Linking love of libraries to a larger scale.

Some Latino people think that the country's race categories are not an accurate depiction of what they identify with. This could be seen as extremely racist.

Would be better to end with making an explicit connection between the ENCODE tissue-specific RNAseq data and the Setd2 knock-down RNAseq data. Would it make sense to focus on loci showing evidence for tissue-specific polyA as well as being dependent on Setd2 for correct splicing?

I would call that marginally significant

use of very long prepositional phrases at the start of sentences makes reading difficult. stick to simple subject- predicate- object sentence structure.

nice and useful figure but: you primed the cDNA synthesis with random hexamers. the qRT-PCR results are therefore not specific to polyadenylated transcripts. so, above figure shows models consistent with the data rather than summarisations of the data (you did not directly measure polyA).

beware that this implies non-polyadenylated transcripts also are represented in the sample

depends in this case on whether you look at the scatter plot or the UCSC genome browser: they are not telling the same story for some reason. my corrections below reflect what UCSC shows, which results in flipping of placenta and thymus.

see above; will stop pointing this out

low conversion rate leads to over-estimation of methylation, which could explain the 45% methylation seen in placenta

primer sets are not tissue-specific; you used them for all tissues; only the measurements themselves are tissue-specific

The host transcript of the CGI is non-coding. Your upstream primers amplify both the coding transcript and the non-coding host transcript. That is a limitation. Could explain the inconsistencies re the RNAseq data.

qRT-PCR cannot show transcription termination: all it can do is verify the RNAseq data, i.e., more relatively more transcription upstream of an active CGI compared to transcription across the CGI. It is important to be precise about what qRT-PCR can and cannot do.

The data do not show transcripts terminating upstream or downstream of the CGI, they are merely consistent with the hypothesis.

This works because of incomplete conversion (<100%), plus actual differences in CpG methylation states.

Bonferroni multiple testing correction: you divide alpha (the significance threshold), typically (by convention) 0.05, by the number of tests, and that gives you the corrected significance threshold.

What you did not do due to lack of time: optimisation of the qRT-PCR assays. That would have included a melt curve analysis to detect primer dimers and/or off-target amplicons, and to then run the same reaction again, but with an additional "read" step during each cycle at a higher temperature than the 55C annealing temperature. The "read" temperature is chosen based on the melt curve so that primer dimers and smaller off-target amplicons have melted (become ssDNA) while the target still is dsDNA. This gives you more target-specific fluorescence measurements.

Any dsDNA will generate fluorescence, including, for example, primer dimers and off-target amplicons. That is why SYBR is considered relatively non-specific. But its is relatively cheap compared to more specific assays like TaqMan.

Fluorescence always is measurable. The threshold cycle is when fluorescence exceeds a given and fixed threshold value, which is chosen to intersect the amplification curves during their exponential phase.

you may be asked if some of the inconsistencies between your results and the RNAseq data can be explained by the genetic differences between the hybrids and the B6 mice used by ENCODE. possibly yes, since Cast is quite distant from B6 in evolutionary terms, i.e., there are many genetic differences that definitely have an effect on gene expression. the next question may be: well, why then did you use hybrid tissue? it's the only option available for some tissues, given our tissue stocks, and we don't have a B6 colony any more.

nucleosome = octamer of histones

indeed, genes encoding histones are treated very differently

It makes sense to me on a technical level but isn't something I would provide in an interface aimed at the general public. My inclination would be to have the default interface not show orphan annotations at all. The new york times front page is a great example. If things started to work, you would rapidly have far more orphans than anything else. Without the context of the annotation its hard to imagine these would provide much value. Perhaps this is something that could be added to a different, non-default view that provided some sort of historical perspective on the URL under consideration.

This argues for capturing a bit more of the context around any given annotation for preservation as part of the annotation. e.g. 150 characters up and downstream.

The text is broken at the beginning. See Liuzzo 2015 for an explanation of this.

I feel the next logical step is to open source my.Enspiral.

I've been thinking about this metaphor, and about comments on blogs vs. blogs linking to blogs. In some ways this is another part of the Wikipedia vs. Federated Wiki question. I say "vs." because the alternatives do become binary at some point in the conversation. But back to the owning vs. sharecropping: in terms of web presence, maybe; in terms of discourse and rhetoric and the ways call and response differ, maybe not. I'll keep thinking. And I'm grateful for the heads-up that Hypothes.is is at last up and running!

Prova nota Unito

essa Carolina é aquela que curte séries, né?

Biocentric includes man and includes him in an appropriately prioritized order. An anthropocentric view should be a biocentric, ecocentric, charitable, human view simply because humans are (among other things) organisms, situated in ecosystems, capable of charity, love, humility and that is in fact what makes us human. What is best for the environment is what is best for humans and everything else.

Interesting idea. The only thing is that the science is not where we would like it to be. Most of the accusing will need to be done in retrospect. In that case, many will have lost culpability due to insufficient knowledge. I just wonder how this will hold up in a court of law for most practical cases. For some large-scale cases, I can see it working, as long as the effects are enormous.

As far as I know: Konjunktiv I und Konjunktiv II are named "present subjunctive" and "past subjunctive" respectively. I am not sure if this terminology is familiar to the English speakers.

Perfect has not been taken into account, I guess because it is an analytic form(?)

But cf. Larson, Richard K. 1988. On the Double Object Construction. Linguistic Inquiry 19: 335-391. for a binary analysis of double object constructions in English, and the theories developing the VP shells (and later the Little vP).

Tolkien, C.S. Lewis, gothic cathedrals, Pachelbel suddenly represent the essence of the good western culture.

These references are not in the pdf

Basically useless unless highly zoomed in...

this is cool.

Ich habe mir auch hier erlaubt ein paar Kommentare anzufügen.

Dies geschah auch mit Hypothes.is, jedoch via des PDF Exports, da andernfalls, weder auf live noch read-only Pads, die Kommentieroberfläche nicht geladen wurde.

Created an account and now I'm ready to test this phenomenal innovation.

It's true!

It's a good image but "blood-clotted cloth" is a tongue twister.

this is a comment

a comment from me

Je ne veux pas assurer leur avenir, je veux le changer.

Schools should address the demands of tomorrow, not those of today.

New comment

history of the development of the individual--

equally, can find things for which we are horrified of them, etc.

satisfy instinct for narcissistic enjoyment

still bound to increase self-destruction

consider in context of Darwinian "survival", and interesting to consider the contrast with Berlant's "Slow Death" concept--hunger to the point of obesity, love striving after objects to the point of depression

Christian Morgenstern (1871-1914) German romantic poet, "Das Wasser": "Ohne Wort, Ohne Wort; rinnt das Wasser immer fort; andernfalls, andernfalls; sprach' es doch nichts andres als: Bier und Brot, Lieb und Treu; und das waere auch nicht neu. Dieses zeigt, dieses zeigt; daß das Wasser besser schweigt."

Is it "self-evident"? Once something surfaces from the unconscious into consciousness, it seems intuitively "self-evident"

I like how in the nltk documentation, they make an effort to be as clear as possibly for beginners or those who do not have a computer science degree. Too often, projects (somewhat understandably) don't bother with this.

ideas backward to the world--all those concepts go back to the body

But the awakened one, the knowing one, saith: “Body am I entirely, and nothing more; and soul is only the name of something in the body.” The body is a big sagacity (having or showing keen mental discernment and good judgment; shrewd, but Vernunft means rational/sane), a plurality with one sense, a war and a peace, a flock and a shepherd.

A magic resideth even in his academic chair. And not in vain did the youths sit before the preacher of virtue. His wisdom is to keep awake in order to sleep well. that is to say, there is not much substanceAnd verily, if life had no sense, and had I to choose nonsense, this would be the desirablest nonsense for me also.

he knows his position in dieser Lehrstuhl

und was macht ein Kuh?

All values have already been created, and all created values — do I represent. Verily, there shall be no ‘I will’ any more. Thus speaketh the dragon. My brethren (Brother?), wherefore is there need of the lion in the spirit? Why sufficeth not the beast of burden, which renounceth and is reverent? To create new values — that, even the lion cannot yet accomplish: but to create itself freedom for new creating — that can the might of the lion do. To create itself freedom, and give a holy Nay even unto duty: for that, my brethren, there is need of the lion. To assume the right to new values — that is the most formidable assumption for a load-bearing and reverent spirit. Verily, unto such a spirit it is preying, and the work of a beast of prey. As its holiest, it once loved “Thou-shalt”: now is it forced to find illusion and arbitrariness even in the holiest things, that it may capture freedom from its love: the lion is needed for this capture.

Its last Lord it here seeketh: hostile will it be to him, and to its last God; for victory will it struggle with the great dragon. What is the great dragon which the spirit is no longer inclined to call Lord and God? “Thou-shalt,” is the great dragon called. But the spirit of the lion saith, “I will.” will vs. want