MathCat

Probably just be yourself and inform them of whatever you prefer. If it is an issue for them to do for the length of a visit it will be an even bigger issue to do for 4 years. So better to know how accommodating they are now (if this is an important issue for you).

Hi,
First thank you, everyone who replied. Your comments were helpful and allowed me to gain some outside perspective on my situation. Also, because I wasn't clear, I am a female. Just wanted to clarify because some of the pronouns got a little confusing while reading the longer replies. 
Anyway, I have joined another lab for the spring semester and the plan is to leave with a non-thesis masters in May. I have not officially switched to the masters program yet, as my new advisor said they wanted to give it 5-6 weeks and reevaluate. New advisor and I work well together and communicate amazingly well. It really is light and day compared with Old Lab and Old Advisor. I am still upset and coming to terms with how things turned out, but at least it was an enlightening experience and I know what to look for once I apply to phd programs elsewhere. 

Of course, I'm still hoping in the back of my mind that I somehow win the NSF GRFP and can, therefore, talk a lab into accepting me for a phd. (There are a few here that I was interested in as a first year but they didn't have funding back then). 

My plans are so up in the air right now! I have submitted the (first wave) of postdoc applications and most of the results will come in the next 4-6 weeks. Just like in the PhD application process, my spouse and I are stressed out since we have no idea where we will end up living later this year. I'm sure you and others who have gone through this process for postdocs can also relate!
Because of immigration status issues, I don't even know when I will be defending. If I end up with a US postdoc position, then I will defend within 1 month of starting the new position. If I am returning to Canada (I only applied to US and Canadian positions) then timing is not that important. If I'm leaving academia, then I will need to defend by the deadline to receive my degree in June 2017. 
But I don't know how much the US government will change its priorities for my field after Jan 20. A lot of planetary atmosphere type work relies on studies of our planet's climate, and that might be in danger. Something that sounds like a great research position now might not be very good in a year or two due to the political climate. 
Being someone who is "Type A", especially in terms of time management and planning ahead, this uncertainty is so very not fun. So, one of my resolutions/"trying something new" is learning better strategies to cope with this stress. Grad school in general is stressful and I have been able to be fairly successful at managing stress in the past 5 years. But this new challenge is a whole new level of stress that I am still learning to manage. I know that I need to let go of worrying about things I cannot change at this point (and I often say this to the grad school applicants on these forums!) but it's easier said than done  I'm improving though.
My other academic goal for this year is to do a better job of decreasing perfectionism so that I can produce more tangible "products". Most of my papers have taken 20% to 30% more time than I wanted to spend on them and the extra time doesn't improve the quality of my work in a useful way. So one big goal for this year is to spend my time more efficiently and knowing when and where to spend energy.

Hello!
First, please take care of yourself during the break. If you haven't taken some time off, doing that could be a good idea. 
Next, I think you are right that you will have to do something or there will be negative consequences down the line. I have not been in your situation, so maybe this won't be the best advice but I hope it provides a useful perspective. I think that most of the problems that students have in grad school are due to unclear communication with the faculty. I think it's really important that you talk to the professors about these issues and get their support, if you are able to be comfortable with doing so.
I think it is worth the risk (responding to the "not knowing who you can trust") because there has been and will continue to be more negative consequences for you if you don't get the right support. Again, I'm not in your shoes and I don't know what the situation is like, but I would ask myself what is worse: being labelled as a bad student and not getting nominated by the department for anything, or having people find out about your disability? I feel like the negative consequences of having the faculty know is unimportant if they are already writing you off as a non-successful student. 
But I'm not considering the emotional impact of having everyone know. I can't know how you would feel and I don't mean to minimize this part of your experience either. If you are finding it challenging to bring up, does your school's disability office have people that can guide you through this? If not, I would go to the school's counseling center and talk to a counselor for advice. It might also be helpful to come up with a plan for things that you need in class to actually help you (not just the recorder). For example, you can probably ask for professors to not call upon you in class (if it's part of the evaluation, then they can come up with an alternate way to evaluate whatever they're looking for). Or, if you want to still participate in this way, let them know to give you a little more time to formulate your response if they call on you. 
Ultimately, it's up to you what to do of course and I don't want to pressure you in any way. From the way you describe the situation, things sound like some action needs to be taken, but it's not too late to change the course of your graduate school. It also sounds like the upcoming semesters will go the same way (unless this first semester of your program is special for some reason?) so that's why I think intervention is better sooner rather than later.
Finally, it's not just your responsibility to "figure it out" by yourself. The department should have some responsibility in ensuring you have access to the support you need to succeed. They accepted you into their program, so they bear some responsibility for your success. I think it is okay to let your new supervisor know what's going on---you don't need her to play "mommy" but it's no longer just a personal issue since it's affecting your academic performance. But maybe she can help you identify some professors you can trust and go to first. And if you decide not to tell the majority of professors, if other faculty mention your performance in reviews or other department meetings, you have an ally that can help you (without revealing the personal details). 
Good luck in the new year. I don't think you need to go through this alone. I hope you are able to find people on campus that you can talk to and get support for your disability.

Definitely take your advisor up on it. If they really are a big shot, it's likely that a bunch of people will stop to say hi and you'll be able to meet them. You might also get tips on navigating the conference you otherwise wouldn't get. I wouldn't even hesitate but would totally jump at this offer.

Most schools will only cover travel in economy and not anything beyond that. You might just ask the school, to be sure, but I wouldn't expect too much. 

I'm sorry to hear that things have not improved
I am surprised that the DGS isn't taking your side more strongly here. Maybe now that you know this about the department, you might not want to stay for a PhD anymore, but finding a new mentor in order to graduate with a MS is not a very supportive action by your DGS. I think if you do want to stay for the PhD, you should have more support from your DGS! My opinion is that once a school accepts you as their student, they (the department as a whole) are responsible for providing the support to see you through your PhD, especially if your PI fails at doing this. The DGS should be helping you talk to other professors in the department and potentially start over as a new student in a new lab. 
I think if you want to stay here for the PhD, you should push for your right to stay and complete your degree as planned. This is a good time to push this because they are considering new students at this stage. It would be easier for a professor to take you into their lab instead of accepting a new applicant. And, if you are serious about wanting to stay, you should push harder on the DGS (although still keep it professional because you'll want a letter if you go elsewhere) because the worst that could happen is that they say no and then you'll know you don't want to stay another 4+ years at this department anyways. 
Just my two cents.

Letting everyone else here take the lead on the LOR and application part, I just want to tell you that you are not alone. No one can tell you whether to report this professor or not, but I would really suggest finding someone to talk to about it, specifically a professional like an advocate, social worker, LMHC, etc. Most schools offer free counseling on campus; that is the one thing I would highly suggest doing because even if you handle applications like a BOSS (which I am sure you will), you don't want the trauma to bite you in the ass out of nowhere when you're kicking a** in your doctoral program. I speak from experience, and as a social worker. Before disclosing the name of the professor, or even the incident, I would ask the counselor a hypothetical, as they may be mandated by Title IX to report to the school, and you don't want to be pressured into disclosing.
Being in a country that isn't where you're from can be really difficult and isolating without sexual trauma. Please find someone to talk to. 
Please keep in touch if you're comfortable. Wishing you all the best.
 

@wlsWKglaemfek I have so many things I want to tell you but let me start by quickly saying this, just on the practical side of things (and please don't take this to mean that I in any way underestimate all the other implications of this terrible thing that has happened to you): I think you may run into trouble if you only submit two letters. At least in some cases, it may automatically disqualify your application because it is an official requirement that you've not met. So asking to only submit two letters would be difficult. If at all possible, I would suggest trying to replace the offender with another letter, even if it's short or not as strong. This may require telling some white lie to some secretary about this person encountering a problem getting letters done in time and asking that they be replaced in the application system, in cases where you may not be able to do this alone (some systems won't let you change LOR info once you've entered it). And I'd say ask someone, anyone, else for a LOR, and do it as soon as you can. It's very often the case that LOR writers get extra time to submit their letters beyond the official deadline given to applicants. So it's worth a try, and they may still have 2+ weeks. If your other two letters are strong, a just so-so third letter shouldn't be a big problem. It's quite often the case that students don't have that many strong personal relationships with professors at the undergrad stage and end up with one letter that's weaker than the others.

Don't reply in an email. Find the student in person and ask if they want to go get a coffee with you or something. Then you can talk to them. What you say is up to your personal comfort. For situations like this, I am most comfortable when I stick to facts and be honest. I'll present events that happened without my judgement or how I feel unless asked directly. I think this is the best way to help a new student because a new student may not react the same way to the events as you would (i.e. what's positive to you might not be positive to others etc.). Being honest would also help me feel ethical about doing this. I would never want to mislead someone into thinking a lab is great when I see a lot of problems with it. But, at the same time, I have to keep in mind that maybe these problems are problems for me but another person can do really well in them. So, I will present the facts and events and remind them that I'm telling them my experience. M goal isn't to convince anyone to do anything, but to provide information so that the other person can make a good decision for themselves. Keeping this in mind helps me avoid getting too personal in these types of conversations.

Usually an acceptance to a PhD program will come with a funding package, often for the duration of the program. Funding will be contingent on you staying in good standing and being enrolled full-time, and sometimes some service is expected in return, e.g. work as a TA or RA. The fact that most of your time will be invested in coursework in the first year doesn't matter, you should still be supported. Some programs are set up such that early on you are supported by the department and later you are expected to find a PI who will take you into their lab and fund you from their own grants. Here too, there is always funding from some source while you are a student there. Some students do TA in their first year, this depends on the particular program, and it's not something we can tell you without knowing more. 

The reality is that no one knows the situation better than you yourself do. But I have to say... if it seems dysfunctional from the outside, imagine how much worse it is from the inside. The fact that two students left is a big red flag - students leaving the group is not something that should be taken lightly.

Definitely still apply. Many places don't care that much about the GRE, and the rest of your application sounds competitive. 
If you have time and money to retake it before apps are due, do so. Perhaps think about if you need to revise your studying methods. Also, if the format of the test threw you, definitely use their online practice tests that have the same software (if you didn't do this the first time).

Definitely still apply. Many places don't care that much about the GRE, and the rest of your application sounds competitive. 
If you have time and money to retake it before apps are due, do so. Perhaps think about if you need to revise your studying methods. Also, if the format of the test threw you, definitely use their online practice tests that have the same software (if you didn't do this the first time).

If you are applying to multiple schools, there's no way you could specify this information for each school. Also, that is not the most important part of the proposal, even if it did impact your friend's proposal. I have done the CGSM app twice now, and neither time did I put this information down, and no one recommended it either time as well.
Just make sure your proposal is clear, well-written, and convincing. Those types of methods-section details are not what you should focus on.

Please talk to the ombudsperson before you do anything else. What you should really be concerned about is not so much this one grade and more so your reputation within your program and your relationships with your professors. It's very easy to say or do the wrong thing, and you are obviously upset and worrying a lot, so don't do something now that you will regret later. Even though you were exonerated, the professor who made the allegation may still believe it has merit and may still be upset. You want to get to the point where you agree to have a truce, even if you never speak to each other again, because you stand to lose a whole lot more than s/he does. Be slow and smart about how you go about getting the grade you deserve without creating more tension than necessary. You may be entirely in the right and the professor entirely in the wrong, but s/he still has the power to hurt you by talking about this to other professors in a way that's not how you would like. (Note again: I am not talking at all about blame and who is right, just about what is smart to do.) So, get an outside opinion about the best next moves from someone who actually knows the school and the procedures. If the paper was ruled to be original work and the allegation was that it was too good to be yours, it doesn't make sense that it got an F. You want to bring that up with the ombudsperson, and at the same time talk about how best to mend the relationship with the professor, or at least part on decent terms. Please take care of both; I understand that you worry more about the grade, but in the bigger picture it's the relationship that matters more. 

Numerous hate messages (including swastikas with Hail Trump written) were seen on my campus, both before and after the election, and I live in California. Police are investigating an Islamophobic hate crime at a nearby university as well, and allegedly the assailants spouted pro-Trump messages during the attack.

You know, next time you think that maybe we should give Trump the benefit of the doubt or look for ways to work with him, or that we should look on the bright side, or that he's not as bad at all that, I want you to stop for a second.
I want you to stop, and I want you to imagine you're one of the women whom he sexually assaulted, who came forward to accuse him of sexual assault. I want you to imagine that woman on election night at the moment she hears Trump declared to be the next president of these United States.
Tell her he deserves the benefit of the doubt. Tell her he's not as bad as all that.

Numerous hate messages (including swastikas with Hail Trump written) were seen on my campus, both before and after the election, and I live in California. Police are investigating an Islamophobic hate crime at a nearby university as well, and allegedly the assailants spouted pro-Trump messages during the attack.

If I were in your shoes, I'd do some informational interviews and CV/resume-stalking before quitting the program. Here's why. You said, "I am still interested in doing program evaluation and legislative advocacy to improve the lives of the poor, but do not feel the PhD is needed for me to do those tasks." I would make sure you really don't and won't need the PhD to do the work you want to do before dropping out of your current PhD program. Talking to those doing this kind of work about the skills and degrees needed not only to get in the door but get promoted is a valuable step and one you really should take.
Assuming that you really don't and won't need the PhD, then I wouldn't wait a few more weeks to let people know that you plan on leaving since they may want the chance to make your funding available to another grad student for the spring or it could be that they need to scramble to find someone to pick up your TA assignment. I'd be honest in talking to the DGS or department head about your reasons for leaving, focusing in particular on your intended career path and how the PhD isn't needed for that. 
Also, assuming you had a funded place in a PhD program, you may want to start applying for jobs now so that you have an income source once you exit your PhD program. Good luck!

Numerous hate messages (including swastikas with Hail Trump written) were seen on my campus, both before and after the election, and I live in California. Police are investigating an Islamophobic hate crime at a nearby university as well, and allegedly the assailants spouted pro-Trump messages during the attack.

No, the problem is exactly that the male faculty are friends with the male student, and the male student receives extra benefits from that friendship that the other students do not. This thread is not about discrimination against the female students, it is about the favoritism toward the male student. The favoritism here is gender based, but it could have been easily been based on race, religion, sexual orientation, marital status, or the faculty and the favorite student all being underwater basket weaving enthusiasts. Many people (myself included) believe favoritism in any form is unethical, but there are still significant numbers of people who see no problem with it or even openly practice it as if it were a virtue. 
Favoritism in any setting breeds resentment, frustration and anger among the unfavored, and sometimes even hopelessness and despair. It gives the favored a sense of entitlement to the inequitable allocations of benefits and a lack of appreciation for the advantages they have received that others have not. It also sets up the favored as a potential target for retribution or sabotage. It encourages conflict, breaks down teams, and prevents work from getting done. Favoritism allows the talents, knowledge, and abilities of the unfavored to go unrecognized, unrewarded, and wasted, instead of being put to effective and meaningful use. Favoritism is usually only seen or sensed by the unfavored, seldom noticed by the favored, and routinely denied by those who practice it (although some will boast about it). Those who practice favoritism, whether consciously or unconsciously, eventually lose the trust and respect of the unfavored and anyone else who can see the favoritism and does not agree with it. 
Eigen, I've seen you give good advice in many other threads, but I, for one, do not take any of your advice or statements in this thread seriously... not because you are male, but because you have clearly stated that you choose to show your male students favoritism and will continue to do so. You choose to perpetuate those double standards. The reason why does not matter to anyone but you, because your actions are what make a difference (or not) in your students' lives. Your female students have no choice but to do without, while watching the males reap the benefits you give them. The reason there are those gender-specific support groups is because that outside of those support groups, there are many, many people who think like you do, who are in positions of authority and can grant resources and opportunities as they see fit, and who view themselves as supporting women, even while continuing to give advantages to men and justifying it in ways like you have written above. You are frustrated that you are not viewed as an ally -- why should you be, when you choose not treat your students equally? (Rhetorical question. Only you need to know the honest answer to that.)
Seriously: you cannot show favoritism to men and expect women to believe that you will have their back. Maybe I've been harsh in my statements, but it's because women live with the much harsher reality of favoritism every day. Because favoritism is the root of why there are not more women and other underrepresented groups in STEM fields, not any of the other excuses that people think can be fixed with school outreach programs and whatnot. Because favoritism promotes the success of the favored through greater assistance and opportunities (even simple things like a prof giving you temporary lodging), and the unfavored move on to other areas in search of receiving the same opportunities as everyone else. Unfortunately, many never do get those opportunities.
I really didn't intend this post to be so long and preachy, but I thought someone had to say this. Not that it will actually change anyone's behavior or point of view -- I gave up trying to do that a long time ago -- but at least Pscott and others going through similar experiences can know that some stranger on the internet believes them and understands how damaging these situations are to all involved.

As I wrote a bit about in another thread, I don't think there is a lot of reason for me to worry about my own individual future as an academic. I don't think Trump has a lot of issues on international student status (to him, we are "legal"). I also don't think I will be personally targeted by Trump's policies. The reasons that this outcome affects my decision is my unwillingness to live in a country that seems to be so much more out of alignment with my personal beliefs and my inability to do anything about it since I'm not a citizen. If this was happening in my own country, although it's fun to joke about moving elsewhere, I would definitely stay and do what I can to change things. And that's partially why I would want to leave the US after my degree---Canada is having an election in ~3 years and I don't want Canada to go this way either. I want to be back to do something about it.

The challenge is that lotsssss of research shows that intergroup factors influence raters' perceptions of candidates' qualifications. e.g., men get hired for potential but women based on past achievement; equivalent resumes are rated as worse if accompanied by a stereotypically female or African American name. Put another way, there's probably no such thing as an objective assessment of qualifications and it's better to recognize than minimize group differences.

Here's my opinion. I am not a parent though. But I work with other students on my campus to advocate for better resources for students who are parents.
The CV and Resume is not the right place for this information. While we're on this topic, I know that CVs and Resumes in North America are quite different from European ones. From talking to friends, it sounds like European CVs often include a lot of personal information, like a photograph, martial status, age, etc. In your CVs to North American schools, you should not include any of this personal information, definitely not family status information.
A SOP is generally more academic and research focussed so I wouldn't generally put information about your child there either. If the school cares about aspects of you that are not-academic, then they will ask for a separate "personal history" or "diversity statement". I think this is the best place to discuss the challenges you experienced as a mother and a student. I would only advise putting a sentence or two about your child in your SOP only if it's directly related to your work or your ability to do some work and you feel like you need to explain it. Otherwise I would not mention it at the application stage.