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venerdì 7 gennaio 2022

# evol: viruses as a facilitator / driver of horizontal gene transfer among eukaryotes


<< Gene exchange between viruses and their hosts acts as a key facilitator of horizontal gene transfer and is hypothesized to be a major driver of evolutionary change. Our understanding of this process comes primarily from bacteria and phage co-evolution, but the mode and functional importance of gene transfers between eukaryotes and their viruses remain anecdotal. >>

AA << systematically characterized viral–eukaryotic gene exchange across eukaryotic and viral diversity, identifying thousands of transfers and revealing their frequency, taxonomic distribution and projected functions. Eukaryote-derived viral genes, abundant in the Nucleocytoviricota, highlighted common strategies for viral host-manipulation, including metabolic reprogramming, proteolytic degradation and extracellular modification. Furthermore, viral-derived eukaryotic genes implicate genetic exchange in the early evolution and diversification of eukaryotes, particularly through viral-derived glycosyltransferases, which have impacted structures as diverse as algal cell walls, trypanosome mitochondria and animal tissues. These findings illuminate the nature of viral–eukaryotic gene exchange and its impact on the evolution of viruses and their eukaryotic hosts. >>️

Irwin, N.A.T., Pittis, A.A., Richards, T.A. et al. Systematic evaluation of horizontal gene transfer between eukaryotes and viruses. Nat Microbiol. doi: 10.1038/ s41564-021-01026-3. Dec 31, 2021. 


<< We knew from individual examples that viral genes have played a role in the evolution of eukaryotes. Even humans have viral genes, which are important for our development and brain function, (..)  We wanted to understand more broadly how HGT (horizontal gene transfer) has affected viruses and eukaryotes from across the tree of life. >> Nicholas Irwin. ️

<< We were interested to find that certain groups of viruses, especially those that infect single-celled eukaryotes, acquire a lot of genes from their hosts, (..)  By studying the function of these genes we were able to make predictions about how these viruses affect their hosts during infection. >> Patrick Keeling.

<< Many of these viral-derived genes appear to have repeatedly affected the structure and form of different organisms, from the cell walls of algae to the tissues of animals, (..) This suggests that host-virus interactions may have played an important role in driving the diversity of life we see today. >> Nicholas Irwin. ️

<< These transfers not only have evolutionary consequences for both virus and host, but could have important health implications, >> Patrick Keeling.️

<< we think that this work serves as an interesting reminder that viruses have also contributed to the evolution of life on Earth, >>️ Nicholas Irwin. 
️
New research shows gene exchange between viruses and hosts drives evolution. University of British Columbia. Jan 5, 2022.


Also

Nonlinear effects in shaping human evolution, the role of viruses. Jan 15, 2019. 


keyword 'evolution'  in FonT


keyword 'evolution' | 'evoluzione'  in Notes (quasi-stochastic poetry)



Keywords: evolution, virus, gene exchange, horizontal gene transfer, HGT


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martedì 4 gennaio 2022

# behav: learning walks related to home burrow navigation (among desert grassland scorpions Paruroctonus utahensis)


<< The Navigation by Chemotextural Familiarity Hypothesis (NCFH) suggests that scorpions use their midventral pectines to gather chemical and textural information near their burrows and use this information as they subsequently return home. For NCFH to be viable, animals must somehow acquire home-directed “tastes” of the substrate, such as through path integration (PI) and/or learning walks. >>️

AA << found that once animals established their home burrows, they immediately made one to several short, looping excursions away from and back to their burrows before walking greater distances. We also observed similar excursions when animals made burrows in level sand in the middle of the arena (i.e., no mound provided). These putative learning walks, together with recently reported PI in scorpions, may provide the crucial home-directed information requisite for NCFH. >>️

Douglas D. Gaffin, Maria G. Munoz, Marielle Hoefnagels. Evidence of learning walks related to scorpion home burrow navigation. bioRxiv 2021.12.28.474378; Dec 30, 2021. 


Also

keyword 'walk' | 'walking' in FonT



keyword 'passo lieve' | 'walk' | 'walking' in Notes (quasi-stochastic poetry)




Keywords: behav, walk, walking, learning walk, NCFH



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lunedì 3 gennaio 2022

# gst: weird but not so weird dynamics, basins with tentacles could be common in high-dimensional systems.


<< Basins of attraction are fundamental to the analysis of dynamical systems (..). Over the years, many remarkable properties of basins have been discovered (..), most notably that their geometry can be wild, as exemplified by Wada basins (..), fractal basin boundaries (..), and riddled or intermingled basins (..). Yet despite these foundational studies, much remains to be learned about basins, especially in systems with many degrees of freedom. >>

AA show that for locally-coupled Kuramoto oscillators << high-dimensional basins tend to have convoluted geometries and cannot be approximated by simple shapes such as hypercubes. Although they are impossible to visualize precisely (because of their high dimensionality), (they) present evidence that these basins have long tentacles that reach far and wide and become tangled with each other. Yet sufficiently close to its own attractor, each basin becomes rounder and more simply structured, somewhat like the head of an octopus. >>

<< In terms of (AA) metaphor, almost all of a basin’s volume is in its tentacles, not its head. This finding is not limited to Kuramoto oscillators. (AA) provide a simple geometrical argument showing that, as long as the number of attractors in a system grows subexponentially with system size, the basins are expected to be octopus-like. As further evidence of their genericity, basins of this type were previously found in simulations of jammed sphere packings (..) where they were described as “branched” and “threadlike” away from a central core (..) and accurate methods were developed for computing their volumes (.,). There is also enticing evidence of octopus-like basins in neuronal networks (..), power grids (..), and photonic couplers (..). >>

<< Figure 4 is a further attempt to visualize the structure of high-dimensional basins, now by examining randomly oriented two-dimensional (2D) slices of state space, either far from a twisted state or close to one. (..) Despite the fact that each basin is connected (..)  the basins look fragmented in this 2D slice. >>

 Fig. 4(a): << Perhaps another metaphor than tentacles—a ball of tangled yarn—better captures the essence of the basin structure in this regime, far from any attractor, in which differently colored threads (representing different basins) are interwoven together in an irregular fashion. >>

Fig. 4(b): << The basin structure near an attractor is strikingly different. (..) the basins near an attractor are organized like an onion. >>

Yuanzhao Zhang, Steven H. Strogatz. Basins with tentacles. arXiv: 2106.05709v3 [nlin.AO]. Nov 2, 2021. 



Also

Reshaping Kuramoto model, when a collective dynamics becomes chaotic, with a surprisingly weak coupling. Dec 27, 2021.


Keywords: gst, dynamical systems, high-dimensional systems, Kuramoto oscillator, attractors, basin of attraction 



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venerdì 31 dicembre 2021

# behav: unfrequent events under radical uncertainty; rats tend to avoid black swan situations.

AA << present a novel experimental design that aims at measuring the extent to which animal subjects are sensitive to rare and extreme events and, in addition, how rats respond to those very unfrequent events under radical uncertainty. (..) the novelty of (AA) design is that it provides two direct measures that help interpreting (..) behavioral data: Total Sensitivity to Rare and Extreme Events, and One-sided Sensitivity to Rare and Extreme Events with Black-Swan Avoidance/Jackpot-Seeking behaviors as limiting cases. >>️

<< First, most rats (..) can be grouped into a moderate to high Total Sensitivity group. This means that most rats diversify their choices across options in such a way that they more often rely on convex ones than on concave ones overall. Therefore, they tend to seek extreme gains/Jackpots and to avoid extreme losses/ Black Swans. In addition, most rats (..) tend to exhibit Black Swan Avoidance, which indicates that, given Total Sensitivity, they tend to try more often to avoid Black Swans than to seek Jackpots. (AA) interpret such a behavior as significant aversion towards uncertainty about rare and extreme losses.  >>️

<< all rats diversify their choices across a set of options, which is reminiscent of observed behaviors such as, for example, bet-hedging in animals and financial portfolio strategies used by humans >>
️
<< results from similar experiments among different species might be of interest for the analysis of neurobiological substrates involved in decision-making and its evolutionary traits in the context of rare and extreme events. >>️

Mickael Degoulet, Louis-Matis Willem, et al. Decision-Making in Rats is Sensitive to Rare and Extreme Events: the Black Swan Avoidance. bioRxiv 10.1101/2021.11.01.466806v1. Nov 04, 2021. 


 Keywords: behav, game, decision-making, bet-hedging, trading, uncertainty, gain, loss, black swan 


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mercoledì 29 dicembre 2021

# game: in a iterated prisoner's dilemma scenario forgiveness turns out to be an adaptation

<< Prisoner’s dilemma is used to represent a range of real life phenomena such as economics, commerce, nature and wildlife. >>

<< Researchers working on iterated prisoner's dilemma (IPD) with limited memory inspected the outcome of different forgetting strategies in homogeneous environment, within which all agents adopt the same forgetting strategy at a time. In this work, with the intention to represent real life more realistically, (AA) improve existing forgetting strategies, offer new ones, and conduct experiments in heterogeneous environment that contains mixed agents and compare the results with previous research as well as homogeneous environment >>

<< in a more realistic environment consisting of all types of agents, in terms of both cooperation probabilities and forgetting strategies, agents who forget defectors consistently outperform other forgetting strategies for all memory ratio values. Moreover, the best performing defectors are also the ones that forget other defectors. In other words, agents who “forgive” defectors are the best performers. Hence, forgiveness is an adaptation. >>

FMC : Forget most cooperator first 
FMP : Forget most played first 
FMU : Forget most unpredictable first 
FR :  Forget randomly 
FLP : Forget least played first 
FMD : Forget most defector first 

Meliksah Turker, Haluk O. Bingol. Forgiveness is an Adaptation in Iterated Prisoner's Dilemma with Memory. arXiv:2112.07894v1 [cs.GT]. Dec 15, 2021


Also

keyword 'game' | 'tit-for-tat' in FonT



keyword 'game' | 'tit-for-tat' in Notes
(quasi-stochastic poetry)



Keywords: game, iterated prisoner's dilemma, forgiveness, adaptation


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lunedì 27 dicembre 2021

# gst: reshaping Kuramoto model, when a collective dynamics becomes chaotic, with a surprisingly weak coupling.

<< The emergence of collective synchrony from an incoherent state is a phenomenon essentially described by the Kuramoto model (..) Collective synchronization is a phenomenon in which an ensemble of heterogeneous, self-sustained oscillatory units (commonly known as oscillators) spontaneously entrain their rhythms. This is a pervasive phenomenon observed in natural systems and man-made devices, covering a wide range of spatio-temporal scales, from cell aggregates to swarms of fireflies >>

<< However, this is only partly true, (..) Kuramoto’s perturbative phase-reduction approach is valid for weak coupling. Specifically, oscillator heterogeneity and interactions appear at zeroth and linear orders in the coupling constant, respectively. >> 

AA << have introduced the ‘enlarged Kuramoto model’; a population of phase oscillators in which three-body interactions enter in a perturbative way. Remarkably, this makes a world of difference, drastically reshaping the traditional Kuramoto scenario. The ‘enlarged Kuramoto model’ exhibits a variety of unsteady states, including collective chaos and hyperchaos. >>

Ivan Leon, Diego Pazo. Enlarged Kuramoto Model: Secondary Instability and Transition to Collective Chaos. arXiv: 2112.00176v1 [nlin.AO]. Nov 30, 2021.


Also

More on the three-body problem (695 families of collisionless orbits). FonT. Oct 16, 2017. 


Keywords: gst, behav, instability, Kuramoto model, three-body interactions, chaos, collective chaos, hyperchaos.

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venerdì 10 dicembre 2021

# life; apropos of #1or2achoos from Wuhan ...

Messrs. A, B, C & D state - between the lines, undertrack, at least a year late -

Commissione DuPre (Dubbio e Precauzione ) live streaming 8/12/2021 


that the official anti covid19 apparatus it appears to be a big, very big mess (i.e. 'un grande pastrokkio') ...

probably Messrs. A, B, C & D could be accused of being thieves, sexual maniacs, they could block their career and make their spouses do twenty years of precariousness ...

their future pensioners' allowance could be taken away or reduced ... 

as well as more ... 

I suppose & anzicheforse ...

luckily for everyone, the 'bushman  variant' of sarscov-2 (Covid-19 B.1.1.529 Omicron) 

Republic of Botswana - new covid 19 variant detected in Botswana -  Presidential covid-19 task force.


could save in short-term, perhaps, the world from this big trouble (i.e.  'grande impiccio').

Here there are three simple questions: 

(a) Why in anticipation of the 'great tea trolley disaster' (after SARS appearance in Nov 2002, Guangdong, China; after MERS in Nov 2012, Gedda, Saudi Arabia) spray forms of antiviral drugs (e.g. remdesivir,  remdesivir like) have not been prepared?


(b) Why in the meantime, hitech reusable anti-viral anti-bacterial fabrics not been studied and tested?

(c) Does it seem serious to propose a vaccine - to treat every six/eight months eight billion people inside a window of 15/30 days - to confine (sic) a mutant virus (one mutation every week) that is transmitted by air? 

Also 

the unmentionable GTTD - Great Tea Trolley Disaster, by Bristow


keyword 'virus' | 'sars-cov-2' | 'sars' in FonT: 




keyword 'virus' in Notes 
(quasi-stochastic poetry):


keyword 'bosciman*' | 'nomad*' in Notes
(quasi-stochastic poetry)





keyword 'bushmen' | 'nomads' in FonT 



keywords: virus, coronavirus, sars, mers, sars-cov-2, covid-19, 2019ncov, bushman  variant, B.1.1.529, Omicron, 1or2achoos, mask


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