NNadir

NNadir's Journal

January 16, 2023

I just realized my kid got an acknowledgement in a Ph.D. thesis for stuff he did as an undergrad.

Apparently he helped a grad student with something when he was interning at ORNL just before his junior year. It was enough to earn an acknowledgement.

The thesis was on the relations between amorphous materials and crystalline materials.

Pretty cool. I have to ask him about it next time I talk to him.

January 16, 2023

In my reading, I came across an interesting quote from a book that caused me to order it.

The book I'm reading now is a picture book for the non-profession on cognition called "How to Win the War on Truth," subtitled:

AN ILLUSTRATED GUIDE TO HOW MISTRUTHS ARE SOLD, WHY THEY STICK, AND HOW TO RECLAIM REALITY

(The author is decidedly on our side of the political spectrum.)

In the chapter called "Bias and the Brain" another work is quoted as follows:

Faced with the choice between changing one's mind and proving there's no need to do so, almost everyone gets busy on the proof.

It's from Robert Trivers, a sociobiologist, and the book in which it appears is called The Folly of Fools.

My library has it. I ordered it, even though I'm very far behind in getting through my reading list.

January 15, 2023

I failed as a father to teach my kid history.

So I told my wife that there was almost a "Tenerife" at "JFK" yesterday.

I can understand not knowing what "Tenerife" (the collision of two jumbo jets on the runway) was, but...

On hearing the remark my son piped in to say "...imagine how embarrassing that must be for a President of the United States..."

"What?" I asked.

"...to be named after an airport!"

It's an internet joke apparently.

January 14, 2023

So I have that new improved souped up XBB.1.5 Covid.

As I noted in a previous post in this space my wife got Covid last week:

The mask is back on. My wife has XBB.1.5 (apparently) Covid.

I commented on some of the science behind this new variant, which apparently is well equipped to evade antibodies generated by vaccines here: Some pretty bad news on the XBB.1 Covid Variant.

My wife was pretty sick for about two days; she's almost completely better, five days out.

My son also tested positive; he had a cough, some lethargy, and congestion. He had to organize an art show he's supervising remotely, so not as to infect people, not an easy trick, but he was not so sick as to be unable to do it.

Now I have it. Like my previous adventure with breakthrough Covid, it feels like a very, very, very bad cold, chills, mild fever, congestion, occasional cough, headache and lethargy. I think the worst was yesterday. I'm feeling better today. I'm still sick, but have been able to read.

I may have a better set of antibodies than my wife had, since I had a breakthrough case between my last "regular" vaccine and the booster. I suspect that this case had some of the mutations now found in XBB.1.5. I'm sure too, the vaccines helped.

The good news is that the cases we all had were not life threatening, annoying but not life threatening.

January 13, 2023

Biggest Sources of Electrical Generation in Canada and the US.

Mapped: Biggest Sources of Electricity by State and Province

We're nearly half a century into "renewable energy" will save us. This is where we are.

Here's another place we are:

January 12: 419.70 ppm
January 11: 418.90 ppm
January 10: 419.15 ppm
January 09: 419.17 ppm
January 08: 419.32 ppm
Last Updated: January 13, 2023

Recent Daily Average Mauna Loa CO2

The broader trend:

Week beginning on January 01, 2023: 419.31 ppm
Weekly value from 1 year ago: 417.55 ppm
Weekly value from 10 years ago: 394.96 ppm
Last updated: January 13, 2023

Weekly average CO2 at Mauna Loa

The first graphic has a small title about an "energy shift."

My opinion is that the shift is from bad to worse.

January 13, 2023

"Renewable Energy" researcher recycles text; ten papers retracted or to be retracted.

Just for fun:

Renewable energy researcher recycled material, agrees to withdraw 10 papers

Investigations at two institutions at Taiwan determined in 2013 that a renewable energy researcher duplicated his own work; the researcher agreed to pull 10 papers. A total of six have been withdrawn or retracted, two in November, 2015.

Shyi-Min Lu is the corresponding author on the two newly retracted papers, from Renewable and Sustainable Energy Reviews. The retractions follow investigations at the Industrial Technology Research Institute, where Lu used to work, and National Taiwan University, his former employer. Lu admitted to committing offenses in 10 papers. He was fired from NTU, where he was a research assistant at the university’s Energy Research Center.

First author Falin Chen — also a co-author on the paper duplicated by the retractions — was not aware that the papers bearing his name had been submitted. He told us how he found out: ...

January 12, 2023

Some pretty bad news on the XBB.1 Covid Variant.

My fully vaccinated wife has Covid and was pretty sick, although she seems to be improving. My son is also not feeling well. I have a slight cough.

This situation motivated me to look into the XBB.1.5 variant that seems to be circulating, which I suspect my wife has.

I accessed this paper this morning: Qian Wang, Sho Iketani, Zhiteng Li, Liyuan Liu, Yicheng Guo, Yiming Huang, Anthony D. Bowen, Michael Liu, Maple Wang, Jian Yu, Riccardo Valdez, Adam S. Lauring, Zizhang Sheng, Harris H. Wang, Aubree Gordon, Lihong Liu, David D. Ho, Alarming antibody evasion properties of rising SARS-CoV-2 BQ and XBB subvariants, Cell, 2022, a corrected proof in press.

The paper is fully open sourced, anyone can read it, but I'll produce the opening paragraphs and a pretty depressing graphic from the paper as well.

The intro:

The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), continues to rage due to emergence of the Omicron variant and its descendant subvariants.1,2,3,4,5,6,7,8,9,10 Although the BA.5 subvariant is globally dominant at this time (Figure 1A), a diverse array of Omicron sublineages have arisen and are competing in the so-called “variant soup”.11 It has become apparent that four new subvariants are rapidly gaining ground on BA.5, raising the specter of yet another wave of infections in the coming months. BQ.1 and BQ.1.1 were first identified in Nigeria in early July and then expanded dramatically in Europe and North America, now accounting for 67%, 35%, and 47% of cases in France, the United Kingdom, and the United States, respectively (Figure 1A). XBB and XBB.1 were first identified in India in mid-August and quickly became predominant in India, Singapore, and other regions in Asia (Figure 1A). BQ.1 and BQ.1.1 evolved from BA.5, whereas XBB and XBB.1 resulted from a recombination between two BA.2 lineages, BJ.1 and BA.2.75 (Figure 1B). These two sublineages are continuing to evolve and diversify, with an ever-increasing complexity of spike mutations. However, the spike protein of the predominant BQ.1 subvariant harbors the K444T and N460K mutations in addition to those found in BA.5, with BQ.1.1 having an additional R346T mutation (Figures 1C and S1). Strikingly, the spike of the predominant XBB subvariant has 14 mutations in addition to those found in BA.2, including 5 in the N-terminal domain (NTD) and 9 in the receptor-binding domain (RBD), whereas XBB.1 has an additional G252V mutation (Figures 1C and S1). The rapid rise of these subvariants and their extensive array of spike mutations are reminiscent of the appearance of the first Omicron variant last year, thus raising concerns that they may further compromise the efficacy of current COVID-19 vaccines and monoclonal antibody (mAb) therapeutics. We now report findings that indicate that such concerns are, sadly, justified, especially so for the XBB and XBB.1 subvariants.

I added the bold.

The XBB virus has been fully sequenced, and the sites of the mutations are known. "K444T" refers to the substitution at the 444th residue in the spike protein of a threonine for a lysine. "N460K" refers to a substitution at the 460th residue of a lysine for an asparagine.

The following graphic shows the evolutionary history of variants of Covid:

The caption:

Figure 1. The rise of SARS-CoV-2 Omicron BQ.1, BQ.1.1, XBB, and XBB.1 subvariants

(A) Frequencies of Omicron subvariants from the Global Initiative on Sharing All Influenza Data (GISAID). Variants were designated according to their Pango dynamic lineage classification.12 Minor sublineages of each subvariant were grouped together with their parental variant. The values in the upper left corner of each box denote the cumulative number of sequences for all circulating viruses in the denoted time period.

(B) Unrooted phylogenetic tree of Omicron subvariants along with other main SARS-CoV-2 variants. The scale bar indicates the genetic distance.

(C) Key spike mutations found in XBB and XBB.1 in the background of BA.2 and in BQ.1 and BQ.1.1 in the background of BA.4/5. Del, deletion. The positions of these mutations on the spike trimer are shown in Figure S1.

This graphic shows the location of the mutations on the spike protein:

The caption:

Figure S1. Key spike mutations of BQ and XBB subvariants, related to Figure 1

(A and B) Key mutations of BQ.1 and BQ.1.1 in the context of BA.4/5 (A), and key mutations of XBB and XBB.1 in the context of BA.2 (B).

See also Figure 1.

And now for the real depressing graphic, showing the decreased neutralization capacity of antibodies:

The caption:

Figure 3. Resistance of Omicron subvariants to monoclonal antibody neutralization

(A) Footprints of NTD- and RBD-directed antibodies tested are outlined, and mutations within BQ.1, BQ.1.1, XBB, and XBB.1 are highlighted in red.

(B) The fold changes in neutralization IC50 values of BQ.1, BQ.1.1, XBB, XBB.1, and the individual mutants compared with BA.4/5 or BA.2, with resistance colored red and sensitization colored green. The raw IC50 values are shown in Figure S2.

See also Figure S2.

The good news, as I understand it, is that this variant does not seem as severe in terms of illness, and there is some protective effect with vaccination status, although how much is on clear.

The authors make the comforting statement I will put in bold:

Therefore, it is alarming that these newly emerged subvariants could further compromise the efficacy of current COVID-19 vaccines and result in a surge of breakthrough infections as well as re-infections. However, it is important to emphasize that although infections may now be more likely, COVID-19 vaccines have been shown to remain effective at preventing hospitalization and severe disease even against Omicron35,36,37,38 as well as possibly reducing the risk of post-acute sequelae of COVID-19 (PASC or long COVID).39,40,41

But it's also clear from my perspective, we're going to need another vaccine. We do have the machinery to do this now, so that is also good news.

The authors conclusions:

Lastly, we found that the spikes of BQ and XBB subvariants have similar binding affinities to hACE2 as the spikes of their predecessors (Figure 5), suggesting that the recently observed growth advantage for these novel subvariants is likely due to some other factors. Foremost may be their extreme antibody evasion properties, especially considering the extensive herd immunity built up in the population over the last three years from infections and vaccinations. BQ.1, BQ.1.1, XBB, and XBB.1 subvariants exhibit far greater antibody resistance than earlier variants, and they may fuel yet another surge of COVID-19 infections. We have collectively chased after SARS-CoV-2 variants for over two years, and yet, the virus continues to evolve and evade. This continuing challenge highlights the importance of developing vaccine and mAb approaches that protect broadly and anticipate the antigenic trajectory of SARS-CoV-2.

I have heard, peripherally, I will now look into it more deeply, that a "master" vaccine that may work against all or most corona viruses, including those responsible for the common cold, is under development.

My wife is suffering from nausea and diarrhea, before taking Paxlovid, and these are side effects of the drug, so she's reluctant to take it.

I'm going to work from home until it becomes clear what the situation is.

The bottom line: Be careful, keep your Covid supplies handy.

Update: My son just tested positive. The historical test kits seem to respond to this variant. He's sick, but not as sick as my wife.

January 11, 2023

The mask is back on. My wife has XBB.1.5 (apparently) Covid.

She, like me, is fully vaccinated, but was pretty sick, nausea, headache, running a low grade fever. The test was run in the doctor's office, flu, A&B; RSV; and Covid all together. Covid won.

Nature News describes XBB.1.5 as "The Great-Grandchild of Omicron."

We're fully stocked with supplies; I'll work from home until next week, and I'll mask up wherever I go. She got a Paxlovid scrip and has been told to quarantine until Saturday.

I'm OK; my son was mildly ill a few days back, but tested negative with a home kit.

I don't feel sick, but if I do, I'll test. I do wonder about the specificity of the test kits I have, since they are generally ligand binding assays, but hey, if I get sick, I'll go to the Doctor myself.

January 8, 2023

Good News! The Wind's Blowing in Germany! German Carbon Intensity Is Only 788% Higher Than...

...That of France! It's 23:45 01/08/23 Sunday evening, Berlin time

Electricity Map Accessed 01/08/23 5:45 pm EST US.

I'm sure everyone loves "percent talk." It's very popular.

January 7, 2023

Telomere Shortening, a Biomarker for Aging, Is Increased by High Ambient Temperatures.

The paper I'll briefly discuss is this one: Higher Daily Air Temperature Is Associated with Shorter Leukocyte Telomere Length: KORA F3 and KORA F4 Wenli Ni, Kathrin Wolf, Susanne Breitner, Siqi Zhang, Nikolaos Nikolaou, Cavin K. Ward-Caviness, Melanie Waldenberger, Christian Gieger, Annette Peters, and Alexandra Schneider, Environmental Science & Technology 2022 56 (24), 17815-17824.

KORA is an abbreviation (in German) of "Kooperative Gesundheitsforschung in der Region Augsburg," a series of longitudinal epidemiological studies conducted in a region of Germany.

Genetic Epidemiology of Refractive Error in the KORA

Germany is a nation that has committed, albeit informally, but nonetheless in a practical sense, to make climate change accelerate, having decided to replace nuclear energy with coal.

Originally the intention was to replace nuclear energy with huge amounts of dangerous natural gas, an idea which their former Chancellor, Gerhardt Schroeder worked to promote when in office. Schroeder is now working as a salesman for Gazprom, Putin's dangerous natural gas company, but Germany rather sheepishly switched from gas to coal after their blindfolds came off to reveal they were funding a vicious war of conquest in Ukraine, a nation with which Germany already has an unhappy history.

The plan, which involves dumping dangerous fossil fuel waste directly into the environment, has left Germany with what is consistently one of the highest carbon intensities for electrical generation in Europe.

Anyway, about the paper based on the German KORA study:

The full paper is open by "authors choice," and there is no need to excerpt it extensively, but a description of what a telomere is, which is quite succinct is excerpted for convenience:

...Telomeres are highly conserved tandem repetitive nucleotide sequences (TTAGGG), which provide a protective cap at the ends of chromosome to maintain genome stability. (12,13) Telomeres are fundamental for cell division and shorten after each round of cell division. (14) Consequently, leukocyte telomere length shortening is evaluated as a potential biomarker for biologic aging, and telomere shortening has been associated with increasing numbers of age-related diseases such as stroke, cardiovascular disease, or cancer. (15?18) A recent large cohort study from the United Kingdom Biobank found that shortened leukocyte telomere length was associated with increased overall cardiovascular, respiratory, digestive, musculoskeletal, and COVID-19 mortality. (19) A further review study showed that telomere attrition was influenced by genetic and environmental factors. (12) Evidence is rapidly growing that telomere shortening can be accelerated by exposure to nonoptimal environmental factors like air pollution, (20,21) and pesticides. (22)...

The introduction continues:

...Air temperature is an important environmental factor, especially in the context of climate change. A study in the three largest English cities (Greater London, Greater Manchester, and West Midlands) found that heat and cold exposure increased the risk of mortality and years of life lost. (23) In addition, high air temperature or heat stress has been associated with higher levels of oxidative stress and inflammatory biomarkers. (24?27) As oxidative stress and inflammation can speed up telomere attrition, (28,29) these findings suggest that air temperature might affect telomere length. However, only one birth study has reported that prenatal high and low air temperature exposures were associated with shorter cord blood telomere length. (30) So far, the effect of air temperature on leukocyte telomere length has not been investigated among an adult population.
Therefore, we aimed to examine the short-term associations between air temperature and leukocyte telomere length in the region of Augsburg, Germany, within two independent adult cohorts...

A brief excerpt from the discussion of the finding:

...We found both significant immediate and lagged effects of air temperature on leukocyte telomere length at lags 0–1, 2–6, 0–6, and 0–13 days. The results indicate that high air temperatures over the preceding 2 weeks are associated with shorter telomere length. A recent epidemiological study based on 1792 participants with overweight/obesity reported a decreasing trend in leukocyte telomere length in association with increasing PM10-levels, which was observed with a lag of up to 2 weeks. (44) These findings suggest that short-term effects of environmental factors on leukocyte telomere length should also be considered as adverse effects with potential health implications. Moreover, this study indicates that the more delayed effects (lags 0–13 days: ?6.69% [?9.04%; ?4.27%]) are larger than the immediate effects (lags 0–1 days: ?2.96% [?4.46%; ?1.43%]). It is conceivable that the immediate effects on telomere length on a day-to-day basis are at least partly compensated. However, the findings of this study suggest that repeated exposure to high temperatures may have compounding effects on telomere length. The reversibility of these effects still needs to be explored, in particular, to determine if there is an exposure level or frequency at which effects become partially or totally irreversible...

Again, the full paper is open sourced. It's an interesting read.

Have a nice weekend.

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Gender: Male
Current location: New Jersey
Member since: 2002
Number of posts: 33,512

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