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With some programming but no formal CS background, to develop fundamental CS knowledge should I get an MS or BS?
I have 3 years of experience as a programmer now. I have worked on some drivers in the automotive domain and some medical applications.
Since I do not have a computer science background, I was thinking of going for a full time masters in computer science. I need to develop my algorithm and data structures, compiler theory knowledge.
I have studied algorithms and data structures through the book written by Cormen, and other stuff through books.
I do not have any published papers from my undergraduate degree.
Would it would be better for me to go for a masters or bachelors degree?

Thanks for the edit. I have removed the part of your post that asks about your chances of admissions, because it's impossible for us to answer that question.

Do you have bachelors degree? If yes, in what field?

This appears to be off-topic because it appears to be about preparation for a non-academic career.

undergrad in electronics and computer engineering

it is about preparation for academic career..I need to apply for masters and choose my research area

So, do you think it makes sense for me to go for higher studies now?

Depends what you are hoping to achieve, of course. However, as you are already working in industry, if your goal is to get better pay or a better programming job, this may not work out the way you hope it would. If the goal is actually to (as you indicate) learn about fundamentals in computer science, going back to university may be the right move. However, note that for these basics, an undergrad may actually be more appropriate. At master level, most programmes would assume that you have a solid working understanding of these concepts from the start.

What will my chances be of getting into a good university?

What is a "good" university for you, and where? There is also the problem that you indicate that your undergrad was not in computer science - this will probably hamper your chances of acceptance to a great computer science programme quite a bit.
Somewhat related: I feel that you are also overestimating the amount of industry experience you have accrued. Frankly, after 3 years, most people would not call you an "experienced programmer". So it is unlikely that your work experience will be sufficient to offset your missing undergraduate degree.

Agreed on the experience part...I just wanted to say that I have some experience....I have studied DS and compiler theory on my own through books....Had RTOS course in my undergrad ...I am an electronics student.

And you are right about my undergrad not being in computer science..That's the reason I want to pursue a degree in the field.


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What should I do if my master's advisor used a figure from my thesis in a publication without citation or acknowledgment?
A year ago, I finished my Master's degree and ended 6 months of working for an incredibly manipulative and demanding supervisor.  We started working on a publication of my Master's results, which is awaiting final approval (post-corrections) at the journal we submitted to.
Last week, I read a paper this supervisor had published recently, which had a figure taken directly from my Master's dissertation.  Our in-press article wasn't cited, and I wasn't co-author, referenced, or even mentioned in the acknowledgements.  No direct reference was given for the figure, but the text surrounding it made it sound as if it had come from another article by my supervisor from last year.
It seems pretty clear to me that this is plaigarism - we worked on this project together, certainly, but the final product was a result of my work and their guidance.
My problem is, I don't know how to deal with it.  We are currently co-authoring a paper, so I don't want to cause a rupture.  I also plan to continue working in this field, and would like to avoid having a senior researcher and previous supervisor to be angry.  At the same time, I don't want them to get away with using my work, and taking all the credit for it.
I will certainly tell them that I feel uncomfortable with how they used my work, but realistically, what can I expect/hope to happen here?
UPDATE - the figure in question is an overview of a simulation model I created, so is pretty much the core part of my Master's work.

Can you elaborate a bit on this "figure"? are we talking about a simple illustration of some concept that you have drawn, or is the figure a research outcome of your thesis? (that is, is this primarily about him using the figure you have drawn, or is it about him selling your research results as his?)

Apart from everything else, there could be a copyright issue if you want to use the figure in your new paper.

There is no benefit waiting for you after pretty much any path you might take here, but you can take this as a valuable lesson in academia: don't get associated with this kind of people.

I don't want to cause a rupture. — You should. Dealing with abuse is more important than one paper.

Just to clarify, do you feel that you should have been a co-author on that supervisor's paper, or is it just his use of the figure that you are concerned about? I started to write an answer addressing the latter case, but my answer won't be that useful if the former case is true.

Contact the editor.

The issue here is somewhat thorny. Relative to you, however, there is unfortunately not much benefit in any event, because citing the figure is not normally enough to merit authorship. All you would have is one extra citation, which would likely get "lost," because the publication with which it corresponds doesn't exist yet.
So I would make sure that your new paper cites the old paper, since it is the first to publish the figure. I would also make sure that you mention politely the concerns that you have over the use of the figure without citing.

I am not sure I understand the suggestion about having the new paper cite the old one. I would recommend that the new paper actually cites your thesis for the figure. If you cited your supervisor's paper for the figure, you would be compounding the problem as you are giving her the credit for your figure. But you don't want to publish the figure without citation as that may breach copyright (because it is already published).

The issue is that the published article is now the "reference" for the figure. You can't reuse it without having the appropriate permissions, which usually includes a citation to the article in question. However, you can also cite the thesis when you use the figure. ("Republished from Ref. X, and adapted from Fig. Y in Ref. Z," for instance.)

I'm not actually sure that's true. The Masters thesis was published before the article and contained the figure. It therefore has the copyright. The supervisor who used the figure would have signed a copyright document but just because she claimed the rights doesn't mean she owns them. In fact, I suspect that the OP could write to the editor of that journal pointing out the copyright breach, but that would create the unwanted rupture.

One possible approach is to discuss this by presenting it as a favor to you (e.g. "I'd have been neat if that number could have been cited to this thesis, because that would help me have more citations a the beginning of my research career") as opposed to accusatory approach of "You ripped me off".

It's hard to fix the past... Rather think of the future... I would (and in past case have) let the person know that you feel you should have either been a coauthor on the paper (preferred outcome usually) or been acknowledged as contributing to the paper (specifically all non-original figures must be acknowledged as to source for copyright reasons and there is the right to be known as author and originator in relation to all aspects of the paper you have contributed to).
If you are one of many students this supervisor has in this area, and/or the figure just encapsulates ideas that your supervisor has provided, then the shoe could be on the other foot, and the supervisor may not even be aware that you feel ownership of the figure (or other aspects of the "joint research").  In your thesis/papers you need to acknowledge where ideas have originated from other people - in a thesis this is likely to be restricted to a specific acknowledgements section.
If a figure is likely to be needed in future papers, I tend to note that it is copyright by me and reproduced with permission in all papers, and thus copyright is not transferred to the first publisher of such a paper.  When I circulate things (even just charts and figures) I sometimes add a copyright if it is something that I am particularly proud of and/or want to retain control of.
If I were in your shoes my aim would be to ensure that I was consulted about future papers (given the opportunity to be an author, or acknowledged, or to waive my rights).

I tend to note that it is copyright by me and reproduced with permission in all papers — Actually, at least in computer science, copyright to figures belongs to the publisher of the first paper that uses them, although many publishers allow authors to reuse the same figures in subsequent papers, as long as the first paper is properly cited.  In practice, of course, nobody follows the rules.

@JeffE: The journal would like to hold copyright, but the assignment is invalid if it wasn't executed by the true copyright holder.  In this case, OP retains copyright to his figure until he assigns it.

It is not hard at all to fix the past. Contacting the editor of the journal is the correct thing to do in these cases.

@nico - It is impossible to change the past, but contacting the editor creates one of many possibly difficult futures. If it is a hardcopy journal, they will not recall all the hardcopies, and even a soft journal is unlikely to change the original. Errata are unlikely to be created for such a minor breach, but might be.  This is likely to cause embarrassment and difficulty to the authors and destroy any possibility to collaborate in the future.  It depends on the significance of the figure and the extent to which which your supervisor contributed, and in this case best to contact them.

@JeffE - No, a copyright assignment covers only those things that are original to the paper, transferred by the author, and not excluded from the transfer as subject to a different copyright arrangement. The first dissemination of the material (figure) need not be a paper, but can be a book, a thesis, lecture notes/handout, or an earlier version of the paper. When a figure is necessary to multiple publications (including thesis, notes, book and/or papers) I am not in general willing to transfer copyright, which is fine even if thesis is university internal or identifiable work is unpublished.

I am not in general willing to transfer copyright — Willing or not, some journal publishers (ACM, for example) do not give you the option of modifying their copyright transfer agreement, which by default covers the entire contents of the paper and requires the author to certify that everything in the paper is original and transferable. In any case, it is necessary to read the actual copyright transfer agreement; you don't retain copyright on your figures just because you say so.

I have had a couple of similar cases before. This is a form of both plagiarism and copyright breach (these two are not necessarily always the same). They had to do 2 things before using your figure in their article: (1) cite you; (2) Provide the journal with the written permission obtained from you, for using your figure in their paper.
The failure to do any of the above 2 items is problematic. In theory, you can (1) write to the journal and ask for the retraction of the plagiarizing article after providing sufficient evidence. (2) write to the publisher and ask the same. (3) write to the authors and ask them to send an erratum to the journal (or ask the journal to ask them). (4) If they did not do anything, sue the irresponsible parties.
What happens in practice though? An article stole a figure and even a table of my article. Interestingly enough, they had not even bothered to re-write the content of my table, but had only take a snapshot of it, and had put it exactly as is, in their own article. They had not stated at any point of their article that those figure/table were picked from my article, nor had they contacted me previously. So I contacted the journal for many times, to no avail. Then I contacted the authors (there was no independent publisher to contact). They did not respond as well! So if I wanted to sue them, I had to fly abroad, and I doubt the court in their country had any stringent rules against such copyright breaches.
So in practice, there is usually little you can do, as journals heavily tend to sweep these issues under the carpet. Another article had plagiarized most of the content of my article, without citing me. I contacted every one (journal, publisher, authors)... After numerous emails, the journal told me they will not retract it, and if I want to sue them, I can go to the court in their country!!!!

I now understand the complexity of the case, in which the author of the copied figure is also the author of the original figure.
Because the journal owns the copyright of the article content, not the authors themselves. So eventhough the author can claim that (s)he has used their own figure twice, the journal still has the right to sue them, since (s)he has breached the copyright of the journal.
But if the original article was an open access one, I think it is fine to use the image twice as its copyright belongs to the author (although it is not a good practice to use repeated content).

The above question is a bit different though, as the supervisor that used the figure is also a co-author in the original article that included the figure. Also what sort of figure we are talking about. I am more than happy to share with my co-authors and students any of my figures if it is necessary as it also helps maintaining a consistent look amongst publications.

Uh I think in that case, they should still seek the consent of the first journal and especially the publisher, in case the work is not open access. I think so, because the journal / publisher owns the copyright of the content of the article, and eventhough the author can claim that (s)he has used their own figure twice, the journal still has the right to sue them, since (s)he has breached the copyright of the journal.
But if the original article was an open access one, I think it is fine to use the image twice (although it is not a good practice to use repeated content).

You could make an anonymous tip about your case to Retraction Watch.

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What can happen if someone acknowledges a grant on papers not related to that grant?
When I was preparing the camera-ready version of a paper, one of my co-author asked me to put in the acknowledgements section that his research was funded by the grant N12345.
Just out of curiosity, I searched the grant number, and found its description: "applying technique X on problem A".
I was very surprised, because my paper is completely unrelated to either X or A. Moreover, I know very well that this co-author has very little background in both X and A, let alone doing research. Although he is a very good researcher, these just are not his expertise.
The grant is for 3 years, and it is going to expire in a couple of months. He has not published any paper related to A or X. However, he has published many papers in completely different topics, e.g. the paper with me, and claimed that they were supported by this grant.
Is it the way to do if your field of research has limited funding? Might he go into troubles if it is discovered by the funding agency that the papers are actually not related to the grant proposal?

I edited the title because it sounded like you were asking about how to write a grant proposal to start working in a different field than the one you were in previously. If you feel the new title misrepresents your question, please [edit] my edit to clarify what it is you are trying to ask :)

Did you read the text of the grant proposal, or just its title?

"Might he go into troubles if it is discovered by the funding agency that the papers are actually not related to the grant proposal". I do not think that any funding agency investigates the papers supported by each grant. That would take ages.

@Alexandros they do, to an extent, that is why funders ask for interim reports.

@NateEldredge: I read the title and the abstract, which is public in the website of the funding agency.

So it's conceivable that the text of the proposal is worded broadly enough that it could include the topic of your paper.

@NateEldredge: first, the topic of my paper can't be related in anyway in solving problem A. It is in completely different domains. Secondly, the technique I used is not related anything to the technique X in the grant proposal. The text of the proposal should be the elaboration of the abstract, and I can't see in any way that I can include the topic in my paper (and his other papers).

@Alexandros, StrongBad is right.  I was once one of those funders who read the papers.

The big underlying question here is what it means for a paper to be "related to a grant". Different funding agencies have different rules on this, either a more "staff-oriented view" or a more "topic-oriented view".

Many pure science funds, for instance the Swiss National Science Foundation, take a liberal stance on what kind of science can be enabled through each individual project. Essentially, while a project is given to support a specific idea, they are fully aware and quite happy that in addition to, and sometimes instead of, this project, other more or less related studies will also happen by the staff paid partly or in full through the project. At the end of the day, the SNF and other similar agencies care not so much about the specific piece of science that is described in the project, but that some valuable science is happening and that PhD students are graduating. Based on this view, researchers funded through SNF are expected to acknowledge them on every paper they do, no matter if it has to do with any of the science described in the project description. The collection of all papers acknowledging this project is then  not understood as "all papers on topic X", but rather "all topics enabled by funding project Y, on topic X and any side projects that the funded students did in addition or instead".
Other, especially more applied funds such as most of the European Commission's Horizon 2020 programme, are much more interested in specific topics than in funding just about any research. For them, acknowledgements have much more the meaning that you seem to imply, that is, that citing this project in the acknowledgements of the paper implies that this contributes to the mission of the project. How strongly this is enforced or checked depends on the project officer. Most people also seem to take a rather liberal approach in practice, but there are certainly project officers that have formally complained about projects using the allocated funds to sponsor other research.

Might he go into troubles if it is discovered by the funding agency that the papers are actually not related to the grant proposal?

So at the end of the day, it really depends on whether the agency actually considers this "topically unrelated but financially enabled by the grant" paper as "unrelated". I would say, in absence of any other information, you can safely assume that your co-author did nothing wrong, and that the agency may be fine with this acknowledgement.

Many grants require progress reports. The NIH system is pretty smart and automatically finds publications by the PI. The system lists if the publication acknowledges the grant. When reviewing officials check the progress report they look to make sure the publications that acknowledge the grant are related and that those that do not acknowledge the grant are not related. They obviously are not experts, but they often know enough to judge what is and is not related.
If they find that the grant was used to fund a lot of research that was very far removed from the aims, the PI might get a nasty email saying do not do it again. If the PI has a history of doing it, at some point the funder might cancel the contract. It might eventually go so far as to blacklist the PI. In the worse case, which I think is unlikely, the funder could probably sue to get the money back. In the US, it is the university who holds the grant, so the PI would have an additional level of bureaucratic protection.

"a lot of research" in numbers or %? For instance, 10 unrelated publications may seem a lot, but if the total for the period is 200 publications, with all the others related to the grant, it isn't significant. For the grants I got, which are not US-based, as long as you reach the milestones that you proposed, whatever else you publish is bonus.

@FábioDias a PI might publish 20 papers in a year and only 1 might be related to the grant. That would be fine if only that one paper acknowledged the grant.

But what if the grant included, for instance, computational resources like a cluster or lab server? You can use that for other projects, without any downside for the grant project. Since you actually used the resource, you'd need to acknowledge the grant as well....

@FábioDias and your point is? In that case, you might get an email from the program officer asking what is up with those papers. As long as you can justify what is happening, it is not a big deal.

When reviewing officials check the progress report they look to make sure the publications that acknowledge the grant are related and that those that do not acknowledge the grant are not related. Do they really care about "over-acknowledgement"?  In math, my impression of the standard is: you write a proposal, do a bunch of stuff, and mention the grant whether the project was in your proposal or not.

Many funding bodies (for example the EPSRC and the Royal Society) explicitly say they are happy with any research you do on a grant they have funded.
That grant has funded this work -- your co-author is spending time which the grant is paying for on your paper.

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List of accepted papers: Why do notifications take 10 more days?
I submitted a paper to an engineering / CS related conference. After several weeks of reviews, a list of accepted papers was published today. However, the notification will be sent out 10 days later, according to their website.
I saw that my paper was accepted since it is included in the aforementioned list. I was not explicitly notified, just the list was put online. I have not received any reviews, yet.
There are several conferences that publish their list of accepted papers before notifications are sent out.
What is the reason for this? The decision must already be fixed, otherwise there would not be a list of accepted papers. But why are the reviews not sent out, yet?
Is the list commonly subjected to change?
I would be happy if someone (program committee, chairs, etc.)  could shed some light onto this, since I am quite interested in the background of this accepted-paper-list.
EDIT: More details regarding this conference.
ACM/IEEE DAC accepted papers:
https://dac.com/2018/accepted-papers
They give a short explanation under "What is the DAC research manuscript timeline?":
https://dac.com/submission-categories/research-manuscript#questions

The second week in February: A list of accepted manuscripts will be posted on the DAC website.
February 20: Accept/reject notices and confirmation forms will be emailed to authors.

Thus, this seems to be intentional and no notification email got lost.
The same was done by the IEEE HOST this year, the accepted paper list was online many days before the notifications were sent out.
EDIT2: I just received the notification. The list of accepted papers was not updated as far as I see.

Is the list necessarily complete?

That's odd. Perhaps they are waiting for reviews to be finalized, which may take a few days after the accept/reject decision is made.

I have never seen or heard anything like this happening in CS conferences. As you say, it makes no sense. There must be some kind of a mistake (e.g. notifications were already sent earlier but for some reason your notification email got lost).

@JukkaSuomela: There is no mistake, I found a note on their website (see edited question). However, it still does not explain their approach.

@Thomas: But how would they be able to decide about acceptance as long as the reviews are not finished?

Most likely, the program committee needs some additional time to edit reviews and provide a summary of the PC's discussion of the paper.  Reviews may require editing to remove bugs (for example, if a reviewer misinterpreted a result, but the misunderstanding was cleared up in discussion), or to professionalize the language (a reviewer might have described an author as a jerk or worse), or to remove references to other submissions under review need to be purged.

Do you think that this is more likely then "it was caused by an error" which seemed to be many people's first responses?

I think you are right, see my edit to my first post. It looks like the time was spent for internal tasks since the paper list was not updated so far.


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Why do most scientists think Brexit is bad for British science?
From what I've seen in the media, almost all British scientists think Brexit is bad for British science. However I don't understand why. Some of the most common reasons I've seen are:
Loss of funding - UK researchers receive lots of funds from EU grants, and these would not last once the UK leaves. But since the UK pays the EU more than it receives in benefits, the UK could simply redirect some of that money into science. It could be that the UK does not actually redirect the money, but that would be because the UK as a whole decided that science isn't worth it, in which case it would be democracy in action and one can't really complain.
Isolation - this seems to be based on the idea that Brexit makes the UK a less attractive place to work in. However the US didn't seem to suffer a similar brain drain after the 2016 elections, so it's not obvious to me that the UK will. Individuals might leave, but there's apparently no shortage of people wanting to move to the UK anyway (e.g. there were record numbers of international applicants to British universities in spite of Brexit).
Loss of collaborations - it's not clear to me why this would happen. The EU presumably doesn't have a "you may only collaborate with other EU researchers" rule, since there're lots of countries that are not part of the EU. But if they don't have such a rule then presumably collaborations can persist whether or not the UK is within the EU. Further, the EU would be incentivized to keep such collaborations because they're presumably win-win. Finally, even if EU collaborations are jeopardized, there's still the rest of the world. There are scientific powerhouses like the US that aren't part of the EU either.
Other reasons I've seen, like "there's no clarity on what we can or cannot do", should be temporary. They might be causing problems now, but five years in the future they should be resolved also.
Is there anything about Brexit that is fundamentally injurious to British science? If not, why do UK scientists so universally regard Brexit as grim?

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

I think it would be better if you would reformulate the post to more neutral. It looks now like a question as a lead, and then answering it on the spot, from an against brexit view. Furthermore, some proof that the majority of the scientists are against brexit, would be also useful. And, if you detail the anti-brexit arguments, you should detail also the pro-brexit ones (but the best would be if you would just ask, and not argument).

@peterh if you're able to write it to be more neutral, please do. I don't know how to do it. As I mentioned in another comment: I could write a 2-sentence question and get comments saying "why didn't you just Google", or I could write something like the OP and get comments like yours. Only thing I can do is add a source that most scientists are against Brexit.

@Allure Hunt for neutral facts and include them into the post. But what is your question? You summarized a view, you essentially answered your question already in the post. What do you want to know what you didn't write in your question already? Brexit is a hot topic, this question generates high visit count and vote counts, but it also generates infights. How can you guarantee that the advantages will be better for the site than the disadvantages?

@peterh questions are posed in the last two sentences and in the question title.

@Allure You stat shows that more than half of the people asked lives out of the UK. I can't see, how could it be representative - I see in this stat more the personal preferences of non-British researchers and British researchers living out of the UK, and not their objective arguments.

@peterh they're still UK researchers even though they don't live in the UK (see 1st question). If you're after a statistic of UK researchers who live in the UK, that's a different thing (and not representative either, since lots of other people can vote).

I'm sure all the people currently subsisting on research grants will be happy to pause their work and live off fairies and moonbeams until all the outstanding issues are resolved.

@perterh are you currently working in a UK university or UK industrial job with R+D component? (FWIW, regardless of your view or my view on either Brexit as an abstract idea or Brexit as it is actually likely to happen given the political realities here and abroad, I agree with your concerns that "Brexit is a hot topic, this question generates high visit count and vote counts, but it also generates infights. How can you guarantee that the advantages will be better for the site than the disadvantages?")

I would comment on your question as a non-UK non-EU researcher who was considering to come to work in the UK before but has completely changed his plans after Brexit was announced. Regardless of other things that could happen, the mobility and width of rights of third country nationals working in the UK definitely will decrease which makes UK much less attractive than, say, Europe. You mentioned that US science did not suffer after 2016 elections - this is not quite true. Many people stopped considering US a place to work and many others (including me) are making effort to leave it asap.

One should maybe convert the term "British science" to "British science and research system" in the question text. After all science can hardly have a nationality.

tl;dr: Although it is possible to have Brexit without British science suffering, this would require meaningful political support, and there is little to suggest that this will be forthcoming in the near future.
A recent report by the Royal Society provides some context. This report is focussed on the British research sector as a whole, rather than on science specifically, but not too much turns on that. Some key figues include:

Britain receives a significant amount of funding from European bodies (e.g. ERC)
A sizeable fraction of the UK science workforce originates from other EU countries (16% of academic staff; 14% of PhD students)
70% of British researchers held a non-UK affiliation at some point in the period 1996-2011, although there is no EU-specific figure.

The overall picture is that British research benefits from EU membership, through direct financial input and through mobility of individuals. British universities are disproportionately well-regarded on the international stage (e.g. the Times Higher Education ranking has 7 British universities in the top 50, compared to 7 from the rest of the EU combined), and so historically Britain has been able to attract excellent researchers from around the world, especially EU neighbours.
It is right to say that Brexit does not need to change any of this. However, maintaining the status quo would require political and financial investment from the government, and there has been little evidence that this will be forthcoming in the short term - especially given the difficulties the government has had in agreeing the basic framework for Brexit. Domestic investment in research has fallen significantly in real terms in recent years, and it is not clear that any more cash will be available in the immediate aftermath of Brexit.
It is also currently unclear how EU citizens currently living in the UK, and British citizens living in other EU countries will be affected. Some progress has been made on this, but (anecdotally) not enough to allay individuals' concerns. This is compounded by (real or perceived) xenophobic attitudes that precipitated the Brexit vote. Numerous UK-based, non-British researchers of my acquaintance are concerned over what the future holds for them, and have started to consider what other options are open to them.
Finally, it is perhaps worth noting that the Brexit vote was correlated with socioeconomic status, and the ideology of Brexit has never enjoyed much support in any of the academic circles I have been familiar with.

worth noting that the other 24% of non-UK PhD students are not from the EU (which is a much larger talent pool than the EU) https://www.vitae.ac.uk/doing-research/are-you-thinking-of-doing-a-phd/who-does-doctoral-research-in-the-uk#the-nationality-of-doctoral-researchers-in-the-uk

@Matt There are issues about funding; there are also issues about quality. I don't think merely quoting that figure makes a compelling argument

@YemonChoi Why would EU students be higher quality?

+1 for explaining how, although some of these effects could be mitigated, the likelihood that they will be mitigated is very low - the possibility that things will be accounted for is not the same as the certainty that they will be accounted for.

Anecdote: My niece (doctor of Physics) is working on an EU funded project. When the funding runs out (this year) they do not know if it will be renewed this time. Nobody knows. So they are all looking for other jobs. Of course they all voted Remain.

@Matt Some non-EU students, who may be admitted for various funding-related reasons, may not be as strong as some who happen to be from the EU. It's a question of competition versus non-competition, not any intrinsic benefit that "being from the EU" confers. I do not wish to say more here but if you are genuinely interested then you can find my contact details easily.

@Matt, the non-EU talent pool is made of 6.5 billion people. The EU27 talent pool is only 440 million. By that measure, EU students are much more represented.

Proposals for some collaborative European projects (such as horizon 2020) require consortia of universities and companies from different EU countries. These projects provide funding as well as opportunity for deep colabortion between different institutions. This is one of the things that leaving EU will make more difficult to participate in.

Some universities in the UK seem to have a slight (mainly with increased tuition fees) for international students. Anyway, my local uni's have been losing EU and non-EU professors recently, this may be linked to Brexit or other factors.

Good answer, +1, but the latter part of this sentence (after the comma) could use a second look. "Some progress has been made on this, but (anecdotally) not allay individual's concerns."

In addition to the practical, and very important answers that others have already given I will make this point about the emotional impact.
I'm a UK citizen in academia, but a lot of my colleagues, collaborators and students (both UG and PG) are from the EU. Before the Brexit vote they had almost exactly the same rights as me to live and work in UK academia. After the vote many feel that they don't, and after the exit they definitely won't (even if the precise nature of that is unclear).
They feel rejected and insulted. Their efforts, working within the UK to teach, and research, and improve our universities, have been deemed less important than the potential benefits of Brexit. I also think that the Brexit vote is an insult and a rejection not just of the EU as an institution but also of its citizens.
I've heard a lot of stories of xenophobic abuse increasing, particularly aimed at students, since the Brexit vote. But that's the nastiest end of the spectrum: most of the hurt that I hear expressed is about the steady normalisation within the UK in general of the idea that EU citizens are a problem.
TL;DR: Brexit supporters intentions and claims notwithstanding, the result is that EU students and academics feel insulted and rejected by Brexit, and this causes emotional damage at least as bad as the practical problems outlined.

Could you tell us the form of this "xenophobic abuse" and where it is coming from?

Most of the stories I've heard are general members of the public, off-campus, insulting obviously non-UK students and staff ("go home, stop scrounging" etc). Few have been academia specific.

If anything, the "precise nature of that is unclear" part exacerbates the problem. If it was clear just what shape Brexit will take, people would be able to plan accordingly; without that certainty, people have to plan for the worst.

It's good to remind that xenophobia and rejection are not limited to people from EU  only. Non-EU people have been treated like this well before Brexit, particularly if they are of non-white origin.

@DmitrySavostyanov This is true, but in my neck of the woods there is a feeling that Brexit has acted as a kind of transistor for increasing said xenophobia. (Actual instances of idiots crowing that Brexit means increased ability to get rid of the <insert ethnic/racial slur of choice here>)

Thank you for providing this answer which doesn't relate to the tangible elements of Brexit. I have left UK academia for another EU country as a result of Brexit, and I always feel it's impossible to convey how much the tone of the public debate has changed, and how hostile it all felt (and still feels).

@camden_kid one year ago I left the UK to go work in one of Northern Europe's top universities. At one of the last department events I mentioned this fact to one of my colleagues, to whom I had rarely spoken. She said "so you trust Juncker more? The EU steals our money and writes our laws". This coming from a university Lecturer. It's not racial abuse, but it was not nice knowing that they bought all Brexiteer's propaganda and would prefer you were not there.

@camden_kid I've had my pregnant (professor) wife be shouted at by an alcoholic lying on the street, I've had my visiting (west-european) father called a paki, a mixed french-english couple had their kids told by classmates they don't belong in the UK. All this in the runup to the Brexit vote, and all in a small Russell League uni city. Then there's uncertainty to what extent uni management will stick up for you; and your continental colleagues have no idea whether having a UK partner in a grant proposal might suddenly make it unwinnable 6--12months after submitting, so they won't include you.

@user3445853 One colleague of mine gave the correct answer to some random person telling her to leave the UK: "If I want to leave, there are 27 countries that will love to take me. If you want to leave, there are none".

The EU organises and funds programmes such as Horizon 2020, the Erasmus programme, and Erasmus Mundus.  None of those can be replaced by the UK government in isolation.
On a personal note.  Why do I feel so strongly?  I am a Dutch citizen and presently a postdoc in England. I have personally benefitted tremendously from freedom of movement and from all three EU programmes mentioned above:

I thoroughly enjoyed an Erasmus exchange in Sweden (incidentally, among 200 exchange students, there were only 2 from the UK, both Scottish; I believe this anomaly may originate from the same island mentality which contributed to the Brexit vote in England, whereas Scotland voted by large majority for Remain; or it may simply be an anomaly/coincidence).
I obtained my Master through the Erasmus Mundus programme where I met my wife.
I am currently funded by Horizon 2020 within the UK.

So I thank my education, my wife, and my job to the European Union.  I was living in the UK at the time of the Brexit vote, which has upset me more than any other vote in my life.
Fortunately, postdocs are exempt from the £35000/year income requirement, or EU postdocs might find themselves shut out of indefinite leave to remain completely (as most earn less than this).  I hope we won't need to apply for a new visa every time a 1-year contract gets renewed by another year, like in the US.

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

"None of those can be replaced by the UK government in isolation." On the other hand, Brexit might not mean that the UK government ends up in isolation. Surely, scientific cooperation is also possible with countries outside of the EU. The EU scientific research programmes might just adapt to include outside contributions over time.

@Trilarion That entirely depends on what post-Brexit deals will be agreed to continue or replace those programmes.  So far, there have been no deals agreed, so according to current information, they will cease.  I would speculate that, in the event of a comprehensive soft Brexit deal in which those programmes essentially continue, opposition to Brexit within British science will lessen.

Just responding to the isolation part...
I am a non-EU postdoc working in UK. Postdocs have short contracts and visas are tied to contracts. I have recently got to 5 years and therefore residency after 4 short term visas. Total visa costs (just for me) over 5500 GBP and no funding provided. Add in my partner's visas to get the full cost.
Also, without residency, a postdoc can't really apply for research funding to the various research councils. This is because you have to make sure your new contract is in place before the current one expires (thrown out of the country at the end of a contract) and therefore the long funding decision cycles mean there's insufficient time to get a decision before moving to the next contract even if the next contract is at the same research group.
This makes UK very unattractive for non-EU postdocs. If postdocs aren't coming to the UK then the next generation of researchers is not going to be based in the UK.
UPDATE: It seems that some commentators were not sure why I was talking about non-EU postdocs. I am expecting that EU citizens in the future will be in a similar position as non-EU citizens now. That is the perspective I was bringing to this question. Barriers are high, so future UK based researchers won't have as broad a professional network because EU citizens are much less likely to do a postdoc in UK and that will lead to separation of the UK from the rest of the research community.

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

"But since the UK pays the EU more than it receives in benefits, the UK could simply redirect some of that money into science. It could be that the UK does not actually redirect the money, but that would be because the UK as a whole decided that science isn't worth it, in which case it would be democracy in action and one can't really complain."
That's the answer.  Democracy in action is not necessarily what's best for science.  The UK receives a disproportionate amount of EU research funding.  There is no reason to think that the UK will maintain this level of funding after Brexit.  The EU (and other systems that I know of) does not apportion research funding democratically, but rather based on perceived scientific merit.  This gives an advantage to some UK universities or researchers.

Exactly, science and research are not democratic, so the purveyors of science will not place democratic interests above their own.

While the EU distributes money on estimated scientific benefit, that's not the full story. Many projects have actively sought British collaborators for non-scientific reasons; a chief reason being that they are native English speakers. While this usually isn't the sole reason to choose a particular collaborator, it does skew the distribution in favor of the UK.

BTW, I agree with your answer. But I'd like to add that the UK's leaving could cause a decline in economic growth (thus a decline in tax revenue), which might invalidate your statement that the UK could simply spend its contributions on the EU on other stuff like academia. It's not as simple as summing direct payments and benefits, there are many regulatory changes that also have an impact (we don't know yet what the impact will be, it depends on many factors like the future relationship with the EU, but also external factors like foreign investments and possibly other trade deals).

I deleted a discussion about the political classification and scientific output of other countries since it had no relevance to this post and was escalating. If you feel the need to discuss these things, please do so nicely in a chatroom.

If the Tory party has to decide whether to spend £1bn to promote science projects in  the UK, or to spend £1bn to bribe the DUP in order to stay in power, who do you think will win?

From my perspective it is mainly about freedom of movement. Within the Union all citizens can move freely between countries without need for visas and other permits (for example work or residency). From a country in the Union to one outside, in general you will need visa and a plethora of permits to be able to start an employment (for example a research position).
If a person needs to pay more and go through more paperwork and wait longer for a position, it is reasonable to believe there is an increased chance that person will rather take some easier, faster and cheaper route in one of the countries within the Union.

I think part of that is that you do not even start to worry moving inside the EU - or if you do, only for seconds. The difference felt between no worry and a little  worry is larger than, between two larger worries of larger, but unclear size.

@VolkerSiegel My guess is that you largely overestimate the worry capability of your people of interest.

Because scientists have political beliefs, and most of them are left of average voter so in general they opposed Brexit.
So they are more likely to pick on the negative sides of Brexit and ignore the good ones. Similar problem is with the news they read: news media read by leftists is strongly anti Brexit, so this exacerbates the problem.
This is not to say that Brexit changes will not cause problems for scientists based in the UK, but there is no reason for that to happen beside UK/EU being incompetent and/or trying to cause problems intentionally(so they can blame Brexit for those problems) or because they are using people as bargaining chips in their petty negotiations.
Again this may sound like conspiracy theory, but consider the example of China/US trade war where China is targeting certain swing states.
And if you want to make Brexit look bad messing up with science is a good way to do that.

What experience do you have of being an academic in a STEM field in a UK university? And why do you think the good sides of Brexit (whatever they might be) would be good/neutral for British science, which is what the question ostensibly asks about?

I'll say one word: Galileo.

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


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Can I use data and images found online in my project report, under the fair use clause in copyright law?
I am a mechanical engineering graduate student, and am working on my final project.  I am doing a finite element analysis of a particular phenomenon.  I was hoping to find test data of that particular phenomenon using a quick google search, and sure enough, I found some.  The test data will be helpful in showing that my analysis results are accurate.  I found the report on a vendor’s website.  Can I reproduce the test data from this report in my final project?  Per the “fair use” clause of the copyright act, since this will be used for scholarship/research (no profit involved), am I covered?
Can I also reproduce images from the report?
Added detail:
Thanks all of you for your answers!  I am certainly going to cite the source of the data and images.  Tom, to explain a little more about the data - it is friction coefficient data that applies to two very specific materials.  Company A did the testing for Company B.  Company B has posted the test report on their website (they are a vendor, and want people to know how low friction their particular material is).  I want to know if I can use the friction data from the report, and one or two images from the report (properly cited).  The reason I ask, is that Company A explicitly states in the report, "This document is provided on the basis of strict confidentiality.  Subject to any statutory requirement, the contents must not be disclosed to a third party, without the prior consent of Company A."  I know that I can contact Company A and ask, but if they do not give me the right to use the data and images... am I still ok?

(Disclaimer: I'm from Europe and speak mainly about [Central] European copy right legislation). Also here, facts (friction coefficient of xxx is y)  are not subject to copyright. But collections of facts (such as an encyclopedia, or a table of friction coefficients) are, given it was enough work to put together that collection.

One way to be sure you can use the report is to ask the company. Being able to write "with kind permission of company" in the caption of the reproduced image does immediately answer all possible copyright questions anyone and in particular any examiner of the thesis may have.
And, who knows, they may be very interested in knowing about graduates who work in the field...


text:
An F grade (in a labor studies class) on the transcript will hurt my admission to mathematics grad school?
So, I'm a third year student studying mathematics. My goal has always been getting a PhD in math. I'm currently doing ok with my math (taking grad courses and stuff). However, as many other students, I have to take courses outside math. I'm currently taking a labor studies class right now. All the class talks about is how bad America is treating its workers, and why don't we raise minimum wage to 50 dollars per hours to help the poor workers and stuff like that. I don't agree with everything I learn in class, and I show my disagree. As a result, the professor gives me terrible grades for saying my opinions. My question is: Will that bad grad hurt my future? Can I explain my situation in my application?

I would be more than happy if anyone who are on the admission committee can read my post and tell me your opinions.

Bad grade in labor studies? Probably not. Focus on keeping your GPA above 3.0 or within the stated competitive average for the department, focus on doing good in your core math courses, focus on a good GRE subject test score in math, and focus on networking w/ math faculty to get 2-3 letters of recommendation for grad admissions.

@Ric: I don't think that is what I'm looking for. I do not think I'm a weak student either. I have completed 33 credit hours of advanced math beyond calculus. But thanks for your comment

Please explain why you think this is different from http://academia.stackexchange.com/questions/38237/how-does-the-admissions-process-work-for-ph-d-programs-in-the-us-particularly we wrote that question and answer exactly for these types of questions.

@StrongBad I suspect the title is culprit, i.e. "I'm actually a rather strong student that goofed up once," but IMO the linked answer does fall in range for this question. Bottom line: do better elsewhere.

It sounds to me like OP might have a genuinely bad professor, one who's grading based on whether students agree with them instead of whether the students are learning. Does anyone else think this is a possibility? I'm honestly not very experienced (I'm just doing my master's degree, and I'm planning on leaving academia when I'm done), so I'm not willing to say that's definitely the case, but I'm a little surprised no one else has discussed that thought.

Ah yes, this brings back memories of a labor economics course I took when I was an engineering undergrad. Three words: pass fail option. :)

This could possibly hurt you.
In grad school, and even more so as a working academic, you will be asked to do various tasks that you might disagree with. For example you might be asked to teach precalculus or college algebra. Occasionally grad students don't like how they are asked to teach these courses and they either raise a big stink, or else simply don't follow instructions. In either case, this can cause huge headaches for the person supervising the TA -- even if the TA's complaints have some merit. Whether fairly or not, the prospect that you may be unwilling to follow instructions might give some admissions committees pause.
Doing tasks which you disagree with and that were assigned by people whom you may or may not respect (and doing them quickly, so that you can get on to the work you actually care about) is a vital survival skill in academia. I recommend that you learn this skill immediately and do what you can to pass the course.


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How to learn programming and designing?
I am a student of automotive engineering and I want to learn programming.
I also want to ask if programming would actually be useful in my field and if so, what type of language should I learn?

Programming is a useful skill in almost every field, especially for all sorts of engineering majors.
Specific language, on the other hand, is less important. I suggest you take a look at the programming and other CS courses provided by your university.
In addition, I suggest you seek the advice of your student/study counsellor. After all, they were hired to give this sort of advice to students.


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Overcoming hostility from a senior PhD student
I am a Ph.D. third year student. In our college for most of the work we have to depend on our seniors as our advisor rarely takes interest in our research. My senior is always rude to me, and never supports me in anything. Sometimes she doesn't talk to me for a whole day, and even sometimes she misguides me. I feel so low. It becomes so difficult to be in a lab where only two people are working and not even talking to each other properly. How can I deal with this?

Remember that the first priority of senior PhD students is their own research and to graduate.  You may be asking for more help than he or she can (or is willing to) provide.

Bear in mind that as a PhD student, you have very few options. It's difficult to switch labs and virtually impossible to switch advisors (at least at this point). You can try talking to them directly if you haven't already, but bear in mind that they're going to prioritize their own success, and that has nothing to do with yours.

Is a recent development or has this been going on for the whole 2-3 years you are in your PhD now?

She could be in a very rough spot. She does not have a senior to ask, the advisor seems to not be helpful. She's trying to graduate and supposed to care for you (which should not be her job in the first place). She might have hoped that at the time she is close to graduation you being in your third year need less guidance and now she's stuck.

"Sometimes she doesn't talk to me for a whole day" - I think this is especially telling that you might be asking for too much. Not speaking to you every day is completely reasonable, you wouldn't expect a faculty advisor to speak to you every day. "...and never supports me in anything." - 'Never' is a dangerous word to use, for your own ability to accurately assess the situation. It's likely if you are feeling like absolute words like that are appropriate, you will be suffering from confirmation bias and make the situation worse.

in CS I would expect a 3rd year to be reasonably independent...

@BryanKrause You wouldn't expect a faculty advisor to speak to you every day. Not even if you're the only two people working in a lab?

@sgf I would expect basic pleasantries if people are actually operating in the same physical space (to me "lab" can either mean a physical room, or it can mean "all of the sum space and personnel under one PI or research group"). But I would not necessarily expect interactions beyond that every day - some people have a focused work style or are very bothered by interruptions. That isn't my style personally, but I wouldn't consider it rude.

Perhaps a more useful question would be something like:  'How do I best approach senior PhD students and my advisor for direction and advice?' or 'How can I gain more research help and direction when my current advisor involvement is low?'

A friend was in a similar situation during her PhD.

I am a Ph.D. third year student. In our college for most of the work
  we have to depend on our seniors as our advisor rarely takes interest
  in our research.

There is really only one bright side to this situation: you will have to become a self-motivated and independent researcher quickly. Even if your advisor does not 'take interest' in your research make sure to meet with them regularly to discuss what you have done and what you are planning to do. This keeps them in the loop and aware of your efforts. To get additional input, you can contact other faculty in and outside your institute to get ideas or feedback on what you are doing. Former students from the same lab are also a good resource.

My senior is always rude to me, and never supports me
  in anything. Sometimes she doesn't talk to me for a whole day, and

As @Dawn pointed out, your senior clearly does not want to be friends. The best you can do is be cordial in person, and keep all important communication over email.

even sometimes she misguides me.

Attributing this to ignorance, rather than malice, is the most productive solution here. You can take her suggestions/answers/advice but make sure to use your own judgement to verify this - whether from other students/researchers, literature, simulation, etc. This will also help you become a better researcher.

I feel so low. It becomes so
  difficult to be in a lab where only two people are working and not
  even talking to each other properly. How can I deal with this?

Treat the lab as your workplace. I have seen labs/groups that feel like family, and others that are unbelievably toxic. Focus on finishing your degree and moving on. Ensure that you maintain a social life with family/friends outside your lab, and get lots of fresh air and exercise.

I agree with you.  As a third year PhD student, it's even more critical that Tina quickly gains an understanding of how to do independent research and constructively interact with her coworkers and advisor. The fact that she seeks advice from someone (who is essentially doing her a favor), then complains about it, is neither productive for her nor for developing a good working relationship with the PhD senior. If I was the PhD senior and became aware of her behavior, I would likely lose interest in helping her whatsoever.

In our college for most of the work we have to depend on our seniors
  as our advisor rarely takes interest in our research.

Have you tried to schedule a meeting with your advisor? Perhaps every two weeks? The advisor may be interested in more interaction as the lab is small with few seniors.

My senior is always rude to me, and never supports me in anything.
  Sometimes she doesn't talk to me for a whole day, and even sometimes
  she misguides me.

This is really difficult to interpret. It may be that your expectations are unreasonable.  If you feel that not talking very much is rude, I would not agree. In some cultures the work environment is very quiet. If you want more social interaction, make friends with people from other groups. In the summer, my workplace is very isolating, so I schedule brown bag lunches with others outside of my office.
In terms of "never supporting" and "misguiding", I think you need to be very clear about the types of support you want/need. She may be misguiding you because she doesn't know the answer and is giving her best guess. You must have realistic expectations for what you need to figure out yourself and what you can rely on her for.
You should try to come to an agreement with her on how she prefers to get questions. Once per day? A set meeting time? You might also consider a more quid pro quo arrangement. If you know she is helping you a lot one week, consider trying to do some of her busy work for her. Offer to do some of the grunt work or to pick up lunch for both of you. Make sure you are also supporting her! Finally, can you get support from people other than her? What about other groups doing similar things?

I feel so low. It becomes so difficult to be in a lab where only two
  people are working and not even talking to each other properly.

I feel sorry for you because you want her to be your friend as well as your work colleague and she does not want that kind of relationship. You should try to make friends with people outside of your lab. Externalize your focus and you won't feel so low. If you continue to feel badly, consider that it may be something unrelated to the lab situation and seek a therapist.


text:
Do “researcher degrees of freedom” invalidate my analysis?
I tested a hypothesis using some observational data, but did not find support for the hypothesis (the difference was not significant at the p < 0.05 level). I subsequently realised that the inclusion of a certain subset of individuals was dubious, since there was some doubt over their measurements. I filtered out those individuals (on objective criteria), and lo and behold, I now find evidence to support my original hypothesis.
I am acutely aware that, had the original hypothesis test returned a significant result, I probably would have found justification to support the inclusion of those doubtful measurements (or perhaps never even stopped to think about removing them). Although this wasn't my deliberate intention, what I have done seems a lot like I have employed my “researcher degrees of freedom” to find a version of the analysis that supports my original hypothesis.
I realise that what I should have done was to plan out my analysis more carefully in advance, and decide whether or not to include the doubtful measurements before carrying out any analysis. But I can’t change what has already happened, so my question is, what do I do with my data/analysis now? I can see a number of options that vary in their sensibleness, but none of which seem ideal:

Continue to use my updated analysis and present a clear argument for why those individuals should be excluded (i.e. ignore the RDF issue).
Continue to use my updated analysis but, in any write-up/publication be fully open about the less-than-ideal path that I took to reach it.
Conduct some kind of multiple-comparisons adjustment to take my multiple different analyses into account (I don’t know if this is even a valid approach in this context).
Sigh and throw the analysis in the bin.

How (if at all) can I make good use of my analysis while still adhering to good research practice?
My field is Ecology, in case that makes any difference.
Edit, in response to close vote: I did consider submitting the question to Stats.SE instead, but I felt that this is more an issue of research philosophy than a detailed statistical question. The answers that I am interested in (and indeed have already received) are connected with a general research strategy, and how to present results, rather than details regarding particular statistical methods, and so I felt that it was appropriate for this site. Having received very useful answers and comments already, it won't make too much difference to me personally if it ends up closed (and I can understand the argument for doing so), but I think the material could be useful to others in a similar situation to my own.

Can you obtain more data? testing your refined analysis on new, independent data is the ideal solution, if it's applicable.

@Tal - not easily, but yes, that may be possible. That is a good point. Though I would still be interested in the answer for the case where further data is too costly to obtain.

Very true. Here the difference in p value was pronounced enough to give me pause though - from p > 0.1 to p < 0.02

You didn't get a negative result. You concluded that you shouldn't reject the null hypothesis. And if you're using a hypothesis test (unless it's a test for trend, which is a rather different thing) there's no 'trend' - you either reject the null hypothesis or you don't. If you're testing with 5% significance and p = 0.06, the null hypothesis stands. There's no 'trend towards significance' - that's a meaningless concept. If you don't like that, find a different analytical model.

I'm voting to close this question as off-topic because it is a matter for the statistics SE

@rhialto I understand all of that. Perhaps "trend" was a poorly chosen word, I was just trying to clarify in response to dan1111's question: there is a difference in the expected direction, but it is not above the threshold to be considered significant. I never used the phrase "trend towards significance".

@ScottSeidman Fair enough. If that is the consensus then perhaps it could be migrated?

@ScottSeidman I disagree that this question is not a good fit here. The parts of the question regarding researcher degrees of freedom, while also on topic on Stats SE, is much better addressed as an academia issue.

Yes... and you know why. Apart from the specifics of "statistics", we all do know that "fudging" (in U.S. English) is not ok. That is, if a thing "fails" (admittedly not as bad a thing as it sounds...), then it does. "Reinterpretation" is not legit, although "learning from past experiments" obviously is so. Just don't think in terms of fake rules, but, instead, visualize the "rules" as though they truly were a guide to protecting us collectively from needless error, and guiding us toward useful risk... Blah-blah-blah!

The discussion of outlier analysis and statistical weight probably called for is best handled by statisticians

@paulgarrett So your feeling is that, having carried out the original, arguably flawed analysis, any attempt to rejig the analysis is "fudging" and so I should start again with new data, learning from my mistake? [This isn't sarcasm, I'm genuinely interested, as it seems to be a slightly different perspective to the one that most others have taken. If I've understood you correctly, perhaps you would consider expanding it into an answer?]

I don't agree that this is off topic here. I will vote to reopen, if it gets a few more reopen votes.

@user2390246, yes, I think anything that isn't starting afresh with new data is "tainted" in some way. Maybe there's a sophisticated methodological way to overcome this, I don't know, but the risk of tainting seems clear. "Learning from mistakes" is a big part of research, I think. Often annoying, true, ...

This question appears off-topic per discussion here.

@dan1111's answer is excellent if you do not have the resources to repeat your experiment, but under ideal circumstances, no matter how your model was created, an independent replication of the experiment would be the best possible evidence of your model's strength.
Much like in experiments involving fitting models to data (such as protein crystallography or data mining), it is perfectly acceptable to refine/train a model after obtaining your initial data, if the model is then fitted with independent results from a different dataset.
For example, you could repeat the data collection (and apply your new filter), and then run your model on the new dataset. If the new dataset confirms the previous one, your model would then be pretty solid.
In any case, no matter which path you take, you should present all of your results in your final publication. If you do in fact have the resources to repeat the experiment, the writeup could go as follows:

I collected dataset A, and then performed analysis using filter 1. However, the results were not statistically significant.
Upon realising that there were a number of flaws in filter 1, I then modified the filter, removing (anomalous values) and changing the filter to filter 2. Upon repeating the analysis, the results were statistically significant.
To reduce the likelihood of "researcher degrees of freedom" affecting the model, I then collected an independent dataset B. Upon repeating the analysis using filter 2, I found that the results replicated the findings of Filter 2 on Dataset A.

dan1111's answer is quite good, and March Ho's answer is also very valuable.
Even though this is a 9-month-old thread, it remains a timeless topic, and so I would like to submit a further thought on the topic for you and/or any other researchers who stumble upon this question.
You asked whether researcher degrees of freedom invalidate your analysis. "Invalidate" might be a bit strong, but it certainly casts serious doubt on the effect you're investigating. Further complicating matters is that, in certain fields (and particularly in certain segments of certain fields), such practices are basically standard operating procedure.
See the story on p. 1 at Nosek, Spies, & Motyl (2012) doi:10.1177/1745691612459058 for a similar kind of scenario. The answer, as I see it, is that you should really treat your results as exploratory, and maintain a healthy skepticism about them. If you want to increase your certainty (and it sounds like you do), then the best answer is to run replications.
Note the plural here. March Ho advocates an independent replication--that is, a single replication. While this can be highly useful, as in the example in Nosek, Spies, & Motyl (2012; linked above), it can lead to further ambiguity if the replication yields a similar, but weaker, effect. Therefore, a single replication may backfire by increasing your uncertainty rather than your certainty! The ideal would be to test the effect multiple times, and look at the results in aggregate. Then, you will be much better able to 1) determine the direction of the effect at the population level, and 2) estimate the magnitude of the effect at the population level.
This approach would take a long time, possibly a lot of money (depending on the nature of your research), and it wades into the murky debate over whether a direct replication or a conceptual replication is more valuable. Despite these limitations, however, the advantage of this method is that you'll end up with a very high degree of certainty about the nature of the effect that you're studying.
If your goal is to increase certainty in your findings, I don't see any viable alternative to conducting multiple replications (both direct and conceptual). If your goal is to generate new findings and you're not terribly concerned about the generalizibility of the results, however, then the exploratory method that you described isn't much of a problem.
At least some academic journals seem to prioritize novelty over certainty. But people who care about the integrity of science seem to prioritize certainty over novelty. I think each approach can be valuable, but not at the exclusion of the other.
For maximum transparency while also maintaining publishability, it would probably be best to follow March Ho's above answer, which provides a great template to solve the issue if further data collection isn't possible.
This is a particularly thorny question! Research methodology and statistical methodology are inextricably linked. I have written about best statistical practice, on a note that is related to this issue; a preprint of the under-review manuscript is available at http://osf.io/preprints/psyarxiv/hp53k/

What does your pre-registered protocol and statistical analysis plan say? You should do that.
If you don't have one, then make sure you do next time.
For the write up here, I think you'll have to present both analyses and explain why you did both.
You should also get away from the belief you seem to have that only results exhibiting a statistically significant result are publishable. That's not the case (see eg https://mobile.twitter.com/trished/status/723202381622730752 from a journal editor). Reputable journals look at the question addressed and the methods used. If you've asked a good question and done the experiment well, then demonstrating the absence of effect is an exceeding positive and publishable finding.
In medicine, that sort of finding would save the country lots of money and spare patient from undergoing needless treatment. I've no idea what would happen in ecology, but publishing it would at least stop your colleagues going down the same fruitless route.

As stated in my question, I understand that it would have been helpful to have a clearer protocol decided in advance, but that does not help me in the present situation. Also, nowhere have I stated or implied that I only care about results that are statistically significant. Sorry to be defensive, but it's only really your third line that addresses my situation.

Once again, referring to a finding of no effect as a negative result is far from helpful - and probably contributes any difficulty in publishing. A definitive finding of no effect is a very positive result.

I have edited to clarity this point - thanks. My original wording was because I was trying to keep from getting into statistical detail, given this is Academia.SE not Stats.SE, but I can accept that this led to some unhelpful implications.


text:
What does "informal application letter" mean?
For an application to a Master programme, I am asked to send:

a description of my study motivation on 2 pages
an informal application letter

What does "informal application letter" mean? Is it something commonly asked for an application? I really don't understand what they want.

It's a letter in lieu of an application form. See Nate's response for more information.

I would interpret that as asking for a short letter that briefly states what you are applying for, your educational background, interests and goals, why you are interested in their   program specifically, and mentions anything else you'd like them to consider.

I agree with the above. I would interpret it as pretty much the same thing as a cover letter that you would normally send along with your application.


text:
Graduate courses as undergrad vs master's degree
I am roughly in the following situation (field: physics/mathematics, location: Europe):
I have enough credits to finish my undergraduate degree this year if I want to. I can also choose to stay as an undergrad for another year.
I have done almost all undergraduate courses at my university that interest me, so I would be doing graduate courses 90% of the time.
With some extra work, I could obtain a master's degree at my university. However, I could also apply for a PhD program immediately after finishing undergrad next year, without getting a master's degree first.
Not counting research experience, is it advantageous to 'formalize' one's graduate courses by getting a master's degree, from the viewpoint of career opportunities?
I am not sure about this because on the one hand, a master's degree may give other people a better indication of one's ability, but on the other hand admissions committees and such may be more demanding from students with a master's degree.

admissions committees and such may be more demanding from students with a master's degree — This is absolutely the case in the US.

Do you plan on doing a PhD after this possible Masters? If so, why not just go for the PhD right away?

@LeoUieda I would like to do a PhD at a top school, and I need recommendation letters for that and apply in October in order to join the next year. Meanwhile, I could apply for a Master's as late as this summer and still get in.

Not counting research experience, is it advantageous to 'formalize' one's graduate courses by getting a master's degree, from the viewpoint of career opportunities?

For industry, yes, it is advantageous to get the Master's degree if you're doing basically the same work.  The Master's degree is generally considered a terminal professional degree for many industries, so there's some value in getting that rather than just a Bachelor's degree.
For academia, no, it's typically not advantageous.  Most US-based PhD programs will require you to do core coursework roughly equivalent to a Master's degree regardless of whether or not you already have one.  (I do not know enough about European programs to comment on them.)  They will also typically present you with an opportunity to earn a Master's on the way to your PhD.  Thus, getting one before you start a PhD program at another university is, perhaps, redundant.  The only exception is if you are planning to switch your focus a bit.  For example, you might get a Master's in Public Health and then start a PhD program in Computer Science focusing on applying computer science research to public health problems.
You also mentioned that you were interested in a PhD, but wanted solid letters of recommendation so that you could have a reasonable chance at a top university.  The best way to do this may not be through coursework.  Obviously, coursework is important, but you may find that working with a research group as an undergrad allows you to more closely interact with a faculty member and get a more personal letter of recommendation.  Professors write letters of recommendation for students based on coursework all the time, but it's more rare for them to write one for an undergraduate with whom they have worked on research projects.  Also, this would allow you to determine whether or not you enjoy research and learn a bit more about what you would like from a graduate school.  Research is quite different from coursework.  It's more of a career than a school experience.

Most PhD programs [in the US and some other countries] will require you to do core coursework roughly equivalent to a Master's degree regardless of whether or not you already have one. In other countries, the situation is very different. (The OP is in Europe)

Thanks!  I've updated the original post to reflect this.

Indeed, for example in Denmark and Finland the master's degree is the standard(at least for now) Like 95% go for master's degree, in fact you are admitted to both undergrad+grad and I think the PhD programs look favorably to those with master's because the structure is different to US PhD.

In Europe, the answer depends on your field and what kind of PhD you apply for but generally (and especially in the UK) a candidate with a masters is more competitive when applying for the PhD and will be more likely to progress to interview.
The reason for this is that with a masters degree you are expected to have completed an extended piece of project work and small thesis. This reassures the admissions committee that you understand the undertakings of a PhD and what it will require and have developed those skills (beyond book learning). The biggest benefit of the masters in the eyes of the PhD admissions committee is not the extra and fairly broad knowledge (a PhD is, after all, very specific) but the experience of planning and undertaking an independent project and writing/presenting a high quality report on it.


text:
How lenient are conferences in accepting and reviewing lately submitted poster presentation abstracts?
There is a conference that my advisor suggested that I attend and present at, but unfortunately as this was just suggested today, I missed the abstract submission deadline by about a week.
I know this is my fault, but I am just wondering how lenient conferences are wrt late registration. I emailed the organizer politely explaining the situation and asking if it would still be possible to register. If anyone is curious, this is for the SIAM annual meeting in Chicago.
I've never attended any sort of conference at this level before (but do have some experience with poster presentations), so I'm wondering should I even expect a reply, let alone a positive one? I think this would be a really great opportunity for me to present my research to people in the field, and I will most likely attend the conference even if I'm not able to present at the poster session.

Edit and update: The organizing committee has agreed to give consideration to my abstract, and said they'd let me know by the end of next week re: acceptance/rejection.

I would expect a large, formally organized meeting like this one to have no leniency.  Sorry.

Some conferences usually/always extend. Others don't. I suggest writing to the organisers and asking - the worst that can happen is that they say no, and they might say yes, even if an extension hasn't been formally announced!

Some conferences (I don't know if it applies for the one you have in mind as well) give the opportunity for the submission of so-called "late breaking posters" even after the official submission deadline until shortly before the conference date.
By this one can present very recent results that did not get ready before the deadline. As a drawback it should be noted that the contribution will normally not be listed in the conference proceedings as they will already go into preparation/production soon after the deadline. Also the reviewers might have a special eye on the originality and the currency of the contribution, so submitting some rather well hung stuff just to get a poster presentation and a reason to attend the conference might not work.

I did miss the breaking posters deadline by about a week. But the conference director let me send her an abstract, which she forwarded to the co-chairs, who ultimately have the final say. Fingers crossed!

Most would not let you submit your abstract. However - I would guess that it  depends on the size of the conference, the amount of submissions, and the committee members themselves.
It doesn't hurt to ask!


text:
Is it possible to do a PhD in pure mathematics after studying aerospace engineering?
I am currently a high school student, and I am considering taking a BSc in Aerospace Engineering (in Delft), hopefully leading into a masters.
I am also very interested in pure mathematics (I am aiming for the Top Scholar award in Mathematics within New Zealand), and want to do a PhD in maths.
Is there any way to continue my studies in Mathematics beyond high school as well as taking aerospace engineering, and while keeping options open for a PhD in maths?

If you want Math, why take a BSc in Aerospace Engineering?

What do you want to do after school?

Do you consider attending a school that would allow you to double-major in Aerospace Engineering and pure math?

Oh, you want everything in life. That's not how life works. And don't pursue degrees but find a professor whom you can work with on some interesting research problem.

The kind of math you'd get exposed to with your proposed BSc would be very much of the applied variety (calc, differential equations, that sort of thing) but it's not going to drive you to any of the backing theory (abstract algebra, real/complex analysis, topology, etc.). It's unlikely a Master's in Aerospace Engineering is going to do you any favors in this regard either. Hence, by the time you want to do your PhD in Math, you will be woefully underprepared for it.
Hence, if you really want a PhD in Math, it's a very, very good idea to do a BA/BS in Math, so I would highly, highly recommend that you dual-major. The good news is that there will be some overlap in classes when you do this, so it's by no means an insurmountable goal. Plus, this will give you a strong sense as to whether to pursue the PhD in Math.
Another option is that, if you just do a BSc in Aerospace Engineering, when you go for your Master's you might consider switching to Math at that time. From a practical standpoint, I'm not sure a Master's in Aerospace Engineering would open many more doors than the BSc would, but a Master's in Math would definitely broaden your knowledge and give you more general appeal. It's possible to proceed with a PhD from there.

Thanks for the answer - I'll definitely have a look at the possibility of a dual major.

@Alex You're welcome! And good luck. :)

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