# gst: apropos of 'reprogrammed by a virus' (2), the case of 'virocells'

<< If it looks like a duck and quacks like a duck, so the adage goes, it must be a duck. But if the duck gets infected by a virus so that it no longer looks or quacks like one, is it still a duck? >>

Viruses reprogram cells into different virocells. DOE/Joint Genome Institute. 

 Feb 11, 2020.

https://m.phys.org/news/2020-02-viruses-reprogram-cells-virocells.html

<< Ocean viruses are abundant and infect 20–40% of surface microbes. Infected cells, termed virocells, are thus a predominant microbial state. Yet, virocells and their ecosystem impacts are understudied, thus precluding their incorporation into ecosystem models. >>

AA << investigated how unrelated bacterial viruses (phages) reprogram one host into contrasting virocells with different potential ecosystem footprints. >>

<< Ecologically, this work suggests that one cell, infected versus uninfected, can have immensely different metabolisms that affect the ecosystem differently. >>

Howard-Varona C, Lindback MM, et al. Phage-specific metabolic reprogramming of virocells. ISME J. doi: 10.1038/s41396-019-0580-z. Jan 2, 2020.

https://www.nature.com/articles/s41396-019-0580-z

Also

keyword 'virus' in FonT

https://flashontrack.blogspot.com/search?q=virus

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

https://inkpi.blogspot.com/search?q=virus

# gst: apropos of 'transitions', liquid-liquid transitions within a one- component system

<< For a long time, the liquid state of pure substances was believed to be a continuous state in which the component atoms or molecules are all equivalent. However, it has now been widely shown that there can be multiple phases within liquids, even those containing only one component. >>

AA << have devised a model based on two factors that describe the ordering of the liquid; the density, and the local organization of the liquid atoms or molecules at a particular point. >>

<< Our Ginzburg-Landau-type model evaluates the system using two order parameters; one that is conserved-density; and one that is not- local structural order (..) What we found was that the growth of the liquid domain we studied was affected by density changes that cause hydrodynamic fluctuations. >> Kyohei Takae.

<< It was shown that when the density changes as a result of the phase transition, hydrodynamic flow is induced leading to changes in both the rate of domain growth and the long-range interaction between the domains. Hydrodynamic interaction was therefore found to be critical to LLT (liquid-liquid transitions) and the pattern evolution and kinetics. >>

But what about flow? The effect of hydrodynamics on liquid-liquid transitions. University of Tokyo. Feb 10, 2020.

https://phys.org/news/2020-02-effect-hydrodynamics-liquid-liquid-transitions.html

Kyohei Takae, Hajime Tanaka. Role of hydrodynamics in liquid–liquid transition of a single-component substance. PNAS. 117 (9) 4471-4479. doi: 10.1073/pnas.1911544117. Mar 3, 2020.

https://www.pnas.org/content/117/9/4471

Also

more on the weirdness of water, "T" and "non-T" Tetrahedral arrangements. Feb 5, 2020. 

https://flashontrack.blogspot.com/2020/02/chem-more-on-weirdness-of-water-t-and.html

Also

keyword 'transition/al' in FonT

https://flashontrack.blogspot.com/search?q=transition

https://flashontrack.blogspot.com/search?q=transitional

keyword 'transizione/i' in Notes (quasi-stochastic poetry)

https://inkpi.blogspot.com/search?q=transizione

https://inkpi.blogspot.com/search?q=transizioni

keyword 'transizionale/i' in Notes (quasi-stochastic poetry)

https://inkpi.blogspot.com/search?q=transizionale

https://inkpi.blogspot.com/search?q=transizionali

# behav: the pulsating, probabilistic approach among parrots (Nestor notabilis)

<< Parrots can learn to choose based on probability, making them the first animal outside of the great ape family that uses statistical modelling in their decision-making process, >>

<< What was most surprising is that they can integrate social or physical information into their probabilistic judgements, >> Amalia Bastos.

Parrots get probability, use stats to make choices: study.  Mar 3, 2020.

https://m.phys.org/news/2020-03-parrots-probability-stats-choices.html

Amalia P. M. Bastos, Alex H. Taylor. Kea show three signatures of domain-general statistical inference. Nature Communication. Volume 11, Article number: 828. Mar 3, 2020.

https://www.nature.com/articles/s41467-020-14695-1

Also 

<< Insects are able to solve basic numerical cognition tasks >>

Hannes Rapp, Martin Paul Nawrot, Merav Stern. Numerical Cognition Based on Precise Counting with a Single Spiking Neuron. iScience. Volume 23, Issue 2, 100852. doi: 10.1016/j.isci.2020.100852. Jan 21, 2020.

https://www.cell.com/iscience/fulltext/S2589-0042(20)30035-3

Quantifying objects: Bees recognize that six is more than four.  University of Cologne. Mar 2, 2020.

https://m.phys.org/news/2020-03-quantifying-bees.html

# gst: the sounds that occur when a soap bubble pops.

<< The popping sound of a bursting soap bubble is acquired using microphone arrays and analyzed using spherical harmonics decomposition. >>

the << acoustic emission originates mainly from the capillary stresses exerted by the liquid soap film on the air and that it quantitatively reflects the out-of-equilibrium evolution of the flowing liquid film. (..) the acoustic signature of violent events of physical or biological origin could be used to measure the forces at play during these events. >>

Adrien Bussonniere, Arnaud Antkowiak, et al. Acoustic Sensing of Forces Driving Fast Capillary Flows. Phys. Rev. Lett. 124, 084502 Feb 27, 2020.

https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.124.084502

Bob Yirka. Measuring the sound of a soap bubble popping. Phys.org. Mar 2, 2020.

https://m.phys.org/news/2020-03-soap.html

# gst: apropos of 'fleeting (transient) interactions'

AA << captured highly transient interactions between transcription factors-proteins that control gene expression-and target genes in the genome and showed that these typically missed interactions have important practical implications. >>

<< Our approaches to capturing transient transcription factor-target interactions genome-wide can be applied to validate dynamic interactions of transcription factors for any pathway of interest in agriculture or medicine, >> Gloria Coruzzi. 

Biologists capture fleeting interactions between regulatory proteins and their genome-wide targets. New York University. Mar 2, 2020.

https://m.phys.org/news/2020-03-biologists-capture-fleeting-interactions-regulatory.html

José M. Alvarez, Anna-Lena Schinke, et al. Transient genome-wide interactions of the master transcription factor NLP7 initiate a rapid nitrogen-response cascade. Nat Commun 11, 1157. doi: 10.1038/s41467-020-14979-6. Mar 2, 2020

https://www.nature.com/articles/s41467-020-14979-6

# life: they used birds to think about and to predict the future.

<< People around the world and throughout history have used birds to think about and predict the future. >>

<< In the Kalahari, southern Africa, !Xõ hunters carefully watch the black-faced babblers after an antelope hunt for signs of where their wounded prey may be. >>

Felice Wyndham. How birds are used to reveal the future. Feb 26, 2020.

https://theconversation.com/how-birds-are-used-to-reveal-the-future-130844

Ethno-ornithology World Atlas

https://ewatlas.net/collection/birds-tell-people-things

Here are some examples ...

'journalists' birds ...

<< Hummingbirds can bring good or bad news. If someone flies nearby you have to say, "You're going to give me good news!" (It's a saying that comes from the Yshir).>>

https://ewatlas.net/digital-heritage/ti%C3%ADnta-polytmus-guainumbi

'ecologist / protester' birds ...

<< If this bird sings at night it warns that white people will be deforesting soon. >>

https://ewatlas.net/digital-heritage/guidob%C3%B3-leptotila-verreauxi

'climatologist' birds ...

<< If one has a gócoco in the house, and the bird digs for a dust bath, it means that the cold weather is coming. It indicates that the weather will be a very rainy and very cloudy weather, but if it sings loud it is warning that the sun will soon rise. >>

https://ewatlas.net/digital-heritage/g%C3%B3coco-chunga-burmeisteri

<< When this bird approaches the Ayoreo village or if you see it in a dive, the noise of its wings warns that a lot of rain will come soon; maybe floods. >>

https://ewatlas.net/digital-heritage/jaac%C3%B3-cairina-moschata

<< This bird announces rain: if it sings in the morning it will rain in the afternoon - she cries because she does not want her nest to get wet. This bird needs high woods and leaves of trees to eat. She is a young lady and she likes young people and always accompanies people every day. >>

https://ewatlas.net/digital-heritage/ngongo%C3%B3-crypturellus-undulatus

<< It may be a warning that if it burns there may be storms or strong winds. >>

https://ewatlas.net/digital-heritage/pi%C3%A1-vireo-olivaceus

<< It says "ti ti ti ti ti ti ti." Warn if the south wind that brings the cold will blow soon. >>

https://ewatlas.net/digital-heritage/totita-hemitriccus-margaritaceiventer-todirostrum-cinereum

Also

keyword 'bird' in FonT

https://flashontrack.blogspot.com/search?q=bird

# gst: continuous, (not intermittent, perpetual) tremors and slips ...

<< Applying deep learning to seismic data has revealed tremor and slip occur at all times—before and after known large-scale slow-slip earthquakes—rather than intermittently in discrete bursts, as previously believed. Even more surprisingly, the machine learning generalizes to other tectonic environments, including the San Andreas Fault. >>

Machine learning reveals earth tremor and slip occur continuously, not intermittently. Los Alamos National Laboratory.  Feb 27, 2020.

https://m.phys.org/news/2020-02-machine-reveals-earth-tremor-intermittently.html

<< Slow earthquakes cyclically load fault zones and have been observed preceding major earthquakes on continental faults as well as subduction zones. Slow earthquakes and associated tremor are common to most subduction zones, taking place downdip from the neighboring locked zone where megathrust earthquakes occur. In the clearest cases, tremor is observed in discrete bursts that are identified from multiple seismic stations. By training a convolutional neural network to recognize known tremor on a single station in Cascadia, we detect weak tremor preceding and following known larger slow earthquakes, the detection rate of these weak tremors approximates the slow slip rate at all times, and the same model is able to recognize tremor from different tectonic environments with no further training. >>

Bertrand Rouet-Leduc, Claudia Hulbert, et al. Probing Slow Earthquakes With Deep Learning. Geophysical Research Letters. Volume 47, Issue 4. doi: 10.1029/2019GL085870. Jan 23, 2020.

https://agupubs.onlinelibrary.wiley.com/doi/full/10.1029/2019GL085870