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1. Genomic Analysis of SARS-CoV-2 Alpha, Beta and Delta Variants of Concern Uncovers Signatures of Neutral and Non-Neutral Evolution

   https://doi.org/10.3390/v14112375  

   Kurpas, Monika Klara; Jaksik, Roman; Kuś, Pawel; Kimmel, Marek (November 2022, Viruses)

   Due to the emergence of new variants of the SARS-CoV-2 coronavirus, the question of how the viral genomes evolved, leading to the formation of highly infectious strains, becomes particularly important. Three major emergent strains, Alpha, Beta and Delta, characterized by a significant number of missense mutations, provide a natural test field. We accumulated and aligned 4.7 million SARS-CoV-2 genomes from the GISAID database and carried out a comprehensive set of analyses. This collection covers the period until the end of October 2021, i.e., the beginnings of the Omicron variant. First, we explored combinatorial complexity of the genomic variants emerging and their timing, indicating very strong, albeit hidden, selection forces. Our analyses show that the mutations that define variants of concern did not arise gradually but rather co-evolved rapidly, leading to the emergence of the full variant strain. To explore in more detail the evolutionary forces at work, we developed time trajectories of mutations at all 29,903 sites of the SARS-CoV-2 genome, week by week, and stratified them into trends related to (i) point substitutions, (ii) deletions and (iii) non-sequenceable regions. We focused on classifying the genetic forces active at different ranges of the mutational spectrum. We observed the agreement of the lowest-frequency mutation spectrum with the Griffiths–Tavaré theory, under the Infinite Sites Model and neutrality. If we widen the frequency range, we observe the site frequency spectra much more consistently with the Tung–Durrett model assuming clone competition and selection. The coefficients of the fitting model indicate the possibility of selection acting to promote gradual growth slowdown, as observed in the history of the variants of concern. These results add up to a model of genomic evolution, which partly fits into the classical drift barrier ideas. Certain observations, such as mutation “bands” persistent over the epidemic history, suggest contribution of genetic forces different from mutation, drift and selection, including recombination or other genome transformations. In addition, we show that a “toy” mathematical model can qualitatively reproduce how new variants (clones) stem from rare advantageous driver mutations, and then acquire neutral or disadvantageous passenger mutations which gradually reduce their fitness so they can be then outcompeted by new variants due to other driver mutations. 

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2. Energy levels of singly ionized and neutral zirconium

   https://doi.org/10.1016/j.jqsrt.2022.108283  

   Lawler, J.E.; Schmidt, J.R.; Hartog, E. A. (October 2022, Journal of Quantitative Spectroscopy and Radiative Transfer)
3. Energy Levels of Singly Ionized and Neutral Hafnium

   https://doi.org/10.3847/1538-4365/ac36d7  

   Lawler, J. E.; Schmidt, J. R.; Den Hartog, E. A. (January 2022, The Astrophysical Journal Supplement Series)

   Abstract Improved energy levels for singly ionized and neutral hafnium of both even and odd parity are determined from Fourier transform spectrometer data using a least-squares optimization procedure. Data from interferometric spectrometers provide much tighter control of systematic uncertainties of line position measurements than can be achieved using dispersive spectrometers. The strong optical and near-UV lines connecting these levels are most likely to be used in the determination of isotopic abundance patterns. Comparisons of new results to published ones strongly suggest that our energy levels have systematic uncertainties in the mK (1 mK = 0.001 cm⁻¹) range or smaller, and that widely used tables of energy levels for ionized Hf have systematic errors of approximately 70 mK. 

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4. The present and future status of heavy neutral leptons

   https://doi.org/10.1088/1361-6471/ac98f9  

   Abdullahi, Asli M; Barham Alzás, Pablo; Batell, Brian; Beacham, James; Boyarsky, Alexey; Carbajal, Saneli; Chatterjee, Animesh; Crespo-Anadón, José I; Deppisch, Frank F; De Roeck, Albert; et al (January 2023, Journal of Physics G: Nuclear and Particle Physics)

   Abstract The existence of nonzero neutrino masses points to the likely existence of multiple Standard Model neutral fermions. When such states are heavy enough that they cannot be produced in oscillations, they are referred to as heavy neutral leptons (HNLs). In this white paper, we discuss the present experimental status of HNLs including colliders, beta decay, accelerators, as well as astrophysical and cosmological impacts. We discuss the importance of continuing to search for HNLs, and its potential impact on our understanding of key fundamental questions, and additionally we outline the future prospects for next-generation future experiments or upcoming accelerator run scenarios. 

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5. Atomic Transition Probabilities of Neutral Calcium*

   https://doi.org/10.3847/1538-4365/ac04b1  

   Den Hartog, E. A.; Lawler, J. E.; Sneden, C.; Cowan, J. J.; Roederer, I. U.; Sobeck, J. (August 2021, The Astrophysical Journal Supplement Series)