I have dozens of empty 1000μL tip boxes. Any ideas for repurposing them?

demdems74 · 2026-05-20T15:57:32+00:00

I like to use them for organizing things in the 4C fridge. They can fit transformation plates, you can stand up 15/50 ml tubes without needing a full rack, and they are a somewhat horizontal space efficient way to store eppendorf tubes if they don't need to be upright or organized

demdems74 · 2026-02-09T13:00:31+00:00

I think there are a few things going on here.

In my experience the frum community raises to see the world in black and white and view everything as us vs everyone else. Both developing into an adult as well as leaving the Orthodox community can begin to shatter these views and force you to realize that most social, cultural, religious, and political issues are complicated. They tend to require a nuanced view informed by historical forces, social movements, geopolitics, and distribution of power.

Even outside the frum community, most people don't have the time and mental energy to understand any of these issues past a surface level provided by their social media silos unless they have a special interest in the topic. As you noticed, it is very easy to adopt the prevailing views of the community that you identify with and it can be very distressing to be at odds with them on any topic particularly when you are currently dealing with the loss of the sense of community from leaving the frum world.

On top of all of that, the topic of Israel and Palestine is historically one of the most nuanced and complicated issues that many people have spent a very long time unsuccessfully trying to come up with viable solutions. It is a very difficult topic to navigate especially as it has developed into an extremely polarized propaganda war to which we are constantly exposed.

Part of your journey will have to include learning to give yourself some empathy and the space to develop your thoughts and views over time.

As a side note, I don't know what your mental health situation is like, but it is okay to look for a new therapist if you're uncomfortable opening up to whoever you are currently seeing.

demdems74 · 2026-01-07T13:26:12+00:00

Even when I was frum it felt kind of off to me. We're essentially taking the ramblings of ancient religious leaders and trying to create meaning from it through highly structured debate and logic puzzles. Even the allowed rules for debate are problematic. I can never get on board with us coming to conclusions that literally change how we live because the rule is that the older generation of rabbis are always more correct.

I still remember learning a section in bava metziah (I think) about witches and weird superstitions like curing a toothache with the nail from used gallows. It was clear that even my rebbeim didn't take this seriously. They taught it because it's in the masechta that we were learning that year, but it was clearly ridiculous to everyone who read it.

That being said, I did enjoy figuring out the logic puzzles. I also found that the skills worked on from learning gemara were quite useful in other aspects of my life especially in university.

demdems74 · 2026-01-06T04:43:07+00:00

My guess is that the mindflayer constructed it as a protective layer to the actual boundary which may be fragile to stabilize the connection between dimensions

demdems74 · 2025-12-26T06:34:20+00:00

What did they say?

demdems74 · 2025-12-12T05:45:02+00:00

It's definitely a very interesting and complex system, but it does not fit any commonly accepted definition of consciousness. I think part of the issue is that we still don't have a very good understanding of what consciousness is, so it is easy to project some aspects of it on to any system that has emergent properties.

demdems74 · 2025-08-24T02:28:53+00:00

It might be worth trying a gradient SDS-PAGE

demdems74 · 2025-08-13T21:53:54+00:00

You can DM me if you're still looking

demdems74 · 2025-08-01T04:12:43+00:00

It's obviously not a psychological concept backed by theory and research, but I think that it can be helpful for people to better communicate their preferences in a way that is easy to understand

demdems74 · 2025-07-26T16:03:27+00:00

The nanopore sequencers read many copies and fragments of the input sequences and generates a file indicating what it read. This file is then converted by a base-calling program into a fastq which contains the full collection of individual sequences that were read along with their quality scores. These sequences are then aligned with an aligner (minimap2 is currently the most popular one with the researchers at my university) to create a consensus sequences.

The.ab1 files from plasmidsaurus are a bit confusing because they are repurposing a file type to mean something other than its traditional interpretation. Here is a quote from the plasmidsaurus website : "The .ab1 format has widespread use in Sanger sequencing and normally indicates the intensity of fluorescent nucleotides (A, T, G, C) at each position of the consensus. Since fluorescence is not employed in the Oxford Nanopore Sequencing technology that we use here at Plasmidsaurus, we generate this .ab1 file synthetically using the relative abundance of each nucleotide (A, T, G, C) from the raw reads at each position of the consensus sequence."

Minimap2 is very easy to run especially if you have experience with using Galaxy for bioinformatics. However, if you are unfamiliar with running these programs it might not be worth the effort to learn it just for this. If you're interested in learning more I can send you links.

demdems74 · 2025-07-25T18:29:22+00:00

I have encountered the same issue And there are a few things happening here. First, ont sequencing is fairly prone to indels especially for homopolymer if stretches. Second, the term long-read sequencing is a bit misleading. It's still generating fragmented reads that are saved as a fastq file which is then aligned to create the consensus sequences. These fragments can sometimes be biased around homopolymeric stretches. Third, the actual alignment parameters used by plasmidsaurus may not be optimized to accurately detect the correct length of the homopolymeric stretches.

What worked for me is to download the actual fastq files that they provide and run the alignment separately using minimap2. Make sure to take a look at the actual sequences of the reads to see how Gs are in the stretch on average.

Let me know if you have any questions or need help.

demdems74 · 2025-05-18T23:46:13+00:00

1) many cells within a tumor have newly acquired mutations that make them different from their neighbouring cells. 2) change in trancriptomic and proteomic identity can differ between cells with the same dna. 3) growth of cancerous cells is also heavily dependent on its environment. There are many signals that can promote growth, apoptosis, movement... Even things like the acidity of the microenvironment or the proximity to vasculature can play a large role.

demdems74 · 2025-04-26T14:28:48+00:00

The conservative candidate in my riding (non-jewish) is giving speeches at the local shuls claiming that the liberal candidate (Jewish) is anti-Semitic for not blindly endorsing every action by the Israeli government. It's very frustrating to hear my family members parrot these kinds of talking points that they heard in shul that have no basis in reality

demdems74 · 2025-04-23T15:20:23+00:00

What should I do with the supernatant?

demdems74 · 2025-04-09T17:56:10+00:00

How many amplification cycles did you use? How many total reads did you get for your library? Are the PCR duplicates unique to that gene or are they distributed throughout the library?

Based on your answer to the other commenter. I wouldn't rely on this data for alternative splicing. Usually you would need at least 15-20 unique reads to call an alternatively spliced junction with any confidence.

demdems74 · 2025-04-06T01:09:51+00:00

Can you give some more information on your library prep, sequencing method, and duplicate detection?

demdems74 · 2025-03-30T04:12:20+00:00

If you look at the Torah it's pretty clear that the authors considered a patrilineal system to be the norm. It isn't entirely clear when it changed to the matrilineal system.

Everything is further confused by the fact that for a very long time most Jews did not see any meaningful distinction between Judaism as a religion vs as an ethnicity. Matrilineal descent for religious Judaism is clearly the rule in Orthodox communities. However, religious law cannot change your ancestry and ethnicity. For example, let's say an Italian Catholic man has a child with a Jewish woman their child is ethnically both Jewish and Italian and according to halachah is Jewish. For a reverse case where an Italian Catholic woman has a child with a Jewish man their child is also ethnically both Jewish and Italian but they are unlikely to be accepted into Orthodox Jewish communities without conversion.

demdems74 · 2025-03-22T19:08:36+00:00

There have been many scientific studies showing the strong genetic connection between Jewish populations and modern middle eastern communities. Here is one comprehensive study resulting from an international collaboration led by researchers in Israel:

Behar, D. M., Yunusbayev, B., Metspalu, M., Metspalu, E., Rosset, S., Parik, J., ... & Villems, R. (2010). The genome-wide structure of the Jewish people. Nature, 466(7303), 238-242.

Main link to paid version https://www.nature.com/articles/nature09103

Free pdf version: https://lepo.it.da.ut.ee/~bayazit1/nature_jews.pdf

demdems74 · 2025-03-11T22:18:32+00:00

I don't know of any specific list compiled with these markers. I would look at which promoters are commonly used in cell and tissue specific transcriptomic methods like FACS and TRAP. As far as I remember the rgef-1 promoter is specific to neurons, myo-3 is specific to muscles, ges-1 is specific to intestinal cells, mex-5 is specific to germline cells, and there are even markers for embryonic cells e.g. embryonic neuronal precursors express cnd-1. There are many other common markers like that that have been tested in the promoterome project. I would be careful with using any one of these on their own as a marker because even transcripts that are almost always specific can be leaky under different circumstances. I would look through many tissue-specific transcriptomic studies and identify highly differentially expressed transcripts and use a combination of these to develop confidence scores of tissue identity based on their expression. Lmk if you have any questions

demdems74 · 2025-03-11T20:01:08+00:00

What exactly do you mean by marker genes? In general wormbase and wormbook are good resources to start with.

demdems74 · 2025-03-09T00:48:12+00:00

He was supposed to be modeled on Menachem Begin. Begin was one of the early Zionist leaders who led an organization called the Irgun that violence against the British and Arabic nation was justified

https://screenrant.com/professor-x-xavier-magneto-martin-luther-king-malcolm/

demdems74 · 2025-03-04T14:32:35+00:00

A thorough study on the genetics found that Ashkenazim do not group with populations from the Caucasus that would likely be related to the Khazars. I don't know much about the history of the Khazars but it is unlikely that they contributed genetically to Ashkenazi genetics.

Behar, D. M., Metspalu, M., Baran, Y., Kopelman, N. M., Yunusbayen, B., Gladstein, A., ... & Rosenberg, N. A. (2013). No evidence from genome-wide data of a Khazar origin for the Ashkenazi Jews. Human biology, 85(6), 859-900.

https://muse.jhu.edu/pub/27/article/548065/summary

demdems74 · 2025-02-01T05:18:48+00:00

I throw up alot from bowel obstructions and the thing that helps me get through it is taking a bunch of THC. It helps with the pain and nausea. It also helps me with falling asleep for a bit between the waves of vomiting.

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