56 Matching Annotations
  1. Feb 2020
    1. Desk Set (1957) is a delightful Tracy-Hepburn comedy about automation and information technology. 

      Love this one. Never thought of it as future forward before, but certainly is!

  2. Jan 2020
    1. In the far future, the [human group] fights a pitched battle against the mighty [alien name] Empire, but deep in the mysterious [region of space], among the ruins of the past, a darker threat looms."

      If I could write a short story or even a novel using only annotations (and info on the web pages themselves, like setting, plot developments, clues)! Might be fun! What cool uses can you think of?

  3. Oct 2019
  4. Jul 2019
    1. he active participation of RBPs in regulated gene expressionmay be pertinent to an emerging concept of phase separationduring gene expression


  5. May 2019
  6. Mar 2019
  7. Jan 2019
    1. arrier bag rather than weapon of domination,

      I need some clarification here. What does Le Guin mean when taking about writing sci-fi in relation to a carrier of words and weapons?

    1. “Well, they believe that when they have listed all His names — and they reckon that there are about nine billion of them — God’s purpose will be achieved. The human race will have finished what it was created to do, and there won’t be any point in carrying on. Indeed, the very idea is something like blasphemy.”

      Sci-Fi Stack Exchange has a good thread on what this story signified https://scifi.stackexchange.com/questions/102956/what-does-the-end-of-nine-billion-names-of-god-signify

  8. Dec 2018
    1. , Octavia Butler

      I discovered Octavia Butler when I was living in New Zealand doing my dissertation research (first stop at research locations was always the public library) and found Kindred on the shelf. I then read the Xenogenesis trilogy, which I just discovered was published as Lillith's Brood.. As a foreign visitor in a mysterious land, both the time travel and the alien visitation appealed to me.

  9. Sep 2018
    1. Reading this article might spark hypotheses as to how intron retention might have regulatory function....

      I find this a great systematic review of how introns appear in the different phases of transcription and how they are found (or speculated) to be involved in amy aspects of :

      • localization
      • timing control on negative feedback loops
      • variable frequency sensitivity in birds
      • marking for transport to nuclear membrane
      • how EJC > 50nt downstream of PTC might be marker for NMD
    1. We then devised a measure of co-transcriptional splicing for each exon by calculating the difference of intronic read coverage at the 3′ and 5′ ends of the flanking introns
      • novel readout to me. Q; is there a gold standard for measuring extent of co-transcriptional splicing (CTS) and is CTS propensity a thing (i.e. is CTS boolean or continuous for a given splice unit?)
    2. Nascent transcripts at different stages of formation throughout the intron generate a gradient. The fact that this slope spans across individual introns, rather than across the entire transcript, can be explained by co-transcriptional splicing.

      Raises question: by this argument, might lack of such a gradient be taken as intron retention as opposed to co-transcriptional splicing? How to distinguish?

    3. Intronic RNAs were abundant in brain tissue, particularly for genes involved in axonal growth and synaptic transmission

      we see similarly in our analysis of genes having > 25% intron retention in wildtype+naive

    1. Finally, the fact that many IRTs are subject to NMD adds an additional layer of complexity, as the gene may be observed as expressed at a lower level due to the specific degradation of IRTs

      I do not expect there is a bioinformatics approach to account for this. The article does not suggest a bioinformatics approach for normalizing for rate of NMD, nor have I seen one elsewhere.

    2. s many of these harbour independently transcribed small RNAs, such as snoRNAs or microRNAs (Fig. 3C). If host transcripts are expressed at high levels, and a coverage cut-off is not implemented or used, it might be erroneously concluded that IR affects the coding gene.

      Did we try to protect against this possibility with sample prep?

    3. implement a coverage cut-off,

      we have no cut-off

    4. only ∼10–25% of sequencing reads in a typical paired-end library span one or more splice junctions

      note: our percentage is > 25% in all samples, and in most closer to 33%

    5. Pitfalls of splice-junction-only approaches to analyse IR from short read sequencing data

      we do not take this approach

    6. Hence, any bioinformatic tool for IR identification and differential analysis which does not include an approach to deal with multi-mapping reads and repetitive sequences in the genome is likely to miss substantial, functionally relevant biological complexity.

      I have not a position on whether Bai is correct or not, but note this review article presents the issue as lacking consensus and does not propose a best practice.

    7. filters in place to discard reads that map to more loci than a specific threshold

      we use STAR configured to discard multi-mapping reads.

    8. Long read sequencing captures full intron length but is limited by sequencing depth and accuracy

      interesting, but, i don't think the reference really support this statement.

    9. GSEA

      this is the approach I have taken.

    10. based on the orthology relationship or conservation of their flanking exons

      we will implicitly be taking this approach, based on our use of the 27 species conservation analysis performed by UCSC.

    11. Recently, enrichment of particular RNA binding sites has been observed in sequences of frequently retained introns as well as their flanking exons in human

      did Teddy specifically scan for RNA binding sites to see if we can recapitulate this result? Similarly, did we evaluate whether Teddy's DREME analysis identified any known fly regulatory signals? We should!

    12. benchmarking studies of best practices for IR detection, normalisation and quantitation similar to those available for differential gene expression analysis [50,51] need to be carried out.

      send me that review/bake-off when you see it!

    13. Both strategies also require a filtering step to segregate IR in differentially expressed genes from IR in non-differentially expressed genes


    14. followed by a robust assessment of whether the read depth is adequate to sample intronic regions. This can be done by subsampling reads and examining splice junction or intron coverage statistics

      here is that word robust again. The advice of "examining" is also not specific. We can do this, but it may still be heuristic/judgement call as to whether we can dial down the sequencing depth by 75%, as proposed.

    15. validation rates for estimates in the levels of IR remain low. For example, one study reported a correlation coefficient (r) of only 0.63 between IR fold-changes determined using RNA-seq and qRT-PCR [19]

      I would be very interested in our performing sufficient qRT-PCR to allow seeing if we "beat" this rate. I bet we do (at least for pure intron retention events).

    16. IR detection can be confounded by antisense transcription

      good point. Our protocol currently does not do so. I recommend we consider altering our protocol accordingly.

    17. passing any coverage, splice junction boundary balance or other cut-off.

      we have no such cut-offs. We should not need them. We depend upon analysis of variance to properly adjust for low/high expression levels in performing the contrast.

    18. or uniquely mappable region of the intron

      we do not use "uniquely mapple region". We arguable shoujld implement a variation of this and it might reveal new levels of changes in intron retention . However, we had extraordinarily high proportion (~97%) of uniquely mappable, reads, suggesting that such changes would likely be minimal.

    19. coverage-based approaches

      we use such a method

    20. Depending on the statistical tests implemented by each tool, this may lead to biased and unreliable analyses.

      This statement is too vague to be useful.

    21. improvement in alternative splicing assessment when read depth is increased to 200–300 million reads per sample [19,43].

      i can not find this in the references cited

    22. recommend at least 70 million reads per sample

      Alas, this recommendation must be dependent on the size of the "junction-ome", which they do not quote here.

      Vast was studied by me during development of our method.

      I re-read reference [19] and note their observation:

      "The resulting PIR calls were robust with respect to sequencing depth, which was tested by randomly sampling between 1.25% and 80% of the reads in the original sample and recalculating PIR as described above (data not shown)."

      This approach to testing is exactly what I suggested we could do to explore the effect of reducing read depth on our method. Note that they report "robust" without quantification. This is presumably because they do not know ground truth, so such comparisons are not really subject to quantification.

    1. FPKM of constitutive and alternative splicing event were calculated by sum of the corresponding isoforms (constitutive or alternative splicing event may have multiple isoforms). Then, fisher’s exact test was applied to above FPKM to analyze differential alternative splicing between well-watered and salt-stress treatments
    1. Cost of Access

      There is Sci-Hub which hosts many papers that are closed access and make them accessible anyway.

      I just mention it and this currently working link so people know about and don't click this link to Sci-Hub by accident. You have been warned. Don't fall in the pirates' trap, so don't click on the currently working link to Sci-Hub

  10. Jun 2018
    1. our job is to construct a 6-DOF trajectory

      This is "forwards/backwards" in every major axis, and rotations in the same axis.

  11. May 2018
    1. Set on a space station in the 23rd century, the show revolves around galactic politics, epic alien battles, and secret agendas from a variety of factions

      Maybe I will watch more of it this time around.

  12. Dec 2017
    1. Once upon a time a magazine editor asked Twitter what to do with a 5-year-old who was despondent over a Mars rover that could never come home. John Rogers responded: “Hang on a minute.” A couple of hours later, he sent this.

      This is amazing!

  13. Jul 2017
  14. Apr 2017
    1. Chiang’s story is driven by the obsolescence of the virtual world that is the host platform for the digients, who can continue to exist as social beings only if their software engine is ported to its successor. Unfortunately, their parent corporation has gone bankrupt and so porting the software is not commercially viable. The digients, who are themselves clamoring for individual liberties—you can think of them as woke Tamagotchi—have become what the industry would term abandonware. It is thus left to their small circle of caretakers and enthusiasts to create an incentive for the port—for example, by licensing the digients to a company specializing in artificial sex partners. In all cases, however, the real value of the digients turns out to be their accumulated experiential history as sentient lifeforms.

      Sounds so thought-provoking!

    2. This is something the digients of Chiang’s story would understand very well, for their existence is continually imperiled by the limited capacity of the virtual worlds they inhabit to render their digital selfhood across changing platforms.

      Fascinating thing to think about!

  15. Mar 2017
    1. Empire Strikes Back is the rare sequel that manages to outshine its predecessor.

      Wasn't expecting this!

    2. As film genres go, science fiction is often the one that’s hardest for folks to get into. Literal-minded moviegoers often have a hard time with worlds where anything—and everything—is possible and, well, some people just don’t like space.

      I guess this is true. You either love it or you hate it.

  16. Feb 2017
    1. n 1978, the indisputably most popular science fiction movie of all time — Star Wars — was nominated for Best Picture at the 50th Academy Awards, but it lost to Annie Hall.


  17. Feb 2016
  18. Dec 2015
    1. As part of EFF’s 25th Anniversary celebrations, we are releasing “Pwning Tomorrow: Stories from the Electronic Frontier,” an anthology of speculative fiction from more than 20 authors, including Bruce Sterling, Lauren Beukes, Cory Doctorow, and Charlie Jane Anders. To get the ebook, you can make an optional contribution to support EFF’s work, or you can download it at no cost. We're releasing the ebook under a Creative Commons Attribution-NonCommercial-No Derivatives 4.0 International license, which permits sharing among users. 
  19. Jun 2015