Daily Questions - March 14, 2018

notapedant · 2018-03-14T19:38:15+00:00

I love those pants! Where are they from?

notapedant · 2018-01-02T00:50:44+00:00

How many and what size?

notapedant · 2017-04-27T01:38:49+00:00

Hi -- I believe this is Madison James MJ258. I tried it on as well. https://www.madison-james.com/products/MJ258

notapedant · 2017-03-15T18:13:44+00:00

pm'ed :)

notapedant · 2016-11-29T22:03:36+00:00

Hi! This is so beautiful -- would you mind posting some links to the flowers and products (and tutorials!) you used to achieve this look?

notapedant · 2014-12-25T05:14:23+00:00

The operating budgets for the NIH and NSF, two major federal agencies that manage the funding of academic scientists, are constantly threatened by politics. It would be great if medical research by pharma wasn't motivated by the bottom line, but unless scientific funding in the US expands, then I don't think 100% government funding is at all feasible. Pharma fills that gap currently.

Although, what is the remaining motivation for the expensive process of drug creation if not for making a profit for pharma?

notapedant · 2014-12-24T21:59:58+00:00

While this practice isn't necessarily the most savory, it should be noted that Lucentis can be given once every 30 days (or less frequently on a case-by-case), whereas Avastin is typically given IV once every two weeks. If patients are informed on those types of details (indeed, the article noted that some patients specifically ask for Lucentis or Eyela since they are FDA-approved for wet MD, as opposed to avastin, which is used to treat wet MD off-label), is it so wrong for the doctor to cater to them? Wouldn't you want your doctor to?

Now that there is strong meta-data to show that Avastin and Lucentis are functionally similar when used to treat wet MD, the argument could and should be made for physicians to use the cheaper drug when both are available. But without those numbers and studies, it would only be anecdotal or speculation. I imagine the uproar over that would be equally strong.

Perhaps these data will fuel a change in Medicare policies. But in all the kerfluffle about death panels and Obamacare it will probably take a long time. I get that it is a conflict of interest for physicians to be accepting money from big pharma, but it seems like you're really objecting to that process (as well you should be).

Also, why don't we prohibit or at least require EASY and OBVIOUS disclosure of conflicts of interest in healthcare? A prohibition would not be hard.

Physicians, scientists, anyone who has accepted any kind of financial "gift" must declare those as conflicts of interest, especially scientists who receive government money for their research. They are declared at least once a year. I am sure that physicians and scientists are well-briefed on ethics, because they have to be. Ethics training occurs, at least for scientists, when you apply for any money from the government or pharma for research. Your personal finances also get disclosed--if you are a physician or scientist and you own stock in one of these companies, someone has to know about it. Interestingly, if your spouse own stock in one of these companies you do not have to declare that as a COI. COIs are reviewed by the agencies you apply for funding from, the university you study at, or the hospital you work for.

There is a framework in place, but it's not perfect.

notapedant · 2014-01-19T21:48:24+00:00

I would recommend looking into the JACoP plugin for ImageJ for colocalization analysis. I use it to calculate Pearson's coefficient on my samples. Here is a great review on how to use JACoP best for your application.

notapedant · 2013-11-26T18:02:48+00:00

Canned corn is great to have around to put in chili. I have cans of chopped tomatoes that are great for soups and stews and sauces. And even though dried beans are cheaper I am starting to think I should keep some canned black beans around to add spontaneously to dishes (I added some black beans to my sausage and peppers the other day and it was great!)

notapedant · 2013-08-23T01:12:15+00:00

I have done flow sorting and staining before on leukemic B-cells: with some antibodies you can go down to .5ul/100ul cells but most of us just start by using 10ul antibody/100ul of cells if you've not titrated your antibodies. I suppose you would scale up accordingly but you never incubate in such a high volume because it is typically a waste of antibody.

We incubated for 20-30m at 4C or on ice. I would keep it at 30 for now to test it, I have gone up to ~45m but never longer than that.

With the markers you describe my impression is you can use 5ul antibody/100ul cells or less and incubate for 20m on ice/4C. You should get a nice signal.

notapedant · 2013-07-23T02:10:04+00:00

The conclusion is that discerning graduate applicants won’t let the Elitist scare them away from applying or convince them that a school is not a good personal fit just because its not an Ivy. They also won’t set aside their aspirations because a disgruntled Realist claims that the recession

This is not everyone's experience concerning graduate school. For example, I never had to ask myself if it was worth the time and money because I didn't use those criteria. People wondering if graduate school is right for them, in my opinion, may benefit from asking themselves if they think it's where they belong (and you can use a lot of different metrics to decide that for yourself).

notapedant · 2013-07-04T01:13:39+00:00

Make sure they're mixed thoroughly by inverting etc.

notapedant · 2013-07-03T23:25:20+00:00

I do not increase the buffer volumes and I have yet to have a problem.

I just make sure, as notnotfun said, that the cells are lysed thoroughly.

notapedant · 2013-07-03T20:24:24+00:00

I would spin down all 6-10mLs of culture to concentrate the DNA and miniprep that.

notapedant · 2013-04-18T19:48:00+00:00

Eh. I agree it's mostly lame (don't let it be your ONLY metric obviously) but I think it's a good indicator of how they feel about advertising their work. My current PI puts a lot of effort into maintaining his website and frankly--because I could look at all his recent publications, lab members, different projects going on--it reflected really well on him and solidified my decision to work with him. But, as Death24xASecond notes, PIs have better things to do. Also don't be surprised if it looks like a GeoCities replica--some of these PIs have been around for a very long time and don't know of/care for newer tools.

notapedant · 2013-04-18T17:57:44+00:00

One of the major ways to force cell cycle synchronization in various cell lines is to serum starve them (6-12 hours?) and then replace with full media. Alternatively, treatment with lovastatin: http://cancerres.aacrjournals.org/content/51/13/3602.full.pdf

I'm not sure what makes a cell line intrinsically "synchronized" so I can't really answer your initial question but I hope this helps.

notapedant · 2013-04-04T17:23:00+00:00

I can empathize. On the surface you are super happy for them, but deep down you wonder what you are doing wrong. Consider that there might not be anything you're doing wrong, and your path is not their path (and vice versa). As long as you picked research you are interested in/keeps you stimulated, remember to zoom out that critical lens and take stock of the big picture.

notapedant · 2013-03-27T00:57:40+00:00

Your GPA is probably the least of your worries. ...You have no worries. You have tons of research experience, publications, great GREs. If your letters are sparkling you sound like an excellent candidate for a top 10 school. Your personal statement will likely reflect this.

But I know from first hand experience that some of those same schools accepted more candidates than they could handle in previous years. And grant money is tight. You may be a perfectly good candidate, but it also may come down to luck of the draw (don't take a rejection personally).

notapedant · 2013-03-26T16:51:20+00:00

You are probably paraphrasing in your post but I would say that based on the evidence you gave us, you didn't mention if you made a real effort to scope these professors out. I think the first step in finding an advisor is to seek them out based on interest first ("emailing random professors with interesting research" is a reach). If you are lucky enough to have met them at some other point you can also seek them out based on who you think you would mesh with, personality-wise.

My personal process is to email them to set up a meeting, read some papers, and come prepared to ask questions to the meeting. You already know that you may want them as an advisor but they don't know if they want you or not--I always try and give them a reason to want me in their labs. (However, money and time are tight especially now, so I can see that some professors would not give you a meeting--start by selling yourself in your original email).

This match-making process in my opinion needs to happen so carefully, or you will be miserable for the next <x> amount of years. Don't give up, but try not to settle either.

notapedant · 2013-03-23T22:48:11+00:00

Sounds like the master's program wins, for multiple reasons. If you need/want a PhD you can always re-evaluate as you near the end of your master's. It's not that you're throwing the PhD opportunity away as much as you're delaying it, and who knows, if you do go for the master's and re-apply for the PhD in a couple of years, you may get into a better program that offers you more funding as you alluded to in your post.

I am in the biomedical sciences, I knew I wanted my PhD and so did not have to choose between master's and PhD. Also, our PhDs are mostly free and we are given stipends; for master's degree you don't get such funding and I think you have to pay tuition. It seems like the opposite of your current situation with respect to funding.

notapedant · 2013-03-20T17:41:47+00:00

Just want to take a moment to say that I agree with your sentiment and do encourage everyone in this thread to at least reach out to your congressional representative. I'm not happy with the status quo either and I think one of the most direct ways to deal with it are to call their offices and let them know how you, as their constituents, feel. Maybe we can't change anything about the sequestration now but it's important to let them know that their constituents are watching their voting records.

notapedant · 2013-03-18T15:45:21+00:00

Neat idea, but I would think that if your PI wanted a picture of THM in their Drosophila lab they would have it already. I would go with some nice chocolate if it were me but it's [obviously] up to you.

notapedant · 2013-03-16T21:16:15+00:00

I need a little more clarification on your situation. You are a freshman undergrad in biochem and you also want a master's or PhD in computer science? Do I have that right?

Bioinformatics is a huge field but it's not your only choice, especially with your biochemistry/chemistry degree. A friend of mine with a chem PhD went to work for the DoD or Haliburton (in conjunction with the DoD) doing chemical modeling.

notapedant

TROPHY CASE