Photoionization from the ground and excited vibrational states of H+2 and its deuterated isotopologues

Photoionization cross sections and rate coefficients have been calculated for all bound vibrational levels of the 1s$\sigma_{\mathrm{g}}$ state of H$_{2}^{+}$, HD$^{+}$, and D$_{2}^{+}$. The Born-Oppenheimer approximation is employed in our calculation of vibrationally-resolved photoionization cross sections. Vibrationally-resolved and local thermal equilibrium photoionization rate coefficients are presented for photon temperatures less than $50\,000$ K and are found to be several orders of magnitude larger than previous results in the literature. Analytic fits for the vibrationally-resolved and local thermal equilibrium photoionization rate coefficients are provided. Near threshold oscillations in the vibrationall-resolved photoionization are observed. A benchmark set of photoionization cross sections are presented. Fixed-nuclei photoionization cross sections are calculated using two-center true continuum wave functions and are verified by comparison with previous calculations and are found to be in excellent agreement in all cases. Data files for our set of benchmark cross sections, rate coefficients, and fitting parameters for H$_{2}^{+}$, HD$^{+}$, and D$_{2}^{+}$ are available on Zenodo under an open-source Creative Commons Attribution license: https://doi.org/10.5281/zenodo.8304060 .Comment: Accepted in ApJ

Antibodies against endogenous retroviruses promote lung cancer immunotherapy

B cells are frequently found in the margins of solid tumours as organized follicles in ectopic lymphoid organs called tertiary lymphoid structures (TLS). Although TLS have been found to correlate with improved patient survival and response to immune checkpoint blockade (ICB), the underlying mechanisms of this association remain elusive. Here we investigate lung-resident B cell responses in patients from the TRACERx 421 (Tracking Non-Small-Cell Lung Cancer Evolution Through Therapy) and other lung cancer cohorts, and in a recently established immunogenic mouse model for lung adenocarcinoma. We find that both human and mouse lung adenocarcinomas elicit local germinal centre responses and tumour-binding antibodies, and further identify endogenous retrovirus (ERV) envelope glycoproteins as a dominant anti-tumour antibody target. ERV-targeting B cell responses are amplified by ICB in both humans and mice, and by targeted inhibition of KRAS(G12C) in the mouse model. ERV-reactive antibodies exert anti-tumour activity that extends survival in the mouse model, and ERV expression predicts the outcome of ICB in human lung adenocarcinoma. Finally, we find that effective immunotherapy in the mouse model requires CXCL13-dependent TLS formation. Conversely, therapeutic CXCL13 treatment potentiates anti-tumour immunity and synergizes with ICB. Our findings provide a possible mechanistic basis for the association of TLS with immunotherapy response

Changes in symptomatology, reinfection, and transmissibility associated with the SARS-CoV-2 variant B.1.1.7: an ecological study

Background The SARS-CoV-2 variant B.1.1.7 was first identified in December, 2020, in England. We aimed to investigate whether increases in the proportion of infections with this variant are associated with differences in symptoms or disease course, reinfection rates, or transmissibility. Methods We did an ecological study to examine the association between the regional proportion of infections with the SARS-CoV-2 B.1.1.7 variant and reported symptoms, disease course, rates of reinfection, and transmissibility. Data on types and duration of symptoms were obtained from longitudinal reports from users of the COVID Symptom Study app who reported a positive test for COVID-19 between Sept 28 and Dec 27, 2020 (during which the prevalence of B.1.1.7 increased most notably in parts of the UK). From this dataset, we also estimated the frequency of possible reinfection, defined as the presence of two reported positive tests separated by more than 90 days with a period of reporting no symptoms for more than 7 days before the second positive test. The proportion of SARS-CoV-2 infections with the B.1.1.7 variant across the UK was estimated with use of genomic data from the COVID-19 Genomics UK Consortium and data from Public Health England on spike-gene target failure (a non-specific indicator of the B.1.1.7 variant) in community cases in England. We used linear regression to examine the association between reported symptoms and proportion of B.1.1.7. We assessed the Spearman correlation between the proportion of B.1.1.7 cases and number of reinfections over time, and between the number of positive tests and reinfections. We estimated incidence for B.1.1.7 and previous variants, and compared the effective reproduction number, Rt, for the two incidence estimates. Findings From Sept 28 to Dec 27, 2020, positive COVID-19 tests were reported by 36 920 COVID Symptom Study app users whose region was known and who reported as healthy on app sign-up. We found no changes in reported symptoms or disease duration associated with B.1.1.7. For the same period, possible reinfections were identified in 249 (0·7% [95% CI 0·6–0·8]) of 36 509 app users who reported a positive swab test before Oct 1, 2020, but there was no evidence that the frequency of reinfections was higher for the B.1.1.7 variant than for pre-existing variants. Reinfection occurrences were more positively correlated with the overall regional rise in cases (Spearman correlation 0·56–0·69 for South East, London, and East of England) than with the regional increase in the proportion of infections with the B.1.1.7 variant (Spearman correlation 0·38–0·56 in the same regions), suggesting B.1.1.7 does not substantially alter the risk of reinfection. We found a multiplicative increase in the Rt of B.1.1.7 by a factor of 1·35 (95% CI 1·02–1·69) relative to pre-existing variants. However, Rt fell below 1 during regional and national lockdowns, even in regions with high proportions of infections with the B.1.1.7 variant. Interpretation The lack of change in symptoms identified in this study indicates that existing testing and surveillance infrastructure do not need to change specifically for the B.1.1.7 variant. In addition, given that there was no apparent increase in the reinfection rate, vaccines are likely to remain effective against the B.1.1.7 variant. Funding Zoe Global, Department of Health (UK), Wellcome Trust, Engineering and Physical Sciences Research Council (UK), National Institute for Health Research (UK), Medical Research Council (UK), Alzheimer's Society

Genomic assessment of quarantine measures to prevent SARS-CoV-2 importation and transmission

Mitigation of SARS-CoV-2 transmission from international travel is a priority. We evaluated the effectiveness of travellers being required to quarantine for 14-days on return to England in Summer 2020. We identified 4,207 travel-related SARS-CoV-2 cases and their contacts, and identified 827 associated SARS-CoV-2 genomes. Overall, quarantine was associated with a lower rate of contacts, and the impact of quarantine was greatest in the 16–20 age-group. 186 SARS-CoV-2 genomes were sufficiently unique to identify travel-related clusters. Fewer genomically-linked cases were observed for index cases who returned from countries with quarantine requirement compared to countries with no quarantine requirement. This difference was explained by fewer importation events per identified genome for these cases, as opposed to fewer onward contacts per case. Overall, our study demonstrates that a 14-day quarantine period reduces, but does not completely eliminate, the onward transmission of imported cases, mainly by dissuading travel to countries with a quarantine requirement

Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission

AbstractUnderstanding SARS-CoV-2 transmission in higher education settings is important to limit spread between students, and into at-risk populations. In this study, we sequenced 482 SARS-CoV-2 isolates from the University of Cambridge from 5 October to 6 December 2020. We perform a detailed phylogenetic comparison with 972 isolates from the surrounding community, complemented with epidemiological and contact tracing data, to determine transmission dynamics. We observe limited viral introductions into the university; the majority of student cases were linked to a single genetic cluster, likely following social gatherings at a venue outside the university. We identify considerable onward transmission associated with student accommodation and courses; this was effectively contained using local infection control measures and following a national lockdown. Transmission clusters were largely segregated within the university or the community. Our study highlights key determinants of SARS-CoV-2 transmission and effective interventions in a higher education setting that will inform public health policy during pandemics.</jats:p

Photoionization from the Ground and Excited Vibrational States of and Its Deuterated Isotopologues

Photoionization cross sections and rate coefficients have been calculated for all bound vibrational levels of the 1s σ _g state of ${{\rm{H}}}_{2}^{+}$ , HD ^+ , and ${{\rm{D}}}_{2}^{+}$ . The Born–Oppenheimer approximation is employed in our calculation of vibrationally resolved photoionization cross sections. Vibrationally resolved and local thermal equilibrium photoionization rate coefficients are presented for photon temperatures less than 50,000 K and are found to be several orders of magnitude larger than previous results in the literature. Analytic fits for the vibrationally resolved and local thermal equilibrium photoionization rate coefficients are provided. Near-threshold oscillations in the vibrationally resolved photoionization are observed. A benchmark set of photoionization cross sections are presented. Fixed-nuclei photoionization cross sections are calculated using two-center true continuum wave functions and are verified by comparison with previous calculations and are found to be in excellent agreement in all cases. Data files for our set of benchmark cross sections, rate coefficients, and fitting parameters for ${{\rm{H}}}_{2}^{+}$ , HD ^+ , and ${{\rm{D}}}_{2}^{+}$ are available on Zenodo under an open-source Creative Commons Attribution license at doi: https://doi.org/10.5281/zenodo.8304061

Cross sections and rate coefficients for photoionization from the ground and excited states of H2+ and its deuterated isotopologues

&lt;p&gt;Photoionization cross sections for all bound vibrational levels of the ground electronic state of H2+, HD+, and D2+. Vibrationally-resolved and local thermal equilibrium rate coefficients have been calculated for radiation temperatures less than 50 000 K. Fitting parameters for an analytic model of the photoionization rate coefficients have been provided. Thermally-averaged photoionization cross sections for gas temperatures of 3 000, 5 000, 8 000, 12 000, 17 000, and 23 000 K have also been included.&lt;/p&gt

Electron-scattering on molecular hydrogen: convergent close-coupling approach

Calculations of electron-impact excitation cross sections for molecular hydrogen have been performed using spherical- and spheroidal-coordinate formulations of the molecular convergent close-coupling method. We present a comparison and find good agreement between the results of these two techniques performed within the fixed-nuclei approximation for excitation from the ground $X{}^1{\mathrm{\Sigma }}_g^{+}$ (v = 0) state of H2 to the $B{}^1{\mathrm{\Sigma }}_u^{+}$ , C 1Πu, $B\mathrm{\prime}{}^1{\mathrm{\Sigma }}_u^{+}$ , D 1Πu, E $,F{}^1{\mathrm{\Sigma }}_g^{+}$ , $b{}^3{\mathrm{\Sigma }}_u^{+}$ , $c{}^3{\mathrm{\Pi }}_u$ , $a{}^3{\mathrm{\Sigma }}_g^{+}$ , $e{}^3{\mathrm{\Sigma }}_u^{+}$ , $h{}^3{\mathrm{\Sigma }}_g^{+}$ , and d 3Πu states. For the spheroidal-coordinate approach the adiabatic-nuclei method has been applied, allowing for a more reliable estimate of cross sections at near-threshold energies. Comparison of the adiabatic-nuclei cross sections with the corresponding fixed-nuclei cross sections is also presented

Kinetic-energy release of fragments from electron-impact dissociation of the molecular hydrogen ion and its isotopologues

We calculate the kinetic-energy release distributions of fragments produced for electron-impact dissociation of the vibrationally excited molecular hydrogen ion H2+ and its isotopologues D2+ and T2+. Here we apply the adiabatic-nuclei convergent close-coupling method and compare results with several different methods, including the δ approximation. Results are presented for a number of dissociative excitation transitions and dissociative ionization as a function of the initial vibrational state of the molecule. We confirm that the square root approximation is a good approximation for the adiabatic-nuclei kinetic-energy release cross sections of H2+. Agreement with experiment, where available, is good