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Contacting references for PhD application
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Hi. Yes you should contact them ASAP. They might take sometime to respond.

PhD Offer Help!
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By the way, it is common in academia that a PI likes your CV very much and is very interested but he/she has no fund. When the fund comes, he/she starts to think also about other candidates and just ignores you without a slight sense of guilt.

PhD Offer Help!
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Hello. Just care for yourself. Uni is the strong party and PhD student is the weak. If a group/PI lost some funding, they are going to survive anyway. But for you, you do not get a position everyday and should take what you think is better for you. Nevertheless, if you feel some guilt regarding their loss, this reflects good manners.
Now to facts. Do you have an offer from Uni B or you must still have to do further interviews? If I were you and both have more or less same pros and cons, I would go with the unconditional offer. Otherwise if you have two offers, just trust your gut and do not regret your choice.

So hard to obtain funding?
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I am sorry for your experience. Funded PhD for non-EU students are rare. You might be wasting your time seeking these very competitive opportunities. The chances in continental Europe are higher although the UK is much better in other aspects.If you want to immigrate to a country where good research jobs are available, you might look for a Master degree in Australia or Canada and apply for jobs there.

Just had a Skype interview--should I thank them through email?
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Do not follow up. Just wait.

Assistance with scholarship application
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Personal reasons like you cannot afford paying tuition fees are not relevant. They want you to state your professional plans after study indicating your "academic ability, energy and commitment to studies."

Tick this box if we can contact your referees before the interview...
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Hi. My post is inference not based on knowledge. I do not think it will affect your chance if you tick that you do not want them to contact references before the interview. I think most of us would prefer that the references would not be contacted at all :) or at least before there is a high chance of getting a job offer.
I can fully understand where the problem is. Every referee has a "quota" for each applicant then she/he might get bored (I put she before he because of women's day, just kidding). You do not want to waste part of your available quota for nothing. I bet 90% of applicants would tick this box to "save" the response of the referee to important occasions.

Publishing things you don´t want because of your advisor
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I agree with Tudor:Queen. If you think there is some kind of misleading or false claim, there is a big problem. If you partially disagree with the hypothesis and the way it is presented, it is not ideal but it happens. Of course freedom is proportional to seniority. The situation is worse outside academia where seniors can even "think" for you.
Think of it in a different way. He is proud of his former work and does not accept it might not be 100% correct. Secondly, he is a senior academic who knows better than you how to "sell" the paper. This might have helped your paper to go through. Reviewers usually think different than authors and he might know how they think in general.

Thinking about quitting my PhD
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let us look from the perspective from someone who left academia to industry. As you already said, pros for quitting are obvious. In particular, you you do not like the project and research direction. I would like to add two important things: If you are not motivated the PhD years may pass and you might not learn a lot to qualify for a job. The second thing, you may find after the fund is over that you won't get even the PhD degree. This is a possibility especially when you are hired as RA and the PhD is not the priority of the supervisor.
Now let us be fair to academia. You know already that you have more freedom. You may have more innovative and interesting tasks than industry. You are driven by funds in academia but to a mire extreme way by projects and customer demands in industry. You have more flexibility in tasks and time in academia.
I do not agree to a general rule that people who do not intend to work in academia should not pursue a PhD. Industry is there and would not go away if you spend a couple of years in academia. What can be really hurting is spending these years in academia demotivated and not learning anything. Academia is a paradox. You have to treat academia carefully. Do not just go and hang around like many guys do and do not kill yourself working 12 hours a day like some guys also. If you have the right motivation and willing to spend 3-4 years working in academia, I would say do not quit. Otherwise, like you and tru, rewt said, quitting would be the best choice (after ginding a job of course).

What happens to funding if switching from full time to part time EPSRC Studentship?
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I do not think it is possible. The reason for funding will exist no more. If you say, I have for private reasons to switch from full time to part time, the funding body might accept. But if you get a full salary, you are not "blocked" from gaining money and you will be like other part time students. You might try to get exemption from tuition fees though.

Self Fund for 1st year or Wait
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Do you want to graduate from a PhD with 30k or more debt? I do not find it a good idea. Search for a real PhD or do something else.
In UK, PhD students are already paid very low (13-14k a year). It is enough just to live as a single person. Do not make it worse by self funding.

Self Fund for 1st year or Wait
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If you pay with own funding this year, no one is going to pay for it next year. It is now or never. PIs want PhD without obligation to pay them. They are not going to search for funding for you. Just wait and apply for a "real" paid PhD.
When they get funding, they may think of other candidates.

Equality irregardless of ethnicity, religion or sexual orientation
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Thanks TQ and AislingB. I have not found this detailed information. I had it several years ago in paper format. Unfortunately it is not in website. Anyway I read them so they existed one day :). Thanks again.

Equality irregardless of ethnicity, religion or sexual orientation
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Thanks TQ. This is useful but brief. I would explain more what I want.
Discrimination against religion in particular is seen differently in each country/workplace. In the UK and Canada for example, speech and writing against some religious beliefs is considered a hate speech. It is accepted for someone to wear anything that is based on his/her belief. It is a taboo to openly discriminate based on religion, even if hidden discrimination exists.
In the continental Europe, they see things differently. The employer can decide a "dress code" which automatically reject some groups. It is not seen as discrimination. They might see some habits (based on religion) as a disrespect to the country "culture".
In summary, some countries see it "do and wear what you want and you will not be disadvantaged based on it". Others see it "we do and hire whom we want based on out metrics which may include how do you wear or behave socially".
What I want is detailed rules emphasising what could be considered as discrimination in particular regarding religion.

Equality irregardless of ethnicity, religion or sexual orientation
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Hi guys, I have a bit strange request from you. I remember when I accepted a job at university in the UK, I received a booklet shows regulations and code of conduct. There was detailed information telling not to have prejudice based on ethnicity or nationality. Also to respect the religion habits of others. Is it possible that someone send me such a booklet of his/her employer? You can hide the logo and name of institution. I need only the text of such paragraphs that state some equality regulations and some examples of how to apply these rules. You can send me a private message if you want.