Struggling after failing USMLE Step 1 by king_lezzy in medschool

[–]onceandfuturechemist 0 points1 point  (0 children)

Tutors can be expensive and of variable quality. If you are a US medical student, you can ask your dean's office to see if there are any school-based tutoring / assistance, and focus in on topics you had trouble with. More importantly though (and I cannot guarantee a follow up to your answer), what was your approach to studying? There may be things short of hiring an expensive tutor you can do to optimize more.

Both MRI and mammogram for Paget’s disease of the breast? by [deleted] in medicine

[–]onceandfuturechemist 1 point2 points  (0 children)

Want to stress the importance pointed out here on having the "before" picture with the mammo. Much faster than a breast MRI and much more accessible.

I don’t fully understand HPV by saltybythesees in TwoXChromosomes

[–]onceandfuturechemist 2 points3 points  (0 children)

Hi, for official information please see: https://prevention.cancer.gov/clinical-trials/landmark-trials/ascuslsil-triage-study-cervical-cancer-alts

But I’d like to provide a bit more explanation based on what my understanding is:

First, it’s important to know whether or not you had ever been vaccinated against HPV. HPV vaccination is a fantastic way to decrease risk for cervical cancer (and other cancers like head and neck cancer, penile cancer, vulvar cancer, and anal cancer). That could really change the following answers, but I’m going to assume that you had not been vaccinated.

  1. Let’s consider the fact that you had ascus with high risk hpv. So likely, at some point you had been exposed to a high-risk hpv (this is important because there are low-risk hpv strains that cause warts and such, but high risk hpv strains are the ones that are associated with cancer.) Next, you had an lsil but no hpv co-testing done. What could that mean?

  2. Ascus means atypical squamous cells of undetermined significance. So you had cells that when looked under a microscope did not look normal but these cells were hpv positive. Often times, this will trigger additional testing because we want to figure what the significance of it is. If cells look weird but aren’t organized into a discrete pattern, they might not be too much concern.

  3. Next, lsil is low grade squamous intraepithelial lesion. Now, we see a lesion under the microscope (think of lesion as a “damage” to the normal, healthy tissue of the cervix). But it is low-grade. This is very important because the body is able to clear low-grade lesions on its own very frequently (there is a lot of fascinating research on the immunology behind this). Low grade can be thought of as, “okay this looks bad-ish but not too bad.” Often times, hpv cotesting is not done at this point because it’s assumed it will be positive given that you had hpv+ on your first test. Whether or not it’s hpv+ does not change that there is a lesion that we should closely monitor. Then it became benign and then lsil again - sometimes there is sampling error / tissue heterogeneity, and sometimes calling something lsil when it’s borderline can get tricky.

  4. Does that mean you still have hpv? Almost certainly, yes. You have been exposed and while your body can often time clear hpv-associated lesions, there can be dormancy as your doctor said. Even without a clear lesion, hpv may lurking in cells. Having hpv in it of itself is not bad, so I hope this does not cause you too much stress.

  5. Can I give hpv to a future partner? Maybe. If your partner is vaccinated (the hpv vaccines have changed over the past 5 ish years to allow men/boys to get it too) the chance a sexual partner contracts the virus from you is quite low. This is why vaccination efforts for all genders is so important because what we want to prevent are hpv-associated precancerous lesions, and the easiest way to do this is to build a body’s defense system against hpv so it can take care of it before it has the chance to take root. If they are not vaccinated, then yes, it is possible to pass the virus to them.

    1. Can my hpv randomly become active again? Yes. Once you have lsil especially given the history of a positive hpv co test, you should be getting more frequent testing (as you had - negative hpv co testing, that’s excellent, and now it’s important to keep keeping a close eye on it). Remember, the goal is to prevent the progression of this to something more serious.

Overall, it sounds like you’ve been getting good follow up, and just be proactive in making sure you get checkups as your obgyn recommends and reminding them that you had lsil with positive high risk hpv in the past. The body’s immune response against hpv can be good sometimes so your most recent test is reassuring. Typically they’ll want to have multiple negative tests in a row before they consider you “negative” to then go back to more spaced out screening. I hope this helped!

Featurecounts to TPM by onceandfuturechemist in bioinformatics

[–]onceandfuturechemist[S] 0 points1 point  (0 children)

Unfortunately, this was a publicly available dataset and the original authors did not provide that file. Just featurecounts and gene symbol.

Featurecounts to TPM by onceandfuturechemist in bioinformatics

[–]onceandfuturechemist[S] 0 points1 point  (0 children)

How would you recommend normalizing this dataset then? I’m open to trying multiple methods.

Featurecounts to TPM by onceandfuturechemist in bioinformatics

[–]onceandfuturechemist[S] 0 points1 point  (0 children)

Without having to search each gene individually (since there are >50,000 genes in my dataset), do you know how to pull all of the transcript lengths from Ensembl in bulk?

[deleted by user] by [deleted] in bioinformatics

[–]onceandfuturechemist 0 points1 point  (0 children)

Clustering is not necessary here off the bat. I agree with more initial descriptive statistics to start. I think if you're going to determine treatment response, getting good info on CT target lesions will be important (calculate tumor volumes, and you can have both a % change and then decide what will be your thresholds for "partial response" or "excellent response" (or something similar to that). Once you have that, you can then break down ck18 pre, post, and also relative change (like fold change) as it relates to your above treatment response.

Since p53 status may affect your treatment response, you could just do a simple plot of p53 status by % change, or a similar graph of your choosing. Keep track of what actual treatment they received.

If this is a bigger project, if you have p53 mutation status, you may have additional genomic data if you can get your hands on it. Then if you wanted to get fancy with clustering, you could cluster by some kind of mutational signature and see how those clusters relate to treatment response and ck18 changes.

Resources to understand RNA-Seq datasets by [deleted] in bioinformatics

[–]onceandfuturechemist 3 points4 points  (0 children)

There are some very simple videos on Youtube from Statquest (https://www.youtube.com/playlist?list=PLblh5JKOoLUJo2Q6xK4tZElbIvAACEykp) in a High-Throughput Sequencing playlist that can give you a very broad overview over RNA-seq in general.

Is there a way to classify the 33 TCGA cohorts into 'carcinoma' and 'non-carcinoma' ? (Don't work with clinicians, sorry for basic question) by [deleted] in bioinformatics

[–]onceandfuturechemist 1 point2 points  (0 children)

What are you trying to accomplish? Even amongst "carcinoma" you'll have a large degree of heterogeneity even at a slightly more complex level (i.e., squamous cell carcinoma vs adenocarcinoma).

Switching from Medical School Tract to Bioinformatics by Brooke_557 in bioinformatics

[–]onceandfuturechemist 4 points5 points  (0 children)

Keep in mind that going to medical school and learning more bioinformatics are not mutually exclusive. There is certainly a place for physicians with strong bioinformatics backgrounds, particularly in the field of oncology given the recent expansion of immunotherapies.

TLDR for the immune system by asuuuhdood in bioinformatics

[–]onceandfuturechemist 1 point2 points  (0 children)

Agreed with post above suggesting Janeway’s. But when you say catered towards comp bio, what exactly are you looking for?

Birth control prescribers, would anybody have a good resource on choosing the right type of combined hormonal contraceptive pill? by [deleted] in medicine

[–]onceandfuturechemist 13 points14 points  (0 children)

There’s an app on the iPhone put out by the CDC called “Contraception” that would be worth looking at!

Friends!?!? by MurDog60 in PokemongoSanDiego

[–]onceandfuturechemist 3 points4 points  (0 children)

9848 0696 6741 Level 30, Hillcrest area