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This is the first post in series dedicated to my research and project I'm
involved in. Also, I'm going to bring here some analysis work I'm doing
just to myself. To find out more follow the tags #myresearch and

This time I'll bring an example of how to use Circos tool to visualize
genomic and transcriptomics data. This tool is visually very appealing, but
more you put on the graph less useful it becomes.

Before we start I want to introduce one basic concept from mycology,
barrage. On figure below barrage shown by arrows and compatible strains'
interactions shown by arrowheads.

In a nutshell barrage or incompatibility reaction is a form of innate
immune response that causes two genetically distinct fungal strains reject
each other. In fungal world most of interactions between strains happen
through hyphal fusion or anastomosis. If all immune signals check and no
disagreement found two strains fuse and continue to exist as a single
individual. But if immune response triggered, two strains form a barrage, a
separation wall made out of dead cells. Barrage separates two strains
restricting exchange of genetic material. It gives us a glimpse into early
evolution of sexual reproduction and immunity. Basically saying if we too
different from each other genetically direct exchange of genes may cause
more damage than good, so lets have sex instead.

Circular diagram below shows genes differentially expressed in C.
parasitica during incompatibility reaction.

This diagram allows to see overall picture of how C. parasitica genes (red
dots) behave in relation to genome map. Plus you can compare them to genes
of P. anserina (purple) and N. crassa (green) in similar reaction. Not
particularly informative, but you certainly can take something out of it.

First of all C. parasitica has much more upregulated genes (pink area) than
other two fungi. Also there are transcriptionally inert areas of genome,
showing no gene activation. And finally lack of correlation in expression
rate between three species. Basically red dots do not appear together with
purple and green, showing different or no expression at all.

Figure caption: Gene differential expression (DE) shown on C. parasitica
genome map (11 largest scaffolds).
Diagrams from outside to inside: Black lines show genome map of 11
scaffolds, each tick mark corresponds to 100,000 bp. Inside the outer black
lines, blue marks indicate previously annotated genes on JGI C. parasitica
genome portal and orange marks indicate novel genes. Novel genes are
transcripts which demonstrated detectable level of expression in areas of
genome previously not annotated on genome portal. First circle shows
expressed genes, and second circle shows DE genes during barrage. Interior
to this are C. parasitica gene IDs of DE genes where black IDs indicate
genes differentially expressed during barrage only in C. parasitica, green
and purple IDs indicate that orthologs of those genes are DE during
Heterokaryon Incompatibility (HI) in N. crassa and P. anserina
respectively. The inner-most pink, grey and blue bands show plots of
individual genes expression. The Y axis indicates genes differential
expression in log2 scale. Y axis pink colour indicates upregulated (y> 2),
blue – downregulated (y< -2) and grey (2>y>-2) indicate non-DE genes. Red
dots indicate C. parasitica genes, green and purple dots indicate DE
orthologs during HI in N. crassa and P. anserina respectively.

[Anabelov Info] Islam

I always have that uneasy feeling when they try to wash religious orthodoxy's face from all the dirt. It looks clean, but now you can actually see how ugly it is. At some point a horrifying thought visits you, that maybe... maybe!.. it was actually better before. O_o
Because before you could easily argue that this is just a piece of shit, lets get rid of it. But now, it would sound more like a prejudice or personal opinion at best.

They can really argue that hijab and burka protect women from unnecessary attention of horny males. However, completely different story is when they say that nobody forces women to wear hijab or burka. That smells the same as shit like 99.99% of North Koreans support their government (remaining fraction are children who can't speak).

So, I have no stylistic issues with hijab, I'm not a fashion police. But, hijab and burka create nasty dichotomy. If you wear it, you are lawful, good, moral person: here's your husband, here's your allowance. If not, you are disgraceful slut and you deserve whatever bad shit happens to you. No pressure (according to modern islamic apologetic).

They may argue that in western world you have to agree to social norms, so you can get certain benefits of living in society. True.
However, important difference with theocratic societies here is that you free to choose the extent of social norms you accept. Of course you have to acquire basic norms, but nobody forces you to accept whole package. You generally free to make up your own personal set of morals and live perfectly fine.

For women in many islamic states this is not an option. You either accept Islamic Law or you disgraceful slut.

So, don't get too excited when you see picture like one below.
For the recent debate over biological differences in males and females when it comes to work in tech or leadership positions.

In short, average person should not care about it at all.

Long: If you a smart girl with IQ over 130 and you decided to hangout only with smart people like you, then prepare to be in predominately male crowd for the rest of your life. Not a big deal. Smart people do not care about penises and vaginas much. If you as IQ130+ person won't be snobbish like that and start to hangout with average people you'll find that all of them, no matter of their sex, are equally stupid. Though sometimes, when you are in a good mood, you can see it as somewhat amusing.

As an average IQ male should I feel pride over the knowledge that there is more males in IQ group over 130?
First, it doesn't change my IQ and second, for a person with IQ 110 there are as much smart men out there as there are smart women. Should a girl with IQ 110 feel bad about the same thing?
For exactly the same reason.

There are biological differences in how brain works between males and females. There is a solid proof of that and it doesn't come from success story magazine. If we look at research on autism there is huge inequality here [1,2]. Ratio of males to females getting autism is like 4.3:1 and this is a general case. Some research shows that for specific cases like Aspergers syndrome it's even worse, like 12:1.

If we start to fight for equality in mental retardation it will be a comedy. We either lower the bar of mental retardation for women (hello XIX century hysteria) or kick out excessive males from care they need. Non of these options are good.

1. Van Wijngaarden-Cremers, PJM, et al. (2014). "Gender and Age Differences in the Core Triad of Impairments in Autism Spectrum Disorders: A Systematic Review and Meta-analysis." Journal of Autism and Developmental Disorders 44(3): 627-635.
2. Fombonne, E. (2003). "Epidemiological Surveys of Autism and Other Pervasive Developmental Disorders: An Update." Journal of Autism and Developmental Disorders 33(4): 365-382.

[Anabelov Info] Pinkillers

Article on opioid epidemics.
While it is really an issue, problem do seems to be a bit overblown.
In these kind of cases I blame how in western countries journalists like first hand experience.
You can never find a report in press generally describing an issue. Informing you on overall matter. It is always have to be accompanied by interviews with real simple folks who got into it.
Of course it gives the problem a human face, something to relate to. But often it creates biases. As people tend to believe testimonies more than to careful analysis.

[Anabelov Info] Gender equality

If at some point government decides to enforce the rule that every workplace has to have exact 50/50 distribution of male and female workers. What you can do to maximise your employment chances?
When they bring you a questionnaire, in line for sex you put none, and declare yourself gender-fluid or gender-neutral. That way your employer can hire you at any quota.

Though for this strategy to work best they have to enforce transgender laws as well. So that at any scrutiny they wouldn't be able to use your birth certificate against you.

[Anabelov Info] History

VV Shulgin is a person with very interesting history. He was Russian nationalist, monarchist, constitutional monarchy advocate and one of the members of white movement (called white as opposed to red,old Russia anti-bolshevik movement). Was a member of all sessions of Duma (first Russian parliament). He was among those who accepted abdication of Nicholas II.

So, conservative, nationalist and one who was fighting communists, after all in 1920 wrote this (highlights are mine):

...our ideas jumped over forefront...they (bolsheviks) rebuild Russian army... It might be terrible to acknowledge that, but it's what it is... Bolsheviks raised the Flag of United Russia... Communist International appeared as weapon... to expand Russia's territory...and Moscow power... no one can deny, russian language again rules over 1/6 of the world and all that in the name of Communist International... bolsheviks: 1) rebuilding Russian army; 2) restoring Russian borders... 3) preparing the return of Russia's Tsar.

Valuable lesson here: Some people may appear wise and insightful, by just being narrow minded. It just happens sometimes that time steps on the same tracks with your narrow point of view. Never for long, though.

[Anabelov Info] Past

He said that only 1 out of 3 smokers die from smoking related illnesses. 30% chance. Almost the same as predicted chance of Trump winning the presidency.

I have only one problem with this article. When do this stupid ganre "he said it -- years ago and still didn't correct himself" end?


[Anabelov Info] Cambodia

Some thoughts about Cambodia.

That was tough experience converting between Riel and USD. And I think they should ban using dollars. It makes everything more expensive. I mean most stuff costs $1, because it's hard to split it further without using local money. Like in Thailand, $1 is about 60 baht. So you can conveniently split dollar at least by 6.


People constantly begging for money almost everywhere. Victims of war, mothers with babies or children with big eyes. Striking thing was not that I never seen it before. I've seen lots of stuff like that back in Russia. It was that I haven't noticed anything like that in Thailand. Still mistery for me.
Sometimes it is interesting what things remind me about my motherland. When I talk with Chinese (esspessially mainland and HK) they remind me Russians by their lifestyle choices and maybe a bit of temperament. And now beggars in Cambodia.

[Anabelov Info] Random thoughts

God created everything in 7 days. Which is usually called as 6 days creation. Where a day is one rotation of Earth around the sun. But because Earth appears only on "second" day, after sun (light) it should be called 5+ days creation.

[Anabelov Info] Climate

This is interesting.

So apparently, Exxon accuses Rockefeller to plot a climate change conspiracy against them.

Interesting times indeed.


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