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NNadir

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Current location: New Jersey
Member since: 2002
Number of posts: 28,552

Journal Archives

Nature: SARS-CoV-2 infection in free-ranging white-tailed deer

I really shouldn't post in GD, but I'm not feeling well, can't get a Covid test, (and neither can my wife who is more ill than I am) and well, what the hell, I'm already in a bad mood, but only mildly ill, not necessarily from Covid.

This paper comes with the following disclaimer from Nature:

We are providing an unedited version of this manuscript to give early access to its findings. Before final publication, the manuscript will undergo further editing. Please note there may be errors present which affect the content, and all legal disclaimers apply.


The full preliminary publication can be found here: SARS-CoV-2 infection in free-ranging white-tailed deer. The full text can be downloaded as a PDF, including graphics and experimental details. I am logged into Nature, but Nature Springer keeps Covid papers open sourced, and the full text should be available to anyone.

The authors are largely from institutions in Ohio, with some participants working at the NIH in Maryland.

I'm personally not panicked by this result; and I live in what may be in a deer festival zone, I can't go outside for more than an hour without seeing one or more deer.

I do not know if any of the deer from this report in Ohio, or the deer all over the place in New Jersey, ever went to a secret lab in Wuhan, or whether any of them bought anything at the Wuhan market, but for what it's worth, here's the report.

Considerable escape of SARS-CoV-2 Omicron to antibody neutralization: Nature Accelerated

...Report.

It's been reviewed and accepted and comes with this note:

ADVANCE ARTICLE PREVIEW

This manuscript has been peer reviewed and accepted for publication in Nature and is provided in this format here as a response to the exceptional public-health crisis. This accepted manuscript will continue through the processes of copy editing and formatting to publication of a finalized version of record on nature.com. Please note there may be errors present in this version, which may affect the content, and all legal disclaimers apply.


It's here: Considerable escape of SARS-CoV-2 Omicron to antibody neutralization: Considerable escape of SARS-CoV-2 Omicron to antibody neutralization


As the paper is in prepublication, the figures are not included in the PDF. I'm logged in to Nature, but I expect the publication is open sourced, whereupon one can read the institutions of the authors, who are in France and Belgium.

We can take it for what it's worth, but it is, as opposed to a tweet, about to published in one of the World's Premier Scientific Journals, if not the Washington Post and the New York Times, or again, a post on Twitter.

However, I speculate that this paper, as opposed to the one I referred to in another post here, is more likely to be picked up by the popular media.

Note that this paper refers largely to therapeutic antibodies (including sera from infected patients) administered by injection as pharmaceutical agents as opposed to antibodies generated by immune response.

Have a happy, safe, and productive New Year.

Broadly neutralizing antibodies overcome SARS-CoV-2 Omicron antigenic shift: Nature Accelerated...

...Report.

It's been reviewed and accepted and comes with this note:

ADVANCE ARTICLE PREVIEW

This manuscript has been peer reviewed and accepted for publication in Nature and is provided in this format here as a response to the exceptional public-health crisis. This accepted manuscript will continue through the processes of copy editing and formatting to publication of a finalized version of record on nature.com. Please note there may be errors present in this version, which may affect the content, and all legal disclaimers apply.


It's here: Broadly neutralizing antibodies overcome SARS-CoV-2 Omicron antigenic shift

As the paper is in prepublication, the figures are not included in the PDF. I'm logged in to Nature, but I expect the publication is open sourced, whereupon one can read the institutions of the authors, which span the globe, and represent every inhabited continent.

We can take it for what it's worth, but it is, as opposed to a tweet, about to published in one of the World's Premier Scientific Journals, if not the Washington Post and the New York Times, or again, a post on Twitter.

Have a happy, safe, and productive New Year.

Weird but fun: Effects of Neutron Transmutation of Silicon to Raise Thermoelectric Figures of Merit.

Wandering around in a desultory fashion in the literature, I came across this paper: Gaidar, G.P. The Effect of Thermal Treatment on the Thermoelectric Figure of Merit of Silicon Doped Using Nuclear Transmutation. Surf. Engin. Appl.Electrochem. 57, 425–430

Recently my son and I were discussing the properties of silicon in a neutron flux in connection with corrosion resistant refractories, not thermoelectric devices, and drifting around the literature I came across the paper linked above. It's something I never would have thought of doing.

Thermoelectric devices convert heat directly into electricity; these devices are mostly known from space mission RTGs (Radioisotope Thermoelectric Generators) used on Space missions to Mars and the outer planets. The Voyager missions now beyond our solar system are still powered by devices of this type launched in the 1970s. As they have no moving parts, they are very reliable.

The downside is their low thermal efficiency and current research is devoted to raising the "Figure of Merit," a dimensionless number reflecting efficiency, which generally varies with temperature.

Precise nanostructure of thermoelectric devices is important in adjusting two conflicting properties, thermal conductivity and electrical conductivity in opposing direction of magnitude, not an easy trick, but doable.

The paper puts it this way:

Hence, a good thermoelectric material must have simultaneously high electric conductivity, high thermo-emf and low thermal conductivity.


In this case the author was studying phosphorous doped silicon as a thermoelectric material and evaluated two ways of making it, one by traditional melt processes in which the phosphorous dissolves in the molten Si forming an impurity, the other involved placing the silicon into a nuclear reactor and irradiating it with neutrons. Under these conditions, one of the isotopes of silicon, Si-30 is transmuted into phosphorous's only stable isotope, P-31.

The rationale for the latter approach was to more precisely locate the phosphorous atoms.

From the text:

During the irradiation of the silicon monocrystals by the flux of slow neutrons, a certain amount of silicon atoms turns into phosphorus atoms, which are uniformly distributed throughout the bulk of a crystal. However, because of a strong interaction of neutrons with Si atoms, the atoms of phosphorus are generally located in the interstitial spaces. In order that all (or at least the majority) of the phosphorus atoms (obtained as a result of the neutron radiation) appeared to be in the lattice nodes and could exhibit electric activity, a special technological annealing is needed (at 800°С for 2 h).


Both processes required annealing, and it was determined the cooling rate was an important factor in performance.

The figure of merit was better for the neutron irradiated material, not enormously so, but better.

Neutron induced transmutation is often discussed with respect to certain components of used nuclear fuel for various reasons, mostly in connection of shortening their half-lives, and in fact, it is a continuous process in nuclear fuels in use. Neutrons are also widely used as analytical tools, most typically in diffraction experiments; my son participated in some of this type of work during an Oak Ridge internship.

I can't recall if I've ever seen an application quite like this however. Maybe I have, but if so, I've forgotten it.

I wouldn't expect it to go commercial, but it's pretty cool, and in my conversation with my son about silicon in neutron fluxes, it's worth discussion.

Don't try this at home.

I wish you a happy New Year.

Whatever. Thanks for all your "critical thinking" here, with emphasis on "critical..."

and your spectacular defense of the science "news" in the Washington post.

You are invited to continue to get your "science" there, but I'll continue to read the primary scientific literature because I can.

Most people - and this is regrettable I think - do not have the same access to the scientific literature that I do but I fully concede your impassioned lawyerly nitpicking is memorable even if, as I suspect, you don't read the primary scientific literature and therefore are not in a position to compare its quality with so called "Mainstream news."

I don't feel that I am required to actually read the Washington Post to have an opinion of it, since I'm an old man who used to take it and other "papers of record" seriously but now feel as if, particularly in recent years, they have the quality of the World Weekly News, especially when it comes to say, Hillary Clinton.

Personally I have a hard time choosing between this: The FBI found 15,000 emails Hillary Clinton didn’t turn over. Uh oh.

The Fix's Chris Cillizza explains the latest on Hillary Clinton's private email server. (Peter Stevenson/The Washington Post)

By Chris Cillizza August 22, 2016

If you scrape away all of the spin and the political positioning that Hillary Clinton's decision to use a private email server has spawned, you are left with these facts:

1. Clinton is the first secretary of state to exclusively use a private email account for official business.

2021 Election: Complete coverage and analysis

2. She is also the first secretary of state to have a private email server housed at her home.


...and this...



"The fix" indeed.

You have carefully read what you say is not worth reading, my post, passionately picking at the flaws, and I have declined to read what I say is not worth reading, the Washington Post's story about how terrifying omicron is, and you rightly critically thought to criticize me.

It was certainly a waste of time for both of us, though wasn't it? I could have carefully read at least five or six papers from the primary scientific literature in the time I spent being annoyed by your nitpicking over the particulars of this case.

You would however, make a good defense lawyer, I think. If you are one or become one, I would advise you, if you are hired by Mark Meadows to defend his private email accounts, I bet you won't find them described with the same "oh oh" that the Washington Post offered us in 2016. This said, I can't know, because I decline to read what is not worth reading and you do read what you think not worth reading. If you take the Meadows case make sure the Trump people pay you up front. I hear they skip paying bills a lot.

Since I don't read it, I won't further speculate whether the Washington Post included a big "uh oh" when describing Meadows email like the one they employed for Secretary Clinton, but the fact of the "uh oh," in 2016 may be one reason that I consider the paper a rag not worth reading, in addition to the current case about Denmark; my impression might have involved that history.

Let's review: I think the paper, the Washington Post is a rag, not worth reading and you think I'm being unfair and I'm not worth reading even though you waste time reading and nitpicking through what I write.

Good for you. Feel free to read the Washington Post all the time and be informed with all that critical thinking you displayed here in its defense, wasting both our time.

Please do me a favor. Since I'm not worth reading, don't waste your time reading what I write. I'm clearly beneath you, if not your consideration of my flaws, and the annoyance I have felt at addressing your "critical thinking" such as it is, led me - my own fault - to waste time I could have used to finish reading papers like this one:

Mechanisms of SARS-CoV-2 Evolution Revealing Vaccine-Resistant Mutations in Europe and America (Rui Wang, Jiahui Chen, and Guo-Wei Wei The Journal of Physical Chemistry Letters 2021 12 (49), 11850-11857)

...in which I never got past this text...

...Although there are 28,912 unique single mutations distributed widely on the whole SARS-CoV-2 genome, the mutations on the S gene stand out among all 29 genes on SARS-CoV-2 due to the mechanism of viral infection. With the assistance of host transmembrane protease, serine 2 (TMPRSS2), SARS-CoV-2 enters the host cell by interacting with its S protein and the host angiotensin-converting enzyme 2 (ACE2) (10) (see Figure 1b). Later, antibodies will be generated by the host immune system, aiming to eliminate the invading virus through direct neutralization or non-neutralizing binding, (11,12) which makes the S protein the main target for the current vaccines. Specifically, there is a short immunogenic fragment located on the S protein of SARS-CoV-2 that can facilitate the binding of SARS-CoV-2 S protein to ACE2, which is called the receptor-binding domain (RBD). (13) Studies have shown that the binding free energy (BFE) between the S RBD and the ACE2 is proportional to the infectivity. (10,14−17)....


...because I was foolishly checked in here and ended up frankly finding myself childishly dicking around with someone interested in dicking around with me.

I'm disappointed in myself for dicking around with dicking around, since the paper I was reading would have been worthwhile, and I stepped away from it for this, which is not worthwhile.

I'm sure I had a thousand more useful things I could have done with this time. How about you? Was there something you could have done that was interesting as opposed to this uninteresting exchange? At least you could have read all about how scary things are in Denmark in the Washington Post, but, wait, you did, which apparently, you were inspired to do in order to get at me. And you did. You annoyed the shit out of me and showed me to be a fool for engaging you here. Congrats.

We value our time differently and I can't believe I wasted it in this dicking around.

Have a happy, healthy and prosperous New Year, and try not to go to Denmark if you can avoid it. It's a very scary place. I heard about it somewhere in the news.

Here's something you don't see often, a 1905 chemistry paper cited 214 times in modern literature.

I came across this paper this evening in my general reading: Villermaux–Dushman Test of Micromixing Characterization Revisited: Kinetic Effects of Acid Choice and Ionic Strength (Pierrette Guichardon, Carlos Baqueiro, and Nelson Ibaseta Industrial & Engineering Chemistry Research 2021 60 (50), 18268-18282.)

It contains the following text:

The so-called Dushman reaction is involved in the Villermaux–Dushman system, composed of rapid multiple reactions, which has a product distribution particularly sensitive to the micromixing (mixing at the molecular scale).
This peculiar system is nowadays widely used for examining the micromixing efficiency either in batch reactors or continuous mixers. It was developed in the 1990s by Villermaux’s team in Nancy. (1−4)...

...The first kinetic investigation of reaction r1 has been carried out by Dushman. (5) Ever since, various contributions have proposed numerous scattered kinetic data, and the confusion surrounding this venerable reaction is still current...


I am always interested in iodine chemistry since it a key component of the (unrelated) sulfur iodine cycle, a famous thermochemical hydrogen cycle that is amenable to continuous flow chemistry, so, being unfamiliar with the Villermaux-Dushman test, I decided to peak into some references.

Reference 5 is this one: Dushman, S. The rate of the reaction between iodic and hydriodic acids. J. Phys. Chem. A 1904, 8, 453– 482.

The ACS posted it to the internet in 2002; it's open sourced.

This is a kinetics paper that was published when Albert Einstein was a young man still working to publish the Special Theory of Relativity.

One doesn't see papers published this long ago on kinetics cited, so I checked out Google Scholar, which lists the paper. The 2002 link says its been cited 214 times since 2002.

Cool...

A Covid Comparison of Popular Media Reporting to Scientific Literature Reporting.

Here's two titles from two different sources reporting on the Omicron status in Denmark:

Title One, from the Washington Post: Highly vaccinated countries thought they were over the worst. Denmark says the pandemic’s toughest month is just beginning.

Title Two, from the scientific literature: Epidemiological characterisation of the first 785 SARS-CoV-2 Omicron variant cases in Denmark, December 2021.

The first is behind a firewall, the second, since all major scientific publishers have made Covid reporting open source, isn't.

I commented on the second over in the Science forum: Epidemiological Classification of Omicron in Denmark, the first 785 cases, with outcomes.

The first headline comes with the implication we're all going to die, vaccinated or not.

The second reports data.

The second reports (Table 2) among 785 confirmed Omicron cases that vaccinated cases of Omicron of people having received two doses of the vaccine is 599, and 56 cases occurred in people who have had booster shots. 111 cases occurred in people who had not been vaccinated at all.

However, the majority of Danes have been vaccinated, close to 80%, 78.2% exactly according to a website maintained by Johns Hopkins University: Johns Hopkins University Coronavirus Resource Center (Accessed 12/29/21, scroll over the map to get a popup with data for a country.) The number of fully vaccinated Danes is 4,549,739. This implies that the population represented by the Johns Hopkins data is roughly 5,818,000 of whom 1,238,000 are not fully vaccinated.

When someone engages in "percent talk" - something against which I often rale in the context of the "success" of so called "renewable energy," which is no success at all at addressing climate change - it is time to turn on one's critical thinking muscles. For example, we do not know whether the 785 cases represent all cases of omicron in Denmark, or whether it is a sample of the total cases. Nevertheless we can get a crude sense of probability using "percent talk" if we assume that the data holds throughout a sampled population. 599 cases represents 0.013% of the vaccinated (total) of vaccinated Danes, 111 cases represent 0.009% of unvaccinated Danes. It would seem on the surface vaccinated people are slightly more likely to have been infected with omicron, but a little critical thinking would note that this calculation ignores behavior. I do not know what restrictions on Danes exist for attending public events but on multiple occasions, both for scientific meetings and for entertainment, I have had to prove vaccination status to attend. I would have been excluded if I wasn't vaccinated. Thus their is a potential behavioral weight not recorded.

The question really revolves, however, over the use in the Washington Post headline of the word "dire."

Hospitalization in the scientific report is not broken down by vaccination status, but of the 785 omicron cases recorded 9 required hospitalization, 1 was admitted to ICU and nobody died. One may compare in Table 2 similar data related to the Delta variant in Denmark, where there is very distinct difference, in "percent talk" and, in fact, in reality between vaccinated and unvaccinated Danes.

No omicron patient died. Zero. Nine were hospitalized. How "dire" is that really?

The quality of the media in this country is devolving faster than the corona virus is evolving. For instance, our media reports both on climate change and on coronavirus overt and obvious lies as if they were part of a legitimate debate. They report insanity as "news."

It thrives on sensationalism and fear and selective attention: "But her emails..."

The Washington Post article, which I did not read beyond the headline, is, again, behind a pay firewall. If you pay for it, you're paying for entertainment, not news.

Here's where we're going with our media:



Critical thinking has never been required more than it is today.

Poland Narrows Down Nuclear Sites.

Poland narrows down nuclear sites

The seaside towns of Lubiatowo and Kopalino in Poland's Choczewo municipality have been named as the preferred location for the country's first large nuclear power plant.

The choice was announced by Polskie Elektrownie Jadrowe (PEJ), the government company that is progressing its policy to deploy up to six reactors at multiple sites by 2040.

PEJ said very detailed environmental and location studies have been conducted on the area since 2017, with the support of Jacobs as a technical advisor. Potential nuclear energy development in Choczewo has been a subject of public discussion since Poland's programme began in 2011. A nationwide effort to raise awareness of nuclear energy has seen three local information centres established in the area, among other efforts. The goal was to "enable everyone to form their own opinion..."

...This confirmed that the province of Pomerania was generally suitable, and more detailed studies began both on Lubiatowo-Kopalino and Żarnowiec. These confirmed that the location of Lubiatowo-Kopalino "is the best option for the environment and safe for people," said PEJ.

"We want the entire investment process in the project of the first nuclear power plant in Poland to be transparent, responsible and to the highest standards from the very beginning," said Tomasz Stępień, chair of PEJ. The "long-term and comprehensive analysis" of locations where the power plant could be built has been a priority for the company in recent years, he added.

PEJ noted a recent opinion poll that showed 74% support for construction of nuclear power plants in Poland as well as 63% support among residents of Choczewo, Gniewino and Korkowa to build nuclear facilities in Pomerania province.


Poland is almost entirely dependent on coal for its electrical generation, including the power it exports to Germany when the wind isn't blowing.

Polish support for nuclear energy is high because apparently, in Poland, the citizenry elevates the reality of climate change over paranoia promoted by generally ignorant people.

Currently, as of this writing (accessed 12/29/21) household electricity prices in Poland are 0.1548 Eu/kwh, compared to 0.1933 Eu/kwh in France, and nearly half of those in that offshore gas and oil drilling hellhole Denmark, 0.29 Eu/kw, which now has for the first time in recent memory the 2nd highest electricity prices in Europe, having fallen below Germany, where electricity prices are 0.3193 Eu/kwh. (Prices can be determined by moving the cursor over the bar graph in the link.)

One hears all the time from people who have huge trouble handling numbers or interpreting bar graphs like the one available at the link above that nuclear energy is "too expensive," to which I ask "for whom?" The "for whom" refers to future generations, on whom, the responsibility for waste, including abandoned wind turbines and the electronic waste of dead solar cells will be dumped.

The current Polish electricity supply is subsidized by future generations, since the Poles are currently allowed to dump the dangerous fossil fuel waste carbon dioxide directly into the planetary atmosphere for free, along with volatized heavy metals like lead, mercury and (gasp) uranium in fly ash, along with sulfur dioxide and sulfur trioxide, which like abandoned wind turbines and electronic waste, will affect every single person born in 2022 for their entire lifetimes.

The Poles find this morally unacceptable apparently and have chosen to embrace the energy profile of France, where used nuclear fuel is contained and is available for use by the generations. These generations will have to clean up the mess we made by not embracing nuclear energy, and/or, well, live in extreme poverty if not die.

(France holds the largest supply of twice through plutonium - used MOX fuel - in the world, an essential resource because of its marvelous isotopic vector. Their infrastructure will hopefully available to the Poles.)

Modern nuclear reactors are designed to operate from 60 to 80 years, meaning nuclear infrastructure, if it takes the Poles ten years to go nuclear, will be available to Poles as the 22nd century approaches. Any nuclear plant built in Poland will be a gift to future generations of Poles.

The lifetime of wind turbines can be readily calculated from the Danish Master Register of Wind Turbines. The last time I used Excel functions to do these calculations, the mean lifetime of a wind turbine in Denmark was about 18 years.

I hope your New Year will be productive and rewarding.

Epidemiological Classification of Omicron in Denmark, the first 785 cases, with outcomes.

Espenhain Laura, Funk Tjede, Overvad Maria, Edslev Sofie Marie, Fonager Jannik, Ingham Anna Cäcilia, Rasmussen Morten, Madsen Sarah Leth, Espersen Caroline Hjorth, Sieber Raphael N., Stegger Marc, Gunalan Vithiagaran, Wilkowski Bartlomiej, Larsen Nicolai Balle, Legarth Rebecca, Cohen Arieh Sierra, Nielsen Finn, Lam Janni Uyen Hoa, Lavik Kjetil Erdogan, Karakis Marianne, Spiess Katja, Marving Ellinor, Nielsen Christian, Wiid Svarrer Christina, Bybjerg-Grauholm Jonas, Olsen Stefan Schytte, Jensen Anders, Krause Tyra Grove, Müller Luise. Epidemiological characterisation of the first 785 SARS-CoV-2 Omicron variant cases in Denmark, December 2021. Euro Surveill. 2021;26(50):pii=2101146.

This one looks like pretty good news. Of the 785 omicron cases, only 9 required hospitalization, 1 patient went into intensive care, no deaths. Only 7.1% of the Omicron cases took place in boosted patients.

Note that these statistics do not include people who did not get either variant of Covid.

Nice overview of Omicron symptoms from an outbreak from a Norwegian Christmas Party.

Outbreak caused by the SARS-CoV-2 Omicron variant in Norway, November to December 2021 (Brandal Lin T., MacDonald Emily, Veneti Lamprini, Ravlo Tine, Lange Heidi, Naseer Umaer, Feruglio Siri, Bragstad Karoline, Hungnes Olav, Ødeskaug Liz E., Hagen Frode, Hanch-Hansen Kristian E., Lind Andreas, Watle Sara Viksmoen, Taxt Arne M., Johansen Mia, Vold Line, Aavitsland Preben, Nygård Karin, Madslien Elisabeth H.. . Euro Surveill. 2021;26(50):pii=2101147)

None of the subjects had a booster dose, but 89% had been vaccinated. 81 out of 111 respondents tested positive. (Six people did not respond to inquiries.) All but one of the positive tested cases had at least one symptom.

The Moderna vaccine did seem more prevalent in the subjects who didn't test positive. Of the 25 attendees who didn't test positive, 12 had Moderna vaccines (Spikevax) and 7 Pfizer vaccines.

My sister-in-law visited for Christmas. Her boyfriend got very sick. (He was vaxxed and boosted.) I've had all three Moderna shots; the boyfriend has not had confirmed Covid, but he was very sick. I'm tired, but then again, I suffered from one of the more intense episodes of insomnia last night. I've been an insomniac my whole life. I did have headaches, but that's not unusual either.

It will be interesting to see if any of us get it. My sons were booth boosted (Pfizer 2 doses, Moderna booster), but my oldest only a few days ago. My wife had all three Moderna shots; she's tired, but otherwise OK.

The incubation time seems shorter with Omicron overall, about 3 days.

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