April 27, 2017

Got the green light to write! (And a little about the graduation process)

Filed under: "Me" updates,Grad school,Research — sanguinemare @ 1:08 am
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Today, I had my (hopefully) last committee meeting before my thesis defense.  Basically, I presented the data I had thus far and asked whether they thought I had done enough work to graduate in the summer.  They said yes, praise God!  So I will be defending my thesis in early June, in time for starting medical school on schedule at the end of June (well, actually I found out that the rest of the class actually starts next week, oddly enough, on block “6A”, whereas the end of June one is called “1A”, but anyway…). The timing only gives me a week or two at home before starting back again, but at least there’s a little break, and it gives me an extra two weeks or so to write than I would have had if we’d done it at the end of May (my PI is out of town until early June, so that was the earliest that was feasible).

I’m not sure if it’s the same at all schools, just to walk you through the graduation process a bit, here’s our rough graduation process.  After the committee agrees you can graduate soon, we have to turn in an “application for degree form”, after which the graduate school will give us an approval form that we need to fill out and return to them 2 weeks before our defense at the latest.  This form will be the official confirmation to the school that we are defending, and they apparently put it on a school-wide calendar.  We also have to turn in our entire written dissertation (usually ~100 pages long) to our committee 2 weeks before the defense date so they can read over all the materials in preparation for the defense.  Then, we have our public, oral defense, where we present our work over the last few years to the public, and then we have a private defense after, where the committee decides whether the student has enough proficiency in their area to be awarded a PhD.  If this thesis defense is passed, we then make the final edits to the dissertation and need to submit the written thesis to the graduate school, where I think it gets bound and also put online.

In my program, the thesis itself can be either in the traditional format (an introduction, a body which has multiple chapters describing work done, and a conclusion), or a “3-paper model”, where essentially 3 individual papers are written up, which become chapters in the dissertation, and they are sandwiched between an introduction and conclusion.  That’s the route I’m going, because it seems the simplest way, especially since I’ve gotten one paper published already.

Ok, time to head to bed – tomorrow’s the all-day orientation for MS-3 year (pretty crazy to think that it’s finally happening!) so better get some rest before that.

Until next time!

April 14, 2017


Filed under: "Me" updates,Grad school,Research — sanguinemare @ 1:16 am
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Ok, a very unprofessional title, and about 10 days or so late (now that it’s officially the 14th, at least here), but just wanted to post a quick update that… after staying up until 4am a couple nights re-creating the figures from scratch because for some reason they were apparently not in good enough resolution the first time and the (semi-)quick fix didn’t work… MY FIRST, FIRST-AUTHOR PAPER GOT ACCEPTED (for publication)!!! WHOO HOO, PRAISE THE LORD!  That means I’m all set for non-thesis related graduation requirements!

Oh how easy it is to bring a grad student joy, haha.

Now all I have to do is… revise paper 2, do all the assays and writing for paper 3, and write an introduction and conclusion… all within a little less than a month now, plus a committee meeting in the middle of that.  Whew.  I’ve actually been pulling 13-14 hour days in the lab every day from last Tuesday until Sunday (minus Wednesday for weather concerns), and then averaging around 9 hours every day since. Apparently this is pretty typical during the end-stage – I ran into a fellow MSTP a year below me in the elevator the other day and after relaying my current schedule, and he was like “what are you doing, trying to graduate?” I blinked a couple times at the irony, then replied with a “why yes, actually!” with a bit of a cheeky grin, and he nodded understandingly, saying “ah, the extremely productive final year huh?”  On a bit of reflection, I suppose that is actually sort of true.  Everyone always talked about the last year being the most productive in terms of both experimental data gathering, and paper-writing, and I suppose technically that has somewhat been the case for me as well.  So there you go – “n of 1” as they say, haha!

Just finished organizing all the miscellaneous parts/templates for my thesis tonight.  It’s starting to feel a lot more real now.  Yikes.

Wish me luck!

March 29, 2017

Struggles of a grad student – Part 1

Filed under: "Me" updates,Grad school,Research — sanguinemare @ 1:49 pm

Today was the epitome of Murphy’s law for a grad student – the classic case of needing to order supplies for a key experiment, and the lab not having it… and then not being able to order it due to a series of unfortunate events: the supply center which I’d sent the order in to yesterday is apparently closing and not accepting any more orders –> the other person we place orders from has an auto-reply e-mail saying they are out having surgery and not to place orders until they’re back tomorrow unless it’s an emergency, then contact person b –> person b also has an automated e-mail reply saying they are out of the office today and won’t be responding e-mails until tomorrow –> another supply center that I found out about from the one that’s closing ALSO has an auto-reply e-mail saying they are out of town right now and will only intermittently check e-mail.  *Sigh*  At least that means I should be able to place an order first thing tomorrow, but it also means that’s another day’s delay before I can start the assays.  At least there’s a few other steps (aka days’ worth of work) that I have the resources for beforehand.

Generally this sort of thing can be avoided if 1) there is good communication in the lab (and/or a good lab manager and/or a good system in place so you can easily check the lab inventory), and 2) you plan ahead.  Both are good practices to have so you don’t need to delay your work just to wait on things to arrive.

Sometimes, however, it is not really avoidable, such as in this case, where the study only recently finished, I only just figured out how many samples I had total, and then found out that there’s a 384-well plate machine on the 2nd floor that we are allowed to use that would make my life a LOT simpler (less reagents used per sample and a lot less plates to run: 12 vs. 46)… but the catch is that we’d have to buy the plates ourselves.  So I decided to try to go for that, and that’s how this happened.  Also decided to order some different primers to try based on the literature, and those need to be custom-made and take time, so yeah.  Timing is so tight right now because I have a committee meeting set for the end of April, and the extractions and processing itself will likely take 2-3 weeks of full day schedules, plus analysis time and putting together a presentation (while writing 2 papers and my thesis).  Additionally, I just found out from the lab I was supposed to get my samples from today that because they aren’t getting in the new freezer until tomorrow, I won’t be able to access my samples until Friday afternoon after they’ve re-put everything back where it needs to be.  These are the little day-to-day things that people don’t really think of being part of research, but are snags that will affect how quickly things can be done.

Anyway!  At least the couple days’ reprieve from retrieving and processing samples means I have time to look over the short students’ Letter to the Editor I wrote with a couple students on a side project that just got accepted with minor revisions, as well as to re-draft my 2nd paper, which my PI and I just decided we should expand to a full manuscript yesterday (as vs. the Brief Report we were originally thinking of submitting it as – there are different lengths and purposes of publications, which I might get into in a future post if anyone’s interested).  So yeah, that’s life at the moment!  No rest for the grad student – at least not one who’s trying to graduate in a couple months.

Catch you guys later!

March 24, 2017

Just sent in my revision for my first paper! (And why that is a big deal)

Filed under: "Me" updates,Grad school,Research — sanguinemare @ 4:12 pm

HELLO all you lovely people (aka the 1 person who may actually see that I have finally posted after months of hiatus)!  I’m so sorry for dropping off the face of the planet, but well, PhD life is somewhat of a struggle and between that and battling long bouts of depression, it’s been difficult to drag myself up to write something substantial like this.  (I have also come to realize that I think almost all graduate students go through a mini existential crisis/period of depression before it’s over, unless they are extremely lucky and really love their work, mentor, and are extremely fortunate in their ability to generate and analyze data, but that is a story for a different day… if I ever get around to it, haha).

… and now that I actually revisited my last post, I realize I have somewhat reiterated myself, so I guess not much has changed over the last… 7 months?  Haha whoops.  Oh well.  Also apologies in advance for the somewhat incoherence of thought on this post as my brain is currently rather fried.


So I literally just clicked “submit” on my revision for my first paper.  This is a big deal for multiple reasons:

  1. It’s a graduation requirement. Of course, this is my first priority right now, so it gets to be first on this list 😛  As a graduate student, at least in the biomedical sciences, we are usually required to have at least one paper published under our name before we are allowed to graduate.  This is because, as I’ve mentioned in my last post, publications are essentially the “currency” of academia, and programs want to help their students show that they are competent and competitive in the scientific world, which will help with their upcoming job search.  The slightly less altruistic reason is that it also reflects well on the department/program/school/institution if they can show that a significant portion of their graduate student population are publishing good papers in peer-reviewed journals (important statistics for funding purposes).

    The publication requirements will vary based on said department/program, school (i.e. school of health professions vs. school of bioengineering) and institution, but my particular one requires at least 2 papers published before graduation, with at least one being a first author paper (*note: review papers – which are essentially summaries of a particular topic based on research that has already been published – do not count towards this second stipulation).  The paper that I have just turned in is my first, first-author paper, and thus is super important to get accepted since I am trying to graduate in May/June, and it has so far seemed to take an average of 2 months for responses from journals, which means timing is really tight right now. Speaking of which…

  2. Revision = higher chance of acceptance (?). Considering this is my first experience with submitting a manuscript, I’m not entirely sure how accurate this statement is, but from what I gather, a revision decision is usually a positive sign for a manuscript to get accepted into a journal for publication, especially if the revisions are minor.

    To give a little walk-through of this whole process thus far, I first started the analysis for writing up this paper a little over a year ago, ~Feb 2016.  The first complete draft was written by June, and after many (many) revisions, we finally submitted this article to a journal in August.  We waited for a long two months, during which one of my co-authors casually mentioned that perhaps it was actually a good sign we hadn’t heard in so long because she had also submitted to the same journal a couple weeks later and had already gotten a rejection letter.  She was right in a way, because in October, we got our paper back with reviewer notes, which is better than an outright rejection since it means that the editors thought it was at least interesting enough to send out to reviewers.  However, the journal ultimately rejected it after the review, though they did give us an option to do an internal transfer to another of the journals in their group.  We took that option and I did revisions based off of the reviewers’ comments.  We then resubmitted it to the new journal this January (there was a brief hiatus on this work as I was out of the town/the country for a little over a month between Nov-Dec).  After waiting another 2 harrowing months, we finally got the decision letter last week, which basically said they thought it was interesting, but reviewers had concerns which made it unacceptable at the present moment. Hopefully that means it will be acceptable after the changes…?  So I made the changes, and sent it in today. (Though a slightly concerning note at the bottom of the letter said that any decision after the revision was final, which induced a minor paranoia as I went to click the submit button earlier today. Heh).  Here’s to hoping it gets accepted!  Which brings us to the last point…

  3. (If accepted =) it’s a milestone as a scientist/researcher.  I kind of alluded to this above, but basically, having a first-author paper in a peer-reviewed journal helps to establish your worth to the scientific community.  The first author is the one who has generally been involved in all the aspects of the study, including conception/design of the study, conduction of the experiments, analysis, reading of the background literature, and writing the manuscript. Thus, in a way, a first first-author paper establishes the level of work others can expect from the author in the future, and is thus like a debut of sorts into the scientific world.

So yeah. In a nutshell, that’s why I’m actually quite happy with myself/life for once, and will likely take this weekend to celebrate (some of us in MSTP are going to Six Flags for a day!) before the massive freak-out session starting next week about how I only

Thanks for reading and see you on the other side (after my defense)!

August 31, 2016

Publishing and Reviews

Oh man, I can’t believe it’s been almost an entire YEAR since I last published here!  I’m so sorry… there’s been a lot going on, and also I’m fairly certain I’ve been actually depressed for the last year or so and only very recently started perking up a bit (like literally a couple weeks ago) so that’s probably part of the reason… PhD life and its ups and (mostly, at least in my case) downs, an unexpected and lengthy authorship battle… etc etc… so it was hard to find anything positive to write about, and/or to summon enough energy/brainpower to write about anything at length in general.  But that’s fodder for another post.

Today what I’m going to write about (briefly) is publishing!  Yay, publishing… the currency and lifeblood of the academic.  In case you weren’t aware, basically what, where, and how much you publish is an important factor for your career, mainly because all the people/agencies with money (institutions looking to hire you, government/other organizations looking to award grants) use it as a kind of surrogate measure of your scientific worth when evaluating whether or not to hire you/give you money.  In a way, it’s like judging you based on your contribution to society’s advancement, which I guess is fair, especially if you’re using, say, government funds to help your research. Where it gets a little tricky however, is when you get into the question of where the articles are being published, and whether quantity > quality, and that’s different for everyone.  There’s a whole discussion to be had about the Impact Factor of journals (which itself has some controversy based on how it is determined), but that might have to wait for another time.  In terms of quantity vs quality, from what I gather, I think (a very big emphasis on “think”) the general consensus is that quality is of course important, but publishing regularly (at least every year or so, even if it’s only a review paper) is highly desired because it shows consistency. Which is bad news for someone like me, who hasn’t even had a single (first author) publication yet, and it’s already my 4th/last year in the program (hopefully anyway), heh.

At any rate, after you submit your paper for publication, assuming it isn’t rejected outright, it goes to a couple reviewers.  These are usually other scientists, usually in a related field of study, but sometimes not.  They review the paper and help the editors of the journals determine whether the paper is ready to be either 1) accepted as is, 2) accepted with revisions, or 3) rejected.  The first two options are obviously preferred 😛 but if it needs to be revised, the manuscript authors need to address all the reviews (either by doing more experiments or rebutting with explanations why they don’t need to), and resubmit.  This process I hear can take anywhere up to a few weeks to a few months!  I just submitted my first PhD-related paper a couple weeks ago, so will try to update on how that process goes after I hear back.  It is currently in the “under review” status (so at least that means it wasn’t rejected outright, hopefully!)

Anyway, what actually prompted this post was that I got an e-mail from the director of the pre-doctoral training fellowship I’m currently on as a follow-up to a discussion we had about hosting a seminar for all the trainees to learn how to review a paper (something we will all be called to do as scientists in the future).  It was quite an amusing article on how to review papers by Greg Gibson, who apparently was a section editor for PLoS Genetics for 10 years, which exemplifies the type of feedback that was often receive from these things… and really, now that I think about it, it must be pretty difficult to have to constantly make executive decisions as an editor as to whose review gets the most weight if they are this scattered, haha!  But anyway, just wanted to re-post that all here for you guys in case you’re curious how these things work.

Until next time!  (Which will hopefully be less than a year from now! ^.^||)

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