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- Nov 2021
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www.science.org www.science.org
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Couzin-Frankel, J. (2021). Antiviral pills could change pandemic’s course. Science, 374(6569), 799–800. https://doi.org/10.1126/science.acx9605
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www.frontiersin.org www.frontiersin.org
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Interesting diffs between IgG1, Ig2, IgG3, IgG4.
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drive.google.com drive.google.com
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high school students learning of biology online in the Netherlands
high school students learning of biology online in the Netherlands
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arxiv.org arxiv.org
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Yang, P., & Colavizza, G. (2021). A Map of Science in Wikipedia. ArXiv:2110.13790 [Cs]. http://arxiv.org/abs/2110.13790
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Following IM administration, the maximum concentration (Cmax) of the injection site muscle was 5,680 ng/mL, and the level declined with an estimated t1/2 of 18.8 hr
Vaccine's halg-life was measured just below a day for mice muscles.
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The spleen and liver had a mean Cmax of 86.9 ng/mL
Spleen & liver had x30 less mRNA concentration than Lymph nodes closest to the vaccine site, and x70 less the injected muscle.
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Proximal lymph nodes had the second highest concentration at 2,120 ng/mL (tmax of 8 hr with a relatively long t1/2 of 25.4 hr)
Lymph-node mRNA half-life is a day.
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Burn, G. L., Foti, A., Marsman, G., Patel, D. F., & Zychlinsky, A. (2021). The Neutrophil. Immunity, 54(7), 1377–1391. https://doi.org/10.1016/j.immuni.2021.06.006
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Possible routes to platelets activation by covid19.
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Thursday, he announced that private-sector businesses with more than 100 employees must make sure their workers are fully vaccinated or be tested each week before coming to work.The
surveillance state: meet the first candidate for a govnerment created retroviral biotracker:
COVID-19 and it's quanta of "so long, freedom"
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Telstra on Twitter: “I’m fully aware this won’t stop ‘the vaxx gave me 5G’ jokes. But #LetsVaxx anyway. Https://t.co/IwM7AwrpJ6” / Twitter. (n.d.). Retrieved September 9, 2021, from https://twitter.com/Telstra/status/1433191938497282051
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twitter.com twitter.com
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Michael Mina on Twitter: “With all the news of vaccines & immunity, did you know measles infections destroy immunity and cause ‘Immune Amnesia’, increasing risk of all other infections Our research in ‘15 & ‘19 discovered this & the abbreviated story is written up nicely here: 1/ https://t.co/t5DKoQljxM” / Twitter. (n.d.). Retrieved September 7, 2021, from https://twitter.com/michaelmina_lab/status/1435037668027641861
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- Aug 2021
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- Jul 2021
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However, human babies are also able to immediately detect objects and identify motion, such as a finger moving across their field of vision, suggesting that their visual system was also primed before birth.
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A new Yale study suggests that, in a sense, mammals dream about the world they are about to experience before they are even born.
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Source: Structural image from Lorenzo Casalino, Univ. California, San Diego (Ref. 1); Graphic: Nik Spencer/Nature
The best diagram of the covid19 spike protein.
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标签蛋白IP或基于标签的pull-down
a very good sumamry of the difference between Pull-down and IP assays. Pros and cons of both methods are described.
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από τις 53 μελέτες που είχαν υποβληθεί από παραγωγούς της γλυφοσάτης στην EFSA μόλις δύο ήταν επιστημονικά αξιόπιστες με βάση τα διεθνή πρότυπα του ΟΟΣΑ. Οι 34 ήταν μη αξιόπιστες ενώ οι υπόλοιπες 17 μερικά αξιόπιστες.
Πάμε πάλι: η Επιστήμη δεν αποφαίνεται για θετικά συμπεράσματα, αλλα μονο διαψεύδει.
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mlech26l.github.io mlech26l.github.io
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In our research, i.e., the wormnet project, we try to build machine learning models motivated by the C. elegans nervous system. By doing so, we have to pay a cost, as we constrain ourselves to such models in contrast to standard artificial neural networks, whose modeling space is purely constraint by memory and compute limitations. However, there are potentially some advantages and benefits we gain. Our objective is to better understand what’s necessary for effective neural information processing to emerge.
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www.sciencedaily.com www.sciencedaily.com
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“Although a seemingly mundane and simple innovation, Linnaeus' use of index cards marks a major shift in how eighteenth-century naturalists thought about the order of nature,” says Mueller-Wille. The natural world was no longer ordered on a fixed, linear scale, but came to be seen as a map-like natural system of multiple affinities.
Ha!
Roughly the idea I'd just written!
The idea of reordering nature this way would have been fantastic, particularly in light of the general prior order of the cosmos based on the scala naturae or Great Chain of Being.
Compare this with Ernst Haeckel's Tree of Man. What year was this in relation? Was the idea of broader biological networks and network-like structure thought of prior to this?
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- Jun 2021
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Zhao, H., Wu, D., Nguyen, A., Li, Y., Adão, R. C., Valkov, E., Patterson, G. H., Piszczek, G., & Schuck, P. (2021). Energetic and structural features of SARS-CoV-2 N-protein co-assemblies with nucleic acids. IScience, 24(6), 102523. https://doi.org/10.1016/j.isci.2021.102523
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Study finds potentially druggable process of SARS-CoV-2 replication. (n.d.). Retrieved June 24, 2021, from https://phys.org/news/2021-06-potentially-druggable-sars-cov-replication.html
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osf.io osf.io
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Singh, Urvashi B., Mercy Rophina, Dr Rama Chaudhry, Vigneshwar Senthivel, Kiran Bala, Rahul C. Bhoyar, Bani Jolly, et al. “Variants of Concern Responsible for SARS-CoV-2 Vaccine Breakthrough Infections from India.” OSF Preprints, June 3, 2021. https://doi.org/10.31219/osf.io/fgd4x.
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An easy access dashboard now provides links to scientific discussion and evaluation of bioRxiv preprints. (n.d.). Retrieved 30 May 2021, from https://connect.biorxiv.org/news/2021/05/14/dashboard .
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blogs.sciencemag.org blogs.sciencemag.org
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This might explain the seemingly higher frequence of this serious complication compared to the mRNA delivery methods which have other problems, in particular related to the ionizable cationic lipid packaging which have strong toxic effects.
On brain tissue damages due to AstraZeneca.
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localhost:8080 localhost:8080
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<small><cite class='h-cite via'>ᔥ <span class='p-author h-card'>Maël Montévil</span> in "I've redone my #academic website using @eleven_ty It is fun to play with various data sources like @CrossrefOrg api as a complement to #webmention. I also took some inspiration and code from @nhoizey https://t.co/ULaTAMDYZC" / Twitter (<time class='dt-published'>05/12/2021 17:52:48</time>)</cite></small>
Theoretical biology AND webmentions? I'm in.
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Cepelewicz, J. (n.d.). The Hard Lessons of Modeling the Coronavirus Pandemic. Quanta Magazine. Retrieved February 11, 2021, from https://www.quantamagazine.org/the-hard-lessons-of-modeling-the-coronavirus-pandemic-20210128/
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- Apr 2021
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theoretical biologist
This field is not well recognized, but hopefully this situation will change!
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Once established, however, it spreads slowly. Unlike aggressive Kentucky bluegrass, which spreads by underground stems called rhizomes, perennial ryegrass is a bunch-forming grass. Like tall fescue, it naturally grows in clumps and spreads through vertical shoots known as tillers, rather than spreading by rhizomes or horizontal above-ground stems, known as stolons.
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- Mar 2021
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en.wikipedia.org en.wikipedia.org
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Annotators
URL
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www.scientificamerican.com www.scientificamerican.com
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Wallis, C. (n.d.). Why Some People Get Terribly Sick from COVID-19. Scientific American. Retrieved August 24, 2020, from https://www.scientificamerican.com/article/why-some-people-get-terribly-sick-from-covid-19/
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collect.readwriterespond.com collect.readwriterespond.com
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As well as the discussion about what is really meant by a ‘domain of one’s own‘
Societies have been inexorably been moving toward interdependence. More and more people specialize and sub-specialize into smaller fragments of the work that we do. As a result, we become more interdependent on the work of others to underpin our own. This makes the worry about renting a domain seem somewhat disingenuous, particularly when we can reasonably rely on the underlying structures to work to keep our domains in place.
Perhaps re-framing this idea may be worthwhile. While it may seem that we own our bodies (at least in modern liberal democracies, for the moment), a large portion of our bodies are comprised of bacteria which are simultaneously both separate and a part of us and who we are. The symbiosis between people and their bacteria has been going on so long and generally so consistently we don't realize that the interdependence even exists anymore. No one walks around talking about how they're renting their bacteria.
Eventually we'll get to a point where our interdependence on domain registrars and hosts becomes the same sort of symbiotic interdependence.
Another useful analogy is to look at our interdependence on all the other pieces in our lives which we don't own or directly control, but which still allow us to live and exist.
People only tend to notice the major breakdowns of these bits of our interdependence. Recently there has been a lot of political turmoil and strife in the United States because politicians have become more self-centered and focused on their own needs, wants, and desire for power that they aren't serving the majority of people. When our representatives don't do their best work at representing their constituencies, major breakdowns in our interdependence occur. We need to be able to rely on scientists to do their best work to inform politicians who we need to be able to trust to do their best work to improve our lives and the general welfare. When the breakdown happens it creates issues to the individual bodies that make up the society as well as the body of the society itself.
Who's renting who in this scenario?
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- Feb 2021
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www.youtube.com www.youtube.com
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Center for Infectious Disease Dynamics—YouTube. (n.d.). Retrieved 21 February 2021, from https://www.youtube.com/channel/UC1dZp4v6sF2jKjutJguk7ng/videos?view=0&sort=da&flow=grid&view_as=subscriber
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www.virology.ws www.virology.ws
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Fredericks DN, & Relman DA (1996). Sequence-based identification of microbial pathogens: a reconsideration of Koch’s postulates. Clinical microbiology reviews, 9 (1), 18-33 PMID: 8665474
Repostulation of Koch's rules in the era of the virueses.
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- Jan 2021
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www.theatlantic.com www.theatlantic.com
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Proteins are made up of building blocks called amino acids. N501Y means that the 501st amino acid was originally an N, which stands for the amino acid asparagine, but has been changed to a Y, which stands for tyrosine.
The takeaway: Amino acids, represented by single letters such as N or Y make up proteins which are part of the coronavirus (as well as other biology such as animals, plants, microorganisms, etc.). Mutations are written with the original amino acid letter followed by the number of the amino acid and the new amino acid letter.
The claim: Proteins are made up of building blocks called amino acids. N501Y means that the 501st amino acid was originally an N, which stands for the amino acid asparagine, but has been changed to a Y, which stands for tyrosine.
The evidence:
Coronavirus is made up of greater than 20 proteins (1). The spike protein helps coronavirus attach and enter human cells which leads to infection and disease (1). The spike protein on SARS-CoV-2, the virus that causes COVID-19, is the target of many antibodies produced by the human body to fight the SARS-CoV-2 infection (2). Changes in the spike protein sequence may necessitate a change in the human immune system to produce antibodies which stop SARS-CoV-2 from infecting human cells. Changes in the amino acid sequence are written as was stated in the claim: original amino acid, number of the amino acid in the sequence, new amino acid.
Sources:
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blogs.scientificamerican.com blogs.scientificamerican.com
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Johnson: Earlier I interviewed you about patrilocal residence patterns and how that alters women’s sexual choices. In contrast, matrilocal societies are more likely to be egalitarian. What are the factors that lead to the differences between these two systems?Hrdy: I think in societies where women have more say, and that does tend to be in societies that are matrilocal and with matrilineal descent or where, as it is among many small scale hunter-gatherers, you have porous social boundaries and flexible residence patterns. If I had to say what kind of residence patterns our ancestors had it would have been very flexible, what Frank Marlowe calls multilocal.
Matrilocality, matrilinearity and egailitarianism.
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- Nov 2020
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www.quantamagazine.org www.quantamagazine.org
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“Half of what you learned in college is wrong,” my biology professor, David Lange, once said. “Problem is, we don’t know which half.”
Very interesting that a biology professor believes that 50% of what we learn can be wrong.
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www.healthline.com www.healthline.com
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Schleiss says a better analogy for COVID-19 is the mumps. For more than 45 years, we’ve had a very effective vaccine for measles, mumps, and rubella (which are also RNA viruses).
The takeaway: Even though mutations happen in all virus, vaccines still work. Current evidence about SARS-CoV-2 indicates that an effective COVID-19 vaccine can be obtained, and that it should be able to provide immunity against the virus.
The claim: A better analogy for COVID-19 is the mumps. For more than 45 years, we’ve had a very effective vaccine for measles, mumps, and rubella (which are also RNA viruses).
The evidence: We are all imperfect and we all make mistakes. For a virus, a mistake means the introduction of a mutation in its sequence, and RNA viruses (like the flu, mumps, measles virus, and SARS-CoV-2) have the highest error rates in nature. Mutations are indispensable for viral survival and evolution; this property is believed to benefit the viral population, allowing it to adapt and respond to different complex environments encountered during spread between hosts, within organs and tissues, and in response to the pressure of the host immune response [1]. How fast a virus is changing can be estimated by measuring its mutation rate, and then they can be classified as changing fast – high mutation rate – like HIV or Influenza, or as stable, like measles or mumps virus. SARS-CoV-2 has a mutation rate three times slower than the flu virus [2], but it's still changing faster than the mumps virus (the mutation rate of influenza is more than 10 times higher than mumps) [3]. Of course, how fast a virus can change has implications in the efficacy of treatments and vaccines, but it's not the only determinant. Even though mutations happen in all viruses, vaccines still work. A great example is the measles virus, as the antigenic composition of the vaccine (the molecules that “wake up” the immune system) used to prevent it has remained efficient since it was developed, in the 1960s, and confers protection against the 24 circulating genotypes [4]. The same is true for the mumps virus, with a vaccine that has been efficient for many decades [5]. Sequencing data suggest that coronaviruses change more slowly than most other RNA viruses, probably because of a viral ‘proofreading’ activity that corrects all the copying mistakes [6]. Taken together, all this evidence indicates that an effective COVID-19 vaccine can be obtained, and that it should be able to provide lasting immunity against the virus.
Sources:<br> 1
2 SARS-CoV-2 mutation rate: 1.26 x 10-3 substitutions/site/year
3 Influenza (flu-virus) mutation rate: 3.68 x 10-3 substitutions/site/year. Mumps mutation rate: 2.98 × 10−4 substitutions/site/year
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- Oct 2020
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core-genomics.blogspot.com core-genomics.blogspot.com
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Kits rock! But understanding what is going on at each stage of the protocol provided with the kit really helps with troubleshooting and modification.
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www.the-scientist.com www.the-scientist.com
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Ideas on how to analyze and predict network behavior have been informed by concepts arising from the computational and social sciences, which are themselves increasingly concerned with understanding networks. The interesting thing about these ideas is that they work at scales ranging from the molecular to the population level.
scale free networks perhaps?
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I had bookmarked this article in the form of tearing out and keeping a paper copy of it in my to read pile back in 2008. Finally getting around to reading it today. It's still an interesting introduction to the broader area which has moved forward, but not significantly enough to date the entire area.
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