I have mentioned in  major chunk of my Statement of purpose about machine learning and my past experience with it. Is it okay or not ?

Actually, the SOP should look to your future, not the past. Your CV tells what you have already done, so you don't need to repeat that. But if you want to talk about machine learning, talk about how that background applies to your future in data science. If you intend, for example to work at the intersection of the two fields, talk about that.

But in general, you want to convince the admissions people that you have realistic goals and are well suited to achieve them. The main focus should be forward looking, not backward.


Failed undergraduate research project: does it belong in my CV? I'm an undergraduate who is going to apply for scholarships and to graduate school in physics in the coming months. At the start of last semester in August, I tried to join a group of a respected professor, where I was assigned a theoretical project. I've met with him maybe three times during the few coming weeks, before we mutually agreed that the assigned problem is pretty much a dead end. The professor had no idea for another suitable project, so I decided to join a different group, with which I stayed until very recently, when an analogous issue occured (but in this case I have actually done some work until that happened).

I was debating whether this "project" deserves being mentioned in my resume, at least for the sake of continuity, and so far have received contrary pieces of advice. Currently, that project is listed on my resume as follows:

  Worked with […] at […] on a project attempting to reformulate the
  definition of quantum-mechanical work for autonomous Hamiltonians.

I am certainly not going to ask for a letter of recommendation from that professor since there are others who know me much better. I only want to know whether the inclusion of the above description in my resume would have a positive or negative influence on my application.

I think for an undergraduate student, it is quite valuable to show that they have experience working on a diverse range of problems with different people, even if some of such projects do not lead to anything substantial.

Usually for grad school application and other fellowships there is an essay component. It may also be useful to mention such projects (briefly), and how such experience clarified your research interest/taught you how to do research/provided cross-disciplinary/cultural experience, etc. The exact messaging of course depends on what you think the program is looking for from the applicants.


Inspiration for great presentations I enjoy creating presentations a lot and I think I have an eye for nice design, however, I tend to always have the same layout/colour scheme/etc. and I'd like to try something new for my defence.

So I've been googling great presentations for hours, and there are heaps of innovative designs but usually these are from outside academia. I still want to convey information in a serious manner. But when looking at websites that intend to give advice for scientific presentations I find the examples horrible and very much 1990s (bullet points...)

So, in short, can you think of any scientific presentations with unpretentious but great design, which can be found somewhere online?

Edit Thank you for your comments, which definitely include heaps of helpful advice, however, I was less looking for "basic" presentation guidelines but more for design elements, which do not distract the audience but which make the presentation a bit more interesting. For instance, a colleague of mine recently gave a presentation and before each section she'd have a slide with just the title of the section and a photo (e.g. "Methods" and a picture of her lab equipment). I liked that because it structures the presentation and is a nice break from charts, diagrams and (in the worst case) bullet points. So, yes, I am really more looking for inspiration on fonts, colours, using white space, ...

There are two aspects to your question, in my opinion: design and function.

Function. Many have criticized PowerPoint and bullet points and perhaps none so much as Edward Tufte in his essay booklet The Cognitive Style of PowerPoint: Pitching Out Corrupts Within. The defaults of PowerPoint and reliance on bullet points is interesting and "forces" users into a particular form of presentation where bullets are more reminders for the speaker than the audience. From this background an alternative is to use the so-called Assertion-Evidence Structure which takes a very different approach to building slides.

In the Assertion-Evidence Structure the heading of the slide is the main point of the slide, a take-home message. The slides use graphics extensively to support and high-light the main point. The structure has been shown to yield significant improvements in both audience understanding than normal bullet-point presentations. Se the linked example of the structure.

The Assertion-Evidence slides are not necessarily pretty but they do the job very well so that brings me to the second issue.

Design. When you look at designing slides it is probably easier to list the don'ts than the do's. In general, anything "fancy" easily becomes boring when overdone. Therefore simple is better. I would also add that subtle is better. Do not use strong colours and avoid backgrounds that can clash with the text, either structurally or in terms of colour, after all you want your message to shine.

So design anything with a principle to do as much as possible with as little as possible and you should be on a good road. I think referring back to Edward Tufte is useful also here.

So taken together, it is not clear what is a well designed presentation depending on whether you are looking at aesthetic impact or factual impact.


How effective is it to fund a researcher as opposed to a research idea? As I understand the funding model, it's generally the funder solicits research proposals, then choose those they find the most interesting/promising. The researcher who wrote the funding application then goes and does the research with the money. In other words, the funder mostly assesses the research idea, not so much the researcher.

Can the funder use a different model where they assess the researcher (not the researcher's ideas), give those they find the most qualified/promising a large sum of money, and let them do whatever they want? How effective would this be relative to the traditional model?

There are a few funding schemes which are working exactly in this direction, giving the researcher lots of freedom in their line of research. Sometimes, the funding comes in form of a "prize" and the prize may only be used for further research topics.

In a smaller scale (you were talking about a larger amount of money) each tenuring decision is such a grant: The university is investing a significant amount of money into a person without any further control about the future research directions (at least in Germany). There is just some hope that people will not stop doing interesting things. If you sum up the regular amount of money a professor recieves, plus the additional staff / expenses granted, you end up with large amounts of money. I must say this freedom is something I really enjoy, and for me it is my major motivation for staying in academia.

Of course, those professors still write grant applications...


Guidlines for keeping adminstrative paperwork I am not sure if this question is best here, workplace.sx, or someplace else ...

I would like to clean off my desk before the semester starts (I am lucky and still have a couple of weeks). My department is far from paperless and many things only get distributed in paper form. While I would love to be organized enough to file away the paperwork from each meeting as it happens, I don't. Instead I have a large pile of all of last years meetings on my desk. I feel like most of these meetings do not directly affect me. I have piles from previous years stuck in my file cabinet. Is it worth saving unorganized papers from meetings or should I just dump them. Is there a better strategy going forward (preferably one that only requires intervention twice a year.)?

Personally, I would recommend that you start taking notes at these meetings and toss all the handouts. Include the name & contact info of the person doing most of the talking in your notes so that you can contact them in the future if necessary. I use an electronic note-taking tool with user-defined tags to keep track of everything, as I've found it easier to search later on; experiment with different approaches to see what works best with you.

This approach works with most types of handouts, but for things like calendars and class rosters you'll still want to work with paper. Personally, I use something like this; I have two on my desk and I haven't needed more in a while, as I throw out folders when done with them. Even if you just stick them in a huge pile, though, it'll still be less huge than your previous pile, so at least you're better off.


What are the health impacts of standing / sitting while lecturing? I often find myself lecturing for 7 hours in one day. This question is not about how to reduce my hours, it is about making healthy choices with my existing constraints.

I am lecturing to different classes during the day (it is not a single group of students for all 7 hours), in case that makes a difference.

I realize that during my lectures, I must choose what to do with my body. Should I sit (blood clots, deep-vein thrombus) or do I stand (I've heard non-lecturers complain about swelling legs when standing too much).

My questions are:

What impacts are known from standing while lecturing for 7 hours per day, 3 days per week?
Is it better to stand or to walk around?
Is it better to sit for the whole time?
Is it best to do a "little bit of everything?" If so, where is the optimal balance?

I realize that this might be specific to the person but I am hoping to find some experiences or, even better, research, which will indicate the best choices to make when one must lecture for many hours.

The health impacts of standing while doing a job are known to be strongly positive, compared to sitting while performing a similar function. For the seminal paper on this, see Morris et al., 1953 in the Lancet (http://www.sciencedirect.com/science/article/pii/S0140673653914950). Morris examined the incidence of heart disease in bus drivers vs. bus conductors. The former spend the day sat at the wheel while the latter spend the day walking around the bus collecting fares and enforcing the rules. This occupation was chosen because drivers and conductors come from the same socio-economic conditions and were expected to be fairly similar in every respect except for their working activity. Naturally the incidence was sharply reduced in the conductors. A casual Google Scholar search will pick up more recent references, and the health benefits of standing vs. sitting are widespread.

One can imagine that standing for very long periods of time repeatedly might cause problems, particularly on the feet or ankles, but seven hours a day a few times a week is not really anything to be excited about. Many people work in bars or restaurants, on building sites, in hospitals and so on doing much more labour intensive work with shift lengths exceeding twelve hours, six days a week.

All I would say is ensure you wear comfortable shoes!


Standard way to specify roles in authorship This question is not really about who can be considered a coauthor of a given journal paper —or maybe it is, after all— but rather about how to specify the different roles, levels of implication or contributions of each of the coauthors, in case this would mean to be done.

My question is: Is there any standard about how to specify the different roles or contributions of the coauthors of a given journal paper? I do not mean the importance of coauthors that can maybe deduced from their order in the author list (see What does first authorship really mean?, Authorship allocation - is it common to grant equal credit to two last authors?, for instance), but a way to explicitly specify the implication of each of the coauthors, in a sort of standard way.

I remember someone saying this could be added at the end of each article, as a way to make the contribution of each coauthor clearer.

Actually, my question is highly related to this previous one: Revamping Paper Authorship, *or* Should Papers Roll Credits, which has only received one answer and is still open at the moment of writing.

I have found some interesting webpages and articles dealing with this subject:

Defining the Role of Authors and Contributors (International Committee of Medical Journal Editors)
The ICMJE's definition of authorship is illogical and unethical (David Shaw)
Is it time for a new approach to authorship? (Leash E.)
A New Standard for Authorship (Paul J. Friedman)

So, maybe my question is actually about the state of the art of this subject: how to credit authorship in a standard way or standard authorship crediting.

Other related questions in this site:

What are the minimum contributions required for co-authorship
Is it ethical for advisors to automatically coauthor papers?
If you make a substantial contribution should you be given the opportunity to satisfy the other requirements for authorship?
Should undergraduate students be included on papers containing data they collected?
Indicating co-PI status on a paper
Can I claim authorship on work I wasn't personally involved in, that uses a framework I developed for my research?

There is no standard way, not even in the same field or sometimes even the same journal.

But when people put contributions at the end, it typically looks something like this:

  Author Contributions
  AB conceived the project. CD and EF designed the experiments. AB and GH performed the experiments. CD and EF analyzed the data. AB wrote the article with input from all the other authors.