“The elegance of quantum mechanics”: An at-distance proposal for secondary school students

INTRODUCTION: THE STATE OF THE ART AND OPEN PROBLEMS Quantum Mechanics has been the focus of physics education research since the 90s and, nowadays, researchers no longer express doubts on the fact that it is fundamental for the culture and the awareness of the individual citizen and of the whole society (Redish, 2000; Besson, 2017). From surveys on teacher training (Stefanel, 2008; Fera, 2011; Giliberti, 2014; Krijtenburg-Lewerissa, 2017), it emerged that most teachers - mainly with a degree in mathematics - often do not have a coherent framework of modern physics in general, and of quantum physics in particular. Furthermore, the didactic path presented in textbooks is limited to a pseudo-historical presentation, which provides a hyper-simplified explanation of the fundamental concepts, in an attempt to bypass the problems associated with students’ lack of adequate mathematical tools, leading to deep misconceptions. OUR COURSE: “THE ELEGANCE OF QUANTUM MECHANICS” In this presentation we describe the work of designing, testing, and evaluating the effectiveness of a course entitled, “The elegance of quantum mechanics”, presented in Academy Year 2021/22. The activity - done online - was offered to teachers and students of the last three years of high school (120 participants overall), from October 2021 to January 2022, through weekly appointments of one and a half hours each. Lessons were integrated with slides, questions with Kahoot! and graphic examples with GeoGebra (https://www.geogebra.org/m/aqf2dgn3). Course effectiveness was assessed by collecting and analyzing different types of data deriving from an anonymous satisfaction survey, 9 Google Forms (given after each of the first nine lessons, with a total of 38 open questions and 24 exercises; for example: https://forms.gle/Nr2umPc53FCCi3KZ9), and 19 individual interviews, aimed at investigating strengths and criticalities. This analysis allowed us to identify the reasoning that students commonly use in facing some conceptual issues of quantum mechanics. The following will be discussed: strengths of the activity, regarding the mathematical aspects, the use of GeoGebra and Kahoot!; criticalities, especially in dealing with spaces with more than 3 dimensions, with the concept of self-adjoint operator, and concerning the confusion between states and operators; materials (https://pls.fisica.unimi.it/materiali/). A new course, implemented with the improvements mentioned above, is expected to start in October 2022. REFERENCES Besson, U. (2017). Didattica della fisica. Rome: Carocci Editore. Fera, G., Challapalli, S. R., Michelini, M., Santi, L., Stefanel, A., & Vercellati, A. (2011). Formare gli insegnanti all’innovazione didattica e all’orientamento, Connessi! Scenari di Innovazione nella Formazione e nella Comunicazione, 411-420. Giliberti, M. (2014). Theories as Crucial Aspects in Quantum Physics Education. Frontiers of Fundamental Physics and Physics Education Research. Springer Proceedings in Physics, vol 145. Springer, Cham. https://doi.org/10.1007/978-3-319-00297-2_51 Krijtenburg-Lewerissa, K., Pol, H.J., Brinkman, A., & Van Joolingen, W. R. (2017). Insights into teaching quantum mechanics in secondary and lower undergraduate education. Physical Review Physics Education Research, 13(1). Redish, E. F. (2000). Who needs to learn physics in the 21st century and why? Plenary lecture, GIREP Conference 2000. Stefanel, A. (2008). Impostazioni e percorsi per l’insegnamento della meccanica quantistica nella scuola secondaria. Giornale di Fisica 49, 15-53

Tunability and Losses of Mid-infrared Plasmonics in Heavily Doped Germanium Thin Films

Heavily-doped semiconductor films are very promising for application in mid-infrared plasmonic devices because the real part of their dielectric function is negative and broadly tunable in this wavelength range. In this work we investigate heavily n-type doped germanium epilayers grown on different substrates, in-situ doped in the $10^{17}$ to $10^{19}$ cm$^{-3}$ range, by infrared spectroscopy, first principle calculations, pump-probe spectroscopy and dc transport measurements to determine the relation between plasma edge and carrier density and to quantify mid-infrared plasmon losses. We demonstrate that the unscreened plasma frequency can be tuned in the 400 - 4800 cm$^{-1}$ range and that the average electron scattering rate, dominated by scattering with optical phonons and charged impurities, increases almost linearly with frequency. We also found weak dependence of losses and tunability on the crystal defect density, on the inactivated dopant density and on the temperature down to 10 K. In films where the plasma was optically activated by pumping in the near-infrared, we found weak but significant dependence of relaxation times on the static doping level of the film. Our results suggest that plasmon decay times in the several-picosecond range can be obtained in n-type germanium thin films grown on silicon substrates hence allowing for underdamped mid-infrared plasma oscillations at room temperature.Comment: 18 pages, 10 figure

Carriers of ADAMTS13 Rare Variants Are at High Risk of Life-Threatening COVID-19

Thrombosis of small and large vessels is reported as a key player in COVID-19 severity. However, host genetic determinants of this susceptibility are still unclear. Congenital Thrombotic Thrombocytopenic Purpura is a severe autosomal recessive disorder characterized by uncleaved ultra-large vWF and thrombotic microangiopathy, frequently triggered by infections. Carriers are reported to be asymptomatic. Exome analysis of about 3000 SARS-CoV-2 infected subjects of different severities, belonging to the GEN-COVID cohort, revealed the specific role of vWF cleaving enzyme ADAMTS13 (A disintegrin-like and metalloprotease with thrombospondin type 1 motif, 13). We report here that ultra-rare variants in a heterozygous state lead to a rare form of COVID-19 characterized by hyper-inflammation signs, which segregates in families as an autosomal dominant disorder conditioned by SARS-CoV-2 infection, sex, and age. This has clinical relevance due to the availability of drugs such as Caplacizumab, which inhibits vWF-platelet interaction, and Crizanlizumab, which, by inhibiting P-selectin binding to its ligands, prevents leukocyte recruitment and platelet aggregation at the site of vascular damage

Gain- and Loss-of-Function CFTR Alleles Are Associated with COVID-19 Clinical Outcomes

Carriers of single pathogenic variants of the CFTR (cystic fibrosis transmembrane conductance regulator) gene have a higher risk of severe COVID-19 and 14-day death. The machine learning post-Mendelian model pinpointed CFTR as a bidirectional modulator of COVID-19 outcomes. Here, we demonstrate that the rare complex allele [G576V;R668C] is associated with a milder disease via a gain-of-function mechanism. Conversely, CFTR ultra-rare alleles with reduced function are associated with disease severity either alone (dominant disorder) or with another hypomorphic allele in the second chromosome (recessive disorder) with a global residual CFTR activity between 50 to 91%. Furthermore, we characterized novel CFTR complex alleles, including [A238V;F508del], [R74W;D1270N;V201M], [I1027T;F508del], [I506V;D1168G], and simple alleles, including R347C, F1052V, Y625N, I328V, K68E, A309D, A252T, G542*, V562I, R1066H, I506V, I807M, which lead to a reduced CFTR function and thus, to more severe COVID-19. In conclusion, CFTR genetic analysis is an important tool in identifying patients at risk of severe COVID-19

The polymorphism L412F in TLR3 inhibits autophagy and is a marker of severe COVID-19 in males

The polymorphism L412F in TLR3 has been associated with several infectious diseases. However, the mechanism underlying this association is still unexplored. Here, we show that the L412F polymorphism in TLR3 is a marker of severity in COVID-19. This association increases in the sub-cohort of males. Impaired macroautophagy/autophagy and reduced TNF/TNFα production was demonstrated in HEK293 cells transfected with TLR3L412F-encoding plasmid and stimulated with specific agonist poly(I:C). A statistically significant reduced survival at 28 days was shown in L412F COVID-19 patients treated with the autophagy-inhibitor hydroxychloroquine (p = 0.038). An increased frequency of autoimmune disorders such as co-morbidity was found in L412F COVID-19 males with specific class II HLA haplotypes prone to autoantigen presentation. Our analyses indicate that L412F polymorphism makes males at risk of severe COVID-19 and provides a rationale for reinterpreting clinical trials considering autophagy pathways. Abbreviations: AP: autophagosome; AUC: area under the curve; BafA1: bafilomycin A1; COVID-19: coronavirus disease-2019; HCQ: hydroxychloroquine; RAP: rapamycin; ROC: receiver operating characteristic; SARS-CoV-2: severe acute respiratory syndrome coronavirus 2; TLR: toll like receptor; TNF/TNF-α: tumor necrosis factor

An explainable model of host genetic interactions linked to COVID-19 severity

We employed a multifaceted computational strategy to identify the genetic factors contributing to increased risk of severe COVID-19 infection from a Whole Exome Sequencing (WES) dataset of a cohort of 2000 Italian patients. We coupled a stratified k-fold screening, to rank variants more associated with severity, with the training of multiple supervised classifiers, to predict severity based on screened features. Feature importance analysis from tree-based models allowed us to identify 16 variants with the highest support which, together with age and gender covariates, were found to be most predictive of COVID-19 severity. When tested on a follow-up cohort, our ensemble of models predicted severity with high accuracy (ACC = 81.88%; AUCROC = 96%; MCC = 61.55%). Our model recapitulated a vast literature of emerging molecular mechanisms and genetic factors linked to COVID-19 response and extends previous landmark Genome-Wide Association Studies (GWAS). It revealed a network of interplaying genetic signatures converging on established immune system and inflammatory processes linked to viral infection response. It also identified additional processes cross-talking with immune pathways, such as GPCR signaling, which might offer additional opportunities for therapeutic intervention and patient stratification. Publicly available PheWAS datasets revealed that several variants were significantly associated with phenotypic traits such as "Respiratory or thoracic disease", supporting their link with COVID-19 severity outcome.A multifaceted computational strategy identifies 16 genetic variants contributing to increased risk of severe COVID-19 infection from a Whole Exome Sequencing dataset of a cohort of Italian patients

A genome-wide association study for survival from a multi-centre European study identified variants associated with COVID-19 risk of death

: The clinical manifestations of SARS-CoV-2 infection vary widely among patients, from asymptomatic to life-threatening. Host genetics is one of the factors that contributes to this variability as previously reported by the COVID-19 Host Genetics Initiative (HGI), which identified sixteen loci associated with COVID-19 severity. Herein, we investigated the genetic determinants of COVID-19 mortality, by performing a case-only genome-wide survival analysis, 60 days after infection, of 3904 COVID-19 patients from the GEN-COVID and other European series (EGAS00001005304 study of the COVID-19 HGI). Using imputed genotype data, we carried out a survival analysis using the Cox model adjusted for age, age2, sex, series, time of infection, and the first ten principal components. We observed a genome-wide significant (P-value < 5.0 × 10-8) association of the rs117011822 variant, on chromosome 11, of rs7208524 on chromosome 17, approaching the genome-wide threshold (P-value = 5.19 × 10-8). A total of 113 variants were associated with survival at P-value < 1.0 × 10-5 and most of them regulated the expression of genes involved in immune response (e.g., CD300 and KLR genes), or in lung repair and function (e.g., FGF19 and CDH13). Overall, our results suggest that germline variants may modulate COVID-19 risk of death, possibly through the regulation of gene expression in immune response and lung function pathways

Pathogen-sugar interactions revealed by universal saturation transfer analysis

Many pathogens exploit host cell-surface glycans. However, precise analyses of glycan ligands binding with heavily modified pathogen proteins can be confounded by overlapping sugar signals and/or compounded with known experimental constraints. Universal saturation transfer analysis (uSTA) builds on existing nuclear magnetic resonance spectroscopy to provide an automated workflow for quantitating protein-ligand interactions. uSTA reveals that early-pandemic, B-origin-lineage severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike trimer binds sialoside sugars in an “end-on” manner. uSTA-guided modeling and a high-resolution cryo–electron microscopy structure implicate the spike N-terminal domain (NTD) and confirm end-on binding. This finding rationalizes the effect of NTD mutations that abolish sugar binding in SARS-CoV-2 variants of concern. Together with genetic variance analyses in early pandemic patient cohorts, this binding implicates a sialylated polylactosamine motif found on tetraantennary N-linked glycoproteins deep in the human lung as potentially relevant to virulence and/or zoonosis

SARS-CoV-2 susceptibility and COVID-19 disease severity are associated with genetic variants affecting gene expression in a variety of tissues

Variability in SARS-CoV-2 susceptibility and COVID-19 disease severity between individuals is partly due to genetic factors. Here, we identify 4 genomic loci with suggestive associations for SARS-CoV-2 susceptibility and 19 for COVID-19 disease severity. Four of these 23 loci likely have an ethnicity-specific component. Genome-wide association study (GWAS) signals in 11 loci colocalize with expression quantitative trait loci (eQTLs) associated with the expression of 20 genes in 62 tissues/cell types (range: 1:43 tissues/gene), including lung, brain, heart, muscle, and skin as well as the digestive system and immune system. We perform genetic fine mapping to compute 99% credible SNP sets, which identify 10 GWAS loci that have eight or fewer SNPs in the credible set, including three loci with one single likely causal SNP. Our study suggests that the diverse symptoms and disease severity of COVID-19 observed between individuals is associated with variants across the genome, affecting gene expression levels in a wide variety of tissue types

Common, low-frequency, rare, and ultra-rare coding variants contribute to COVID-19 severity

The combined impact of common and rare exonic variants in COVID-19 host genetics is currently insufficiently understood. Here, common and rare variants from whole-exome sequencing data of about 4000 SARS-CoV-2-positive individuals were used to define an interpretable machine-learning model for predicting COVID-19 severity. First, variants were converted into separate sets of Boolean features, depending on the absence or the presence of variants in each gene. An ensemble of LASSO logistic regression models was used to identify the most informative Boolean features with respect to the genetic bases of severity. The Boolean features selected by these logistic models were combined into an Integrated PolyGenic Score that offers a synthetic and interpretable index for describing the contribution of host genetics in COVID-19 severity, as demonstrated through testing in several independent cohorts. Selected features belong to ultra-rare, rare, low-frequency, and common variants, including those in linkage disequilibrium with known GWAS loci. Noteworthily, around one quarter of the selected genes are sex-specific. Pathway analysis of the selected genes associated with COVID-19 severity reflected the multi-organ nature of the disease. The proposed model might provide useful information for developing diagnostics and therapeutics, while also being able to guide bedside disease management. © 2021, The Author(s)