What can I do when some people stole my master thesis work and published it as their own work? Google scholar suggested a paper for me to read, I opened it and boom it was my master thesis work. My work was based on  Arabic language but they claim their work is based on Telugu language. Even they did not bother to change the title. they just switched the Arabic to Telugu. Not only that, they even did not bother to change the experiment results numbers or the figures. They copy/pasted everything with small minor noticeable changes. I tried to contact the journal but I could not find any contact details for the editor. What should I do now?

Link to my master thesis:https://dspace.aus.edu/xmlui/bitstream/handle/11073/7503/35.232-2014.09%20Soha%20Galalaldin%20Ahmed.pdf?sequence=1&isAllowed=y

Link to the journal paper:http://www.j-asc.com/gallery/18-august-2018.pdf

Any guidance would be highly appreciated.

Update

I have contacted the journal's editor and as expected, no reply.
I have also contacted Google via the link provided by Stig Hemmer and they have thankfully removed the links to the papers from Google search results after asking me to identify the exact content that I claim infringe upon my copyright.

Update 2

When I contacted the journal editor, I have sent a carbon-copy to the papers' authors to let them know I am aware of their plagiarisms. Nobody replied until Google removed their papers from the search result and put the following statement instead.

  In response to a complaint we received under the US Digital
  Millennium Copyright Act, we have removed 1 result(s) from this page.
  If you wish, you may read the DMCA complaint that caused the
  removal(s) at LumenDatabase.org.

Then, one author contacted me claiming that his student stole my work without his knowledge and that he would take the right measure to ensure pulling the two papers from the journal.

I hope this gives hope to anyone who has been a victim of plagiarism. You should not give up and you should stand up for your self and your work and God will assist you.

Thank you for all your comments, pieces of advice, and direction. I would not have been able to protect my right without the StackExchange community guidance.

I have this one paper that has already gotten copied and submitted to some spam journals 5+ times. It literally happens multiple times per year (it has a catchy title that seems to appeal to a certain class of plagiarizers). I also usually learn about this through a Google Scholar alert.

The first two times it happened, I tried exactly the steps recommended by other answers. I contacted the authors (no reply ever), raised a stink with the journals (no reply ever), and contacted IEEE (the copyright holder of my original paper). IEEE indeed did react that they will look into it after quite some time, but nothing ever came out of it.

My lesson learned was that these things are basically impossible to fight. The authors or journals could not care less about ethical integrity, and for IEEE the measurable damage of one of their papers being "reprinted" in a different title and with slightly different words in an obscure scam journal that nobody ever reads is not large enough so that they would make an effort hunting down who is legally behind these shopfront journals.

The good news is that it is also completely irrelevant to you. I can assure you that your scientific contribution will not in any way be lessened by this paper existing, nobody will read the other paper (because nobody reads these "journals", period). For future promotions etc., the existence of this paper will not be in any way an issue for you. Science as a whole suffers (to a degree that we could argue about), but the fact that it happened to be your paper that they copied (as opposed to a paper by me, or somebody else) makes no difference at all.

I think this became very normal nowadays. I heard, that the number of publications doubles every 12 years. I just found data for certain fields where it's actually much worse. Consequently, the quality goes down by more than the increase modifier.

Journals do not care if you send them a mail that experiments are not reproducible and why. People start to publish old PhD or master thesis works by using scripts. Peer-Review became more and more useless to the point were the reviewers often do not understand real issues and mis-interpret pro-arguments because they are maybe just inexperienced students. Scientists startet to send work to fake journals.

This is all fueled by three things. 1) There are thousands of PhDs entering their own publication phase every year. 2) They have pressure to publish anything within 3 years to get out of this phase. 3) At least in my country, there are no not-time-limited PostDoc positions in my age class. So the pressure is forwarded to the next hierarchy level.

Solution to your problem:
The whole system is broken and needs an update. I expect that the publication rates will further increase, review process will become worse. One day, it will be close to impossible to find any valuable information in any recent paper.

Number of publications in some fields:

  Number of publications per year containing the term "PTR-MS"

  Number of publications per year with keywords “cancer pain”


How should I interpret an almost-but-not-quite-alphabetical author list? I just noticed a weird aspect about this paper (which was of interest here and recently came up again here). If you look at the author list, it reads

  L. P. Gaffney, P. A. Butler, M. Scheck, A. B. Hayes, F. Wenander, M. Albers, B. Bastin, C. Bauer, A. Blazhev, S. Bönig, N. Bree, J. Cederkäll, T. Chupp, D. Cline, T. E. Cocolios, T. Davinson, H. De Witte, J. Diriken, T. Grahn, A. Herzan, M. Huyse, D. G. Jenkins, D. T. Joss, N. Kesteloot, J. Konki, M. Kowalczyk, Th. Kröll, E. Kwan, R. Lutter, K. Moschner, P. Napiorkowski, J. Pakarinen, M. Pfeiffer, D. Radeck, P. Reiter, K. Reynders, S. V. Rigby, L. M. Robledo, M. Rudigier, S. Sambi, M. Seidlitz, B. Siebeck, T. Stora, P. Thoele, P. Van Duppen, M. J. Vermeulen, M. von Schmid, D. Voulot, N. Warr, K. Wimmer, K. Wrzosek-Lipska, C. Y. Wu and M. Zielinska

In particular, it splits into an initial, non-alphabetic component,

  L. P. Gaffney, P. A. Butler, M. Scheck, A. B. Hayes, F. Wenander

and then an alphabetic list from M. Albers through M. Zielinska.

How should I interpret this authorship convention? What fields is it used in, and to what purpose? My initial reaction would be to assign to the initial component a ranking down in 'importance' more akin to the "first author did most of the work, middle authors supported, and last author sponsored and oversaw the work" convention used in fields with smaller collaborations (at least in physics), but that leaves the alphabetic component in an awkward position, so I'm not sure my interpretation is right.

How should I interpret this authorship convention?

The first (non-alphabetic) authors are likely the main contributors in order of contribution significance as you guessed. Starting from the alphabetic ordering the authors would be those with lesser contributions (but equal to each other).

What fields is it used in, and to what purpose?

I do not know what fields this is specific to, but I would not be surprised if this is a common strategy for papers with many authors irrespective of the field. Ordering a long list of authors with equivalent contributions in some manner simply seems sensible and alphabetic ordering is a simple and common ordering scheme. Unless the publisher has a policy on how this should be handled, alphabetic ordering seems to be a simple go-to strategy.

I would make an ideological suggestion: Don't interpret it at all.

I believe that the custom of choosing author list positions to express degrees of contribution, seniority, who-is-whose-daddy etc. is unbecoming and should be discouraged in favor of alphabetical author lists. To this end I would suggest applying a sort of "color-blindness" to the order of listing.


Is citation bias a studied issue? I have noticed in a number of papers, including those in top journals, a common dirty practice which consists of self citing your previous works and omitting other important references in the area (I admit some of them at least include the classic references). For instance Prof. John Doe writes a paper and his references look like:

[1] John Doe (1970). Paper 1.
[2] John Doe (1971). Paper 2.
...
[200] John Doe (2014). Paper 200.
[201] Issac Newton (1687). Philosophiæ Naturalis Principia Mathematica.

I am aware of the concept of Publication Bias, which is related to a bias with regard to what is published. I wonder if there is also something related to self-citation bias or citation bias (it might also be the case that a person only cites a group of researchers (friends?))?
This, of course, is not just a matter of taste, but it is a practice that complicates the literature review in a certain area.

This problem has been receiving significant attention in recent years.  Among other thing, there was a recent scandal around "citation cartels", in which journal editorial staff organized not only to ensure their own journals self-cited but also so that groups of conspirator journals would cite one another in order to raise impact factor while adding a layer of indirection to make it harder to track.  Such journals also sometimes strong-arm authors into adding citations to other publications within the same journal.

I don't know if anybody has tried to further tease apart the different between intentional (i.e., citation cartel) and unintentional citation bias.  It would be interesting to study, but may be difficult given the amount of intentional bias that some are using the game the system.

In this article you find empirical evidence for the self-citation bias:

Marc Brysbaert & Sinéad Smyth,
SELF-ENHANCEMENT IN SCIENTIFIC RESEARCH:
THE SELF-CITATION BIAS, Psychologica Belgica 2011, 51-2, 129-137.


Supervisor wants me to support a diploma-thesis software tool after I graduated During my last year of MSc. studies, I was part-time employed on the university project. The project was related to my diploma thesis, and my task was to create a data-mining software and run experiments using this software.

I've finished the software, run the experiments in it, successfully graduated, and finished the studies. It was a huge success for me and for the university as the diploma thesis was awarded in a student's competitions, being top 10 among 2000 diploma theses.

Despite this success, the software I developed is not production-ready, rather just a prototype. For my experiments I considered only happy-case scenarios and if there are some unexpected inputs from the user/from connected systems/uploaded CSV files do not match specification, etc., the software crashes and cannot be used.

My supervisor wants to use the software usually twice a year. When he runs into some troubles with it, he emails me to deploy fixes so that he can run the experiments. In the first year and a half after I finished the project and the software, I did it three times. Now he is asking again to debug the problems in the software and fix them. I do not want to do it, because:

I have no time for it because of very time-consuming projects in my current job.
I am working in a different industry now and during two years I forgot many things from the software development and specific solutions I used.
I already lost accesses to the production environment at the university, so I am not able to deploy fixes.
I feel stressed out by the requests. As this was a prototype I did not set up logging, and I usually struggle to find and fix the error cause. I sometimes even cannot reproduce the errors locally and then I really do not know how to fix it.

I wrote these reasons to him, but he insists that I should still help them with it. He offered me they will pay me again some hour rate to support the software, get production accesses again, etc. But the money is no matter for me; I just do not want to continue with supporting the tool.

I feel there was some misunderstanding from their side about what are difference between diploma-thesis prototype and production-ready software. We never agreed officially that I would support it. We just once talked about that I would support it "for some time if some problems occurs", which I believe I did (three bugfixes and approximately three months of work during a year and a half after I graduated).

Is there a way how to politely refuse while still keeping good relationship with the supervisor as he is always very nice and polite?

I was thinking to offer him a one- or two-day workshop for some of the current university employees where we could go through the code on GitHub, and I would officially hand it over to the current employee. But it would not be a solution for him, as there are only a handful of postgraduate students in their group, and they are not programmers, so they cannot take the software over.

And I feel bad about writing to him: “I do not have a solution, I do not want to continue with that, and I do not care that you cannot use the software any more...”

I think you are being generous and, given what you say, should be able to step away from the project with a clear conscience.

If he needs the software he should be willing to find a way to pay for support, maybe not you, I think, but some support person.

I would see him if possible or send an email giving much of the information you've given here. The fact that you are doing very different things now and that support is disruptive to your main goals should be definitive.

But I agree that it is good to find a way to keep a good relationship with him if you can also achieve your main goal.

Be honest and tell him you struggled to find a resolution that would satisfy everyone involved but finally realized it was beyond the limit of your abilities at which point you reached out for help and received much valuable feedback and that you would be grateful if it were to be improved on further by the inclusion of his own perspective and insight at Supervisor wants me to support a diploma-thesis software tool after I graduated

The fact of his seeing this helps ensure finding a course of action that results in the most good for the most number.

Also, better that you be the one to tell him now than he find this some other way.


What to do if bullied by students? I've recently been the subject of bullying by a group of students. I taught a difficult module alongside another module, which was taught by somebody else. The other module was much easier and offered huge amounts of support. Students described having their hands held in this module. One student told me that this module felt like students were being treated as newbies, whereas my module felt like they were being treated as second year students at a Russell Group university. The university where I work is more teaching focused.

Having heard feedback from students, I think that the tasks I set them were quite challenging, and I don't think they were used to it. I'm still adjusting to the level that the students are operating at in this university, and were I to I teach in the module again, I would adjust the level.

However, the main issue is that students posted rude, personal and abusive feedback in the module evaluations and also posted nasty comments on the module forum. I also got nasty emails from some students, and although I passed this up to management, nothing was done and I was left to deal with this alone.

It has affected my self esteem and my confidence as a lecturer. I've always had plenty of good feedback before and I've always felt competent in my role. I don't know if I have any rights in terms of being bullied by students, but one student has just told me that there is a Facebook group where I was being slated and there were really personal comments. The student I spoke to today described it as a bit of a hate group, directed at me. One student even copied an email that I had sent her (a photograph of it) and posted it on a Facebook group. I'm not sure if this contravenes any confidentiality regulations.

Anyway, I just wondered if anyone else had experienced this and if anyone had any advice. I've been teaching for 10 years and I was on the verge of quitting my job, and I don't feel like I can easily face teaching these students again. On a personal level, I see it as an opportunity to develop greater resilience, but I can't help the fact that it really feels undermining and threatening to be in this situation.

Any advice or support would be appreciated.

In short, the behaviour of your students is not acceptable - no matter how good or bad your teaching was.

If something like this were to happen at my university, I as vice dean for teaching would invite the whole group for a face-to-face meeting and explain to them how adults should solve problems.

In fact, this is something you should aim for, since the problem will persist and affect others as well, since the students' behaviour will not change.

We had good success with early feedback opportunities (not just the end term evaluation), micro-evaluations (anonymous feedback which can be a one-liner) which are discussed with the whole group, an honest open door policy, and with involving student organizations and representatives early on. Some course formats have to be explained to students over and over again... This might be helpful in the future, but won't help for now.

If you are still teaching this course, I'd suggest an intervention (if possible with the help of another neutral professor) where you address the problem in front of the class. If possible, summon an extra meeting which does not take place in your usual teaching room.
For such a setting, I would suggest just asking the students about feedback regarding your lecture, but ask them to follow commonly accepted feedback rules. Afterwards, tell them what you took as the take home message from the feedback.

Afterwards, you should tell them that you prefer direct communication about any issues.

In the best case, they should be ashamed afterwards...

If you are working in an institution where you are assessed based on your student feedback, you have two choices.

You can leave and get a job where you will be supported and developed by your employer.
You can make your course so easy that even the dumbest students get B's and spend way over your paid time to hold their hands (when they want it, rather than in office hours). But over time the students will get dumber and you will lose the will to live.

So, I would recommend looking for a new job, probably outside of academia.


My potential future PhD supervisor ask me to peer review a paper I have been working for two years after my Master and I am now looking for a PhD. I got a PhD offer from one university, met the person who would supervise me and told them I am very interested, while making it clear that I also applied to other PhD offers and am waiting for answers. They said that that it was not an issue for them.

But now he just sent me an anonymous paper and suggested to me peer-reviewing it to help me "get a foot on the ladder". I am really confused by this proposition since:

I am still working for my company
I am still searching for PhD offers to apply, which takes me all my free time,
I never reviewed a paper before.

So, I am not really in the mood to do this now since I have more urgent concerns. However, I do not want to upset this potential supervisor, nor make them believe that I am not motivated.

So, should I do this review or not, and if I don't, how can I refuse without upsetting this potential supervisor?

Let me precise that I am likely to do my PhD there if my other applications don't get accepted.

EDIT

The paper in question is anonymous and I am asked to peer review it for a journal publication. The paper subject is in my field of research but not really in the field of my potential supervisor.

Maybe it's a matter of question formulation, but I find this to be a very peculiar request and would be equally confused as you seem to be even if I wasn't busy with other stuff.

Specifically, you're not qualified to review a paper, yet.

If he's asking your analytical opinion on a paper, kind of like a journal club style dissection of the content, then sure I guess that's no big deal. But if you are given a manuscript, written by someone else and submitted to a journal, I find this request unrealistic and even unethical.

Also, in a way disagreeing with the previous answers here, I don't think it's a reasonable request even if you were given the article in a more relaxed, journal club-like format. Because you are supposed to learn to read and understand the scientific literature, it's part of your training as a PhD student. To use that during the recruitment process, as a test is a bit unfair in my eyes.

  that was my first feeling actually, that he was assigning me some of
  his work while I am still in the application phase. The paper is
  anonymous and I am asked to peer review it for a journal publication.

The above alone, would even deter me from considering to start there. I think it might be worth thinking about what kind of work environment you want to get yourself into for the coming 3-X years of your life.

But again, it's possible that I misunderstand something in the OP. Just my two cents...

A literature review is an effecient way for you to have general overview about the state-of-the-art development in you research area. Most supervisors require their Phd students to do a literature review before starting the actual research.


Why do professors obfuscate their email addresses on their websites? I've always wondered why professors write their emails like this:
john dot doe @ harvard dot edu
I am trying to figure out some benefit of this but I can't think of one. It is definitely not more clear. It is more work if you are actually trying to email the person. Why not just write your actual email?
I come from math so maybe this is just a math thing? I have no idea.

It's most likely to avoid Email address harvesting. There are bots that scrape webpages to pick up email addresses for spam purposes. An easy way to avoid this is write your email in a way that's harder to read for a bot that's scanning for email addresses.

As user2723984 notes, academics often scramble their email addresses ostensibly to prevent web crawlers from harvesting their email address and spamming them. But it still allows humans to obtain their email address.
The effectiveness of this is debated.
While it is true that more sophisticated web crawlers could circumvent much of this, most are not sophisticated. Thus it does help protect against generic spam (but that stuff is mostly caught by spam filters anyway).
However, most academics continue to receive plenty of academic spam. This is because academic spammers harvest email addresses from papers via repositories like arxiv, where people do not use any kind of protection. (I know this because I receive academic spam at email addresses that only are in my papers.)
At this point, I think it is more of a piece of academic culture than a well-motivated practice. At least in computer science, most people do it. This encourages others to copy the practice and so it carries on. Some people go a bit further, e.g., "firstinitial dot lastname at thisuniversity dot edu", where you must fill in the name of the university as well as their name. (I personally find these riddles annoying. I put my email in an image on my website, but with the usual riddle as alt-text for blind people.)


Is it ethical/legal to obtain journal articles from reddit? My university's subscription is really limited (I come from Lebanon). I never found any paper related to my research or essays using the database that my university is subscribing to; even the basic pioneering papers in business. Yesterday, I started writing my master's thesis and the very basic papers behind my topic cannot be accessed through my university's portal (cannot simply ignore them) and I, obviously, don't have access/cannot pay for individual papers. What to do in this case? Someone here recommended a Reddit page that provides and shares papers upon requests. How legal/ethical is that? The page claims that all the shared papers are based on the concept of fair use.

Eventually, I have 3 options: Follow this way, adopt a bad scholarship behavior by not tracking down original references to check myself (which is out of the question) or I just go home and forget about writing a master's thesis or a literature review because it's almost impossible to access those papers without the help of option 1. As for emailing individual authors, well none have replied so far so it isn't always a practical option as I cannot wait days for 1 particular paper to be received (if any).

Legally, I am not sure --- it depends on the laws on the country as well. Ethically, I don't see anything wrong about it. Academia is about building and sharing knowledge: if anything, I would consider it unethical to put papers behind a paywall.

The legality of copyright is a mine field. As I said here, I think that redistributing a paper goes against the wishes of the publisher and is therefore unethical. I think the real issues are

  I cannot wait days for 1 particular paper to be received

and

  papers behind my topic cannot be accessed through my university's portal

I find it hard to believe that your research is progressing so fast that a couple of day delay receiving a paper is going to be catastrophic. Additionally, while electronic access is nice, you should check with you library regarding paper versions. Additionally, Lebanon seems to be developing an "Interlibrary Loan and Document Delivery Services" called LIDS. In the absence of your university helping you obtain a copy of the paper, you should talk to your supervisor. They may have a colleague at a university with a better library. Only after exhausting all other opportunities would I consider buying the paper from the publisher or using a general list server to obtain a copy.


Should I offer to come to campus if given a phone interview? I applied to a faculty position at a university (a small state school) near my hometown and I just received an email invitation for a Skype interview later this week. Coincidentally, I am visiting my parents' house this week, which is about a 20 minute drive from the institution offering the interview.

Would it be weird if I mentioned that I am nearby and/or offered to come in and meet some of the members of the department in person while I'm here?

I didn't mention anywhere in my application that I grew up nearby nor did I indicate that I have family here. I did all of my studies out-of-state and I'm currently living on the other side of the country. However, I am excited about the opportunity to move back "home"!

It is worth asking and is probably worth a visit even if they would rather stick to a Skype interview. They may prefer that so as to treat all candidates equally, but if that isn't necessary, they might prefer you to come in person.

It is a good way to get a feel of a place and to meet a few students and several faculty. I don't see any downside in asking.

"I'm actually quite close and could easily arrange a face to face visit. Would that be preferable?"

Do not offer to come by as it might be interpreted as a request for special or biased treatment.  You can mention that you are nearby.  It is highly likely that all candidates will be interviewed using the same technology, even if they work on campus, because it is considered fairer.


Author states that he is owner of his photographs but they have been published in various journals I'm editing a volume and I am responsible to obtain permissions for figures and photographs the authors wish to use in their respective chapters.

Now I have an author A who included several of his own photographs within his chapter which is great. My problem is that most of them have been previously published - in several different journals under several different authors (A is always among the authors). The author stated explicitly that these are his photographs but I'm not so sure. Do journals not normally claim figures along with the text and require even the authors to ask for permission to reuse "their" own content?

Does this apply only to figures or also to photographs? I checked the image caption in several of the publications and it never explicitly states "Photograph taken by A".

Do I need to obtain a permission from the copyright holder/owner of the journal? Should I just create a statement along the lines of 'Photo taken by A, previously published in A et al. 2010'? Should I make A sign a document stating that he always retained the copyright and can therefore license it for use in the present chapter? Should I contact our publisher instead of asking this on StackExchange? Probably, but you guys are much faster ;)

Context: The edited volume will be published in the U.S.A. by a STM-signatory.

The responsibility of certifying and negotiating copyright issues is typically the responsibility of specialized staff at a publishing organization, not that of the scientific editor of a work.

The responsibility of an editor here is just to make sure that the authors follow the process the publishing organization asks the editor to have them follow, which typically includes making copyright assertions or providing contact information to the people who will actually ask them to make copyright assertions.

Thus, if you have concerns, you can convey them to your contacts at the publisher to be sure that they are aware of these concerns and can sort them out. If you aren't the legal personnel responsible for sorting out the details, however, you shouldn't be trying to make any arrangements yourself: that is likely to create more problems than it solves.

When authors publish their work in scientific journals the copyright is almost always transferred to the publisher as a condition of publishing. Therefore the author no longer has copyright on their images. To republish the same images in a new work, written permission from the copyright holder (journal publishing house) is required. In practice all of the journal publishing houses I am aware of have simple webforms to fill out for obtaining such permission. Sometimes you can get this for free in as little as a week, in other cases there could be a delay of a few months and a fee imposed. Depends on the Publisher!


The position I applied for was advertised as Associate Professor with Tenure, but now they’re saying it’s tenure-track Associate Professor I am an associate professor, who has received tenure in the US in 2014. After receiving tenure, I moved to Europe to help my family with some health issues, and found an associate professor position in a country where tenure is 'by law' meaning the position cannot be revoked or taken away. I am now looking to return to North America, and have begun to apply for associate professor job openings.

I have applied for a position as tenured associate professor. I interviewed and was told I was selected by the department as their top candidate. However, the dean at the new institution just emailed me that the new position will be associate professor "tenure-track," meaning I would need to apply for tenure within 4 years.

Clearly, what I had applied for is not what I am being offered. In my view, there is a flaw in their advertising. The position description clearly stated "the University of X invites applications for a tenure-track Assistant Professor or Tenured Associate Professor in...."

While I understand that each university has its own interest in mind, this seems like a very bad start of a relationship. If I accepted this demotion, I would probably do so with some resentment. The University in question is academically equal to the one I first received tenure from.

I am seeking advice on how to respond to this proposition and would be very grateful to hear people's opinions.

Based on what you've said,

  In my view, there is a flaw in their advertising. The position description clearly stated "the University of X invites applications for a tenure-track Assistant Professor or Tenured Associate Professor in...."

Well...yes, you're exactly right.  It sounds like the department and the dean were not on the same page when the position announcement was posted.

  While I understand that each university has its own interest in mind, this seems like a very bad start of a relationship. If I accepted this demotion, I would probably do so with some resentment. The University in question is academically equal to the one I first received tenure from.

Again, I agree completely.  You've had two different tenured positions, including one at a US institution of (you say, and I'm going with it) comparable academic quality to the one you're applying for.  You applied to this position and interviewed for it -- presumably taking some trouble doing so, since you now live in Europe and have family there -- based on the information you received in writing that it would come with tenure.  Only at the end of the process have you been informed otherwise.  Well...yes, that's a seriously alarming bait and switch.

In my opinion there is really only one thing to do.  You should respond by calling attention to precisely the facts you mentioned to us, especially that (i) the position was advertised as with tenure and that's why you applied for it and (ii) your last two academic jobs have had tenure, including at US institution X (you don't need to explicitly say that it's of comparable academic quality; I would leave them to claim otherwise if they want to), that you are very excited and interested in the job, but only under the original terms: you are not contemplating making an international move from a permanent academic job to a possibly temporary one.

In other words, I think the issue is serious enough to prevent you from taking the academic job...again, for exactly the reasons you say.  The type of employer who will not be held to what they told you before is exactly the type of employer to cause you N years of deep worry that they might not give you tenure, and nothing in your question suggests that you should subject yourself to that.

I really hope that they respond well to your holding your ground. Good luck!

The only verbiage you present from the university is:

  "the University of X invites applications for a tenure-track Assistant Professor or Tenured Associate Professor in...."
  [bolding mine]

That sounds to me that applications that are submitted will be considered for a Tenured Associate Professor or a tenure-track Assistant Professor. Perhaps there is more information that you are leaving out, but based on what you have presented, I don't see any reason to be confident that a tenured position would be offered. If distinction was important to you, you should have asked for it to be clarified.

As for how you should respond, you should decide whether you are willing to accept these terms. If not, then tell them that you are not willing to accept anything short of tenure, and be prepared to not get the job. They might be able to work something out, but don't count on it.

Also, "demotion" is not an entirely accurate term in this context, since it is not within a particular institution.

EDIT:
In English, words often distribute over "and" and "or". For instance, in "You can have soup or salad", "you can have" distributes over "or", giving the implicit meaning "You can have soup, or you can have salad". What distributes depends on context and can be ambiguous. You seem to have interpreted this as "the University of X invites applications for a tenure-track Assistant Professor or applications for Tenured Associate Professor in...." That is, some applications are for a tenure-track Assistant Professor, and some applications are for Tenured Associate Professor. However, without this distribution, it can be interpreted as meaning that each application is for a position that will either be tenure-track Assistant Professor or Tenured Associate Professor. The university could have been more clear, but you shouldn't have just assumed that the interpretation that favors you is the correct one.


Advisor likes MS Word, I like LaTeX I have an issue with my supervisor: he likes to write papers in MS Word and I like to write in LaTeX. We have had issues with editing and formatting, since it is difficult to do it, while working on different platforms.

Does anyone have any advice on how to resolve this situation?

In the end, once the paper is published, nobody will worry about what software was used to generate it. The software is just a means to an end.

So, if your advisor has a strong preference for Microsoft Word then - regardless how you feel about that preference - if you can't easily convince your advisor to use LaTeX you should switch to Word. There are much more important things to worry about, and there is no reason to make life difficult for your advisor for something so unimportant.

Converting your paper from LaTeX to Word is not likely to produce ideal results, as you have noticed. By the time you go through and fix things, you might as well simply work in Word from the beginning. In other words, the "efficient" way to do this is to convert the content in your head as you are writing it in Word, rather than trying to convert the content to Word after it is written.

You should simply stick with using LaTeX and not bother about any problems this gives with formatting. The last thing you want to do is learn using MS Word just to get this paper finished, as working with MS Word can be extremely awkward if you are dealing with technical mathematical text. Formatting issues are very minor issues and should be given low priority. Stick to the subject and stick to any requirements of the IEEE journal by using the correct LaTeX templates for the journal and forget about  your advisor's preference.

This then means that you have your LaTeX version and your advisor has a Word version that may look slightly differently, but content-wise are equivalent. That's not a problem worth worrying about, it's a massive waste of time to do so.


Student caught cheating when leaving class after handing me the exam Usually I am quite clear that cheating and plagiarism are unacceptable. Although every semester I have to deal with several cases of plagiarism, I had not expected students to brazenly cheat in exams. A few seconds after one student handed me the exam, as she was leaving, I noticed that she had written answers on her hand. She was showing it off to a classmate and laughing as they left. In my country, just writing anything on the hands or anywhere they can read (including the table) is usually considered cheating. Students can check their answers when they are given their corrected exams back.

I know I could have created a scene on the spot, prevented the student from getting out as she was leaving the classroom, provided evidence of cheating, and graded her exam as 0. But other students were handing me their exams at the same moment, and many others were still writing down their answers. That would surely cause a commotion. I was paralyzed and did not know how to react. I am still not sure how I should have reacted, or how I ought to react in the future. I feel being aquiescent may have an impact on other students' behavior, and also on my feeling of self-respect.

Now I'm facing a dilemma. The student was not caught in flagrante delicto. The evidence for cheating is also gone. If it matters, the student's grade wasn't great either (4,8/10). I cannot decide myself between leaving the issue alone and forgetting about it, grading the student more severely in the next exams, or somehow lowering the student's grade (the last option is a little risky as the student could denounce me).

Exact rules will depend on where you are.  But normally the student has due process rights: to be confronted with the evidence of her cheating, and to appeal to some higher administrator or body if she desires.    Two of your options (grade more harshly / secretly lower grade) are things that you would do unilaterally, without the student's knowledge, and without giving her the right to challenge.  In my view, these options are therefore totally inappropriate and unethical.

The evidence against her is your testimony about what you observed.  If you think this would be sufficient evidence under your university's rules, then it is appropriate to pursue formal punishment as the rules dictate.  If you don't think it's sufficient, then do nothing, and let the student complete the rest of the course without prejudice. (Though of course you can watch her more closely in the future, and perhaps institute procedures to deter this kind of behavior in general.)

I don't think that you can do anything right now about it.

If you would bring it up now, she could just say you are lying and since it is her word against yours and you don't have any evidence, the administration is mot likely to take her side.

So I wouldn't do anything about it right now, but for the next exam I would pay more attention towards her and if she is doing it again, you can call her out on it.


Why do computer science students working in computational biology domain need to give biological validation for their prediction? I am in my 3rd year of PhD. I am doing my PhD on Computational Biology, with a background of purely Computer Science. Since I am under pressure to publish 4 more journal papers, apart from my review, I am always in a hurry to do the same. What I have noticed for this field is that if I predict something, I need to provide biological validation for my result. Why so? Is biological validation not the work of biologists? How can a computer science student provide biological validation for his/her prediction? Isn't our job just to predict? Why do the journals want biological validation for the results? I did a prediction job, where I predicted some proteins to do a particular function. I communicated it to the Molecular BioSystems Journal. They rejected it saying I have no biological validation. If biologists are the one with the final say, then what point do we have in working in this domain? Whatever we predict would be questioned.

I am always in a hurry to do the same. What I have noticed for this
  field is that if I predict something, I need to provide biological
  validation for my result. Why so?

Because this is how one knows if your results are correct and useful. A prediction is nothing if it hasn't been evaluated. The field is littered with predictions that turn out to be nonsense, only hold up under very narrow circumstances, etc.

  Is biological validation not the work of biologists?

No more than it would be if a biologist said "I just developed this algorithm, proving it's correct is the work of a computer scientist."

Beyond that, there's no reason for them to do so. "I've made an arbitrary prediction, anyone want to validate it?" is going to be met with a resounding "No" - the biologists have their own work to do.

  How can a computer science student provide biological validation for
  his/her prediction? Isn't our job just to predict?

No, it's your job to provide useful results. Validated predictions are useful. Just predictions are not.

As people have noted, there are a number of ways to validate a prediction. Existing data, or even simulated data based on known biological patterns, might be sufficient. If no such data exists, it's time to find a collaborator.

  Why do the journals want biological validation for the results?

Because anything else is just speculation.

  I did a prediction job, where I predicted some proteins to do a
  particular function. I communicated it to the Molecular BioSystems
  Journal. They rejected it saying I have no biological validation. If
  biologists are the one with the final say, then what point do we have
  in working in this domain? Whatever we predict would be questioned.

Do you know that it was rejected by a biologist? There's a number of computer scientists I know who would have rejected such a paper for having no biological validation. Beyond that, your "point" in working in the field is to generate those predictions and evaluate their correctness. The latter part is also an aspect of good computational biology.

Always look at the literature,

If you are doing thermodynamics work, the biological validation will probably come from isothermal titration calorimetry studies. One can get entropy, enthalpy, and Gibbs Free Energy from that alone.

If you are doing protein folding work, the validation will probably come from some form of either fast protein liquid chromatography (FPLC) or High Performance Liquid Chromatography (HPLC) with the main difference being that FPLC appears to be more often used for analysis, purification, and extraction from a complicated matrix, while HPLC is for analysis. The critical difference of either case is the choice of column which is for extraction of hyrophilic/hydrophobic proteins, or specific proteins which are usually retrieved by affinity chromatography binding antigens or antibodies to a column. Another technique is to clone a  polyhistadine tag into the a protein from the extracted DNA via polymerase chain reaction (PCR) to exponentially increase the original concentration of DNA. Critical segments must then be spliced with endonucleases and transcribed/translated into proteins. These proteins will have the polyhistidine tag which will bind to nickle in the column and everything else washes out.

If you are doing ensemble work of the functions of whole protein families, then please pick a family of proteins that you would like to study such as the heat shock proteins (HSPs), receptor tyrosinase proteins, histone proteins, efflux pumps, etc. The biological validation for this informatics work using comes from     microarray experiments, running lots of proteins on an electrophoresis gel to determine their size, or even mass spectrometry which tells a researcher the those of a protein.

If your research does not match up with the literature, it does not necessarily mean that you are wrong. For example, in the nightshade plant, antifreeze proteins were only found in the plant in the months of November and December, but not in September and October, if I remember correctly. That means that temperature drop induced the formation of the antifreeze proteins only when it was really cold. After the cold season, the proteins are probably just destroyed completely.

Here is a little information about how temperature influences the existence of antifreeze proteins in the plant Nightshade:

http://link.springer.com/article/10.1023/A:1014062714786

The whole protein network of a plant can change in response to chemical stress, heat stress, species differences in a family of plants, age, species differences, or competitive parisitosis. I expect the same to be true for animals, where especially solution is very important. Is the solution fully acqueous, with phosphate buffered saline, blood serum, cerebrospinal fluid, urine, etc?

If you want to ask scientists questions about the matter, check out ResearchGate. It has high marks from lots prominent reporting groups.

https://www.researchgate.net/