Risk of Severe Acute Respiratory Syndrome Coronavirus 2 Infection Following Prior Infection or Vaccination.

BACKGROUND: The extent to which infection versus vaccination has conferred similarly durable severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) immunity during the Omicron era remains unclear. METHODS: In a cohort of 4496 adults under continued serological surveillance throughout the first year of Omicron-predominant SARS-CoV-2 transmission, we examined incidence of new infection among individuals whose last known antigenic exposure was either recent (<90 days) or remote (≥90 days) infection or vaccination. RESULTS: We adjudicated 2053 new-onset infections occurring between 15 December 2021 through 22 December 2022. In multivariable-adjusted analyses, compared to individuals whose last known exposure was remote vaccination, those with recent vaccination (odds ratio [OR], 0.82 [95% confidence interval {CI}, .73-.93]; P = .002) or recent infection (OR, 0.14 [95% CI, .05-.45]; P = .001) had lower risk for new infection within the subsequent 90-day period. Given a significant age interaction (P = .004), we found that remote infection compared to remote vaccination was associated with significantly greater new infection risk in persons aged ≥60 years (OR, 1.88 [95% CI, 1.13-3.14]; P = .015) with no difference seen in those <60 years (1.03 [95% CI, .69-1.53]; P = .88). CONCLUSIONS: During the initial year of Omicron, prior infection and vaccination both offered protection against new infection. However, remote prior infection was less protective than remote vaccination for individuals aged ≥60 years. In older adults, immunity gained from vaccination appeared more durable than immunity gained from infection.

Serological response to vaccination in post-acute sequelae of COVID.

BACKGROUND: Individuals with post-acute sequelae of COVID (PASC) may have a persistence in immune activation that differentiates them from individuals who have recovered from COVID without clinical sequelae. To investigate how humoral immune activation may vary in this regard, we compared patterns of vaccine-provoked serological response in patients with PASC compared to individuals recovered from prior COVID without PASC. METHODS: We prospectively studied 245 adults clinically diagnosed with PASC and 86 adults successfully recovered from prior COVID. All participants had measures of humoral immunity to SARS-CoV-2 assayed before or after receiving their first-ever administration of COVID vaccination (either single-dose or two-dose regimen), including anti-spike (IgG-S and IgM-S) and anti-nucleocapsid (IgG-N) antibodies as well as IgG-S angiotensin-converting enzyme 2 (ACE2) binding levels. We used unadjusted and multivariable-adjusted regression analyses to examine the association of PASC compared to COVID-recovered status with post-vaccination measures of humoral immunity. RESULTS: Individuals with PASC mounted consistently higher post-vaccination IgG-S antibody levels when compared to COVID-recovered (median log IgG-S 3.98 versus 3.74, P < 0.001), with similar results seen for ACE2 binding levels (median 99.1 versus 98.2, P = 0.044). The post-vaccination IgM-S response in PASC was attenuated but persistently unchanged over time (P = 0.33), compared to in COVID recovery wherein the IgM-S response expectedly decreased over time (P = 0.002). Findings remained consistent when accounting for demographic and clinical variables including indices of index infection severity and comorbidity burden. CONCLUSION: We found evidence of aberrant immune response distinguishing PASC from recovered COVID. This aberrancy is marked by excess IgG-S activation and ACE2 binding along with findings consistent with a delayed or dysfunctional immunoglobulin class switching, all of which is unmasked by vaccine provocation. These results suggest that measures of aberrant immune response may offer promise as tools for diagnosing and distinguishing PASC from non-PASC phenotypes, in addition to serving as potential targets for intervention.

Superconducting boron allotrope featuring pentagonal bipyramid at ambient pressure.

Elemental boron has evoked substantial interest owing to its chemical complexity in nature. It can form multicenter bonds due to its electron deficiency, which induces the formation of various stable and metastable allotropes. The search for allotropes is attractive for finding functional materials with fascinating properties. Using first-principles calculations with evolutionary structure search, we have explored boron-rich K-B binary compounds under pressure. A series of dynamically stable structures (Pmm2 KB5, Pmma KB7, Immm KB9, and Pmmm KB10) containing boron framework with open channels are predicted, which can possibly be synthesized under high pressure and high temperature conditions. After the removal of K atoms, we obtain four novel boron allotropes, o-B14, o-B15, o-B36, and o-B10, which exhibit dynamical, thermal, and mechanical stability at ambient pressure. Among them, o-B14 contains an unusual B7 pentagonal bipyramid and appears in a bonding combination of seven-center-two-electron (7c-2e) B-B π bonds, which is the first time to be identified in three-dimensional boron allotropes. Interestingly, our calculation reveals that o-B14 can act as a superconductor with a Tc value of 29.1 K under ambient conditions.

Paradoxical sex-specific patterns of autoantibody response to SARS-CoV-2 infection.

BACKGROUND: Pronounced sex differences in the susceptibility and response to SARS-CoV-2 infection remain poorly understood. Emerging evidence has highlighted the potential importance of autoimmune activation in modulating the acute response and recovery trajectories following SARS-CoV-2 exposure. Given that immune-inflammatory activity can be sex-biased in the setting of severe COVID-19 illness, the aim of the study was to examine sex-specific autoimmune reactivity to SARS-CoV-2 in the absence of extreme clinical disease. METHODS: In this study, we assessed autoantibody (AAB) reactivity to 91 autoantigens previously linked to a range of classic autoimmune diseases in a cohort of 177 participants (65% women, 35% men, mean age of 35) with confirmed evidence of prior SARS-CoV-2 infection based on presence of antibody to the nucleocapsid protein of SARS-CoV-2. Data were compared to 53 pre-pandemic healthy controls (49% women, 51% men). For each participant, socio-demographic data, serological analyses, SARS-CoV-2 infection status and COVID-19 related symptoms were collected by  an electronic survey of questions. The symptoms burden score was constructed based on the total number of reported symptoms (N = 21) experienced within 6 months prior to the blood draw, wherein a greater number of symptoms corresponded to a higher score and assigned as more severe burden. RESULTS: In multivariable analyses, we observed sex-specific patterns of autoreactivity associated with the presence or absence (as well as timing and clustering of symptoms) associated with prior COVID-19 illness. Whereas the overall AAB response was more prominent in women following asymptomatic infection, the breadth and extent of AAB reactivity was more prominent in men following at least mildly symptomatic infection. Notably, the observed reactivity included distinct antigens with molecular homology with SARS-CoV-2. CONCLUSION: Our results reveal that prior SARS-CoV-2 infection, even in the absence of severe clinical disease, can lead to a broad AAB response that exhibits sex-specific patterns of prevalence and antigen selectivity. Further understanding of the nature of triggered AAB activation among men and women exposed to SARS-CoV-2 will be essential for developing effective interventions against immune-mediated sequelae of COVID-19.

Symptomology following mRNA vaccination against SARS-CoV-2.

Despite demonstrated efficacy of vaccines against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the causative agent of coronavirus disease-2019 (COVID-19), widespread hesitancy to vaccination persists. Improved knowledge regarding frequency, severity, and duration of vaccine-associated symptoms may help reduce hesitancy. In this prospective observational study, we studied 1032 healthcare workers who received both doses of the Pfizer-BioNTech SARS-CoV-2 mRNA vaccine and completed post-vaccine symptom surveys both after dose 1 and after dose 2. We defined appreciable post-vaccine symptoms as those of at least moderate severity and lasting at least 2 days. We found that symptoms were more frequent following the second vaccine dose than the first (74% vs. 60%, P < 0.001), with >80% of all symptoms resolving within 2 days. The most common symptom was injection site pain, followed by fatigue and malaise. Overall, 20% of participants experienced appreciable symptoms after dose 1 and 30% after dose 2. In multivariable analyses, female sex was associated with greater odds of appreciable symptoms after both dose 1 (OR, 95% CI 1.73, 1.19-2.51) and dose 2 (1.76, 1.28-2.42). Prior COVID-19 was also associated with appreciable symptoms following dose 1, while younger age and history of hypertension were associated with appreciable symptoms after dose 2. We conclude that most post-vaccine symptoms are reportedly mild and last <2 days. Appreciable post-vaccine symptoms are associated with female sex, prior COVID-19, younger age, and hypertension. This information can aid clinicians in advising patients on the safety and expected symptomatology associated with vaccination.

Prediction of a novel robust superconducting state in TaS2 under high pressure.

In this work, we performed first-principles structure-searching calculations to investigate the behaviors of tantalum disulfide (TaS2) under compression. Beside the well-known 1T and 2H phases at ambient pressure, our results reveal two new phases with the space group of C2/m (in the pressure range of 27-59 GPa) and I4/mmm (stable above 59 GPa). The C2/m and I4/mmm phases adopt three-dimensional covalent framework structures possessing highly eight-fold and ten-fold coordinated Ta, respectively. Strikingly, we observed an unusual superconductor-metal-superconductor transition in TaS2 with the increase of pressure. The predicted C2/m structure exhibits metallic character, while all the other low-pressure (1T and 2H) and high pressure (I4/mmm) phases of TaS2 show superconductivity under pressure. A robust superconductivity of I4/mmm-TaS2 is predicted up to a maximum transition temperature of 7.62 K at 60 GPa and can be stable up to 200 GPa. Our findings, therefore, provide important information to further understand the intrinsic physics of pressure-driven behaviors in transition metal dichalcogenides and related materials.

Pressure-induced unexpected -2 oxidation states of bromine and superconductivity in magnesium bromide.

Finding novel compounds with unusual crystal structures and physical properties is always an important goal for the materials and chemistry community. Pressure becomes attractive due to its unique ability to break down many fundamental rules by modifying the chemical properties of elements, overcoming reaction barriers and shortening interatomic distances, leading to the formation of some novel materials with unexpected properties. In this work, for the first time we have analyzed the high-pressure phase diagram, crystal structures and electron properties of the Mg-Br system up to 200 GPa using unbiased structure searching techniques. Besides the already known MgBr2, here we report that three unusual stoichiometries of Mg-Br compounds can be stabilized at high pressures as MgBr3, MgBr and Mg4Br. Firstly, among the predicted stable compounds, we find that the Mg4Br in the I4/mmm structure stabilized at 178 GPa behaves as a typical electride, indicating that the formation pressure of an electride for Mg can be significantly reduced by bonding with Br atoms. Secondly, it is surprising that the unexpected oxidation states of Br approaching -2 are observed in the predicted I4/mmm Mg4Br and Pm3[combining macron]m MgBr compounds. Furthermore, P21/m MgBr3 and I4[combining macron]2m MgBr3 phases are predicted as superconductors with an estimated Tc of 23.2 and 0.49 K, respectively. Our work represents a significant step toward understanding the high pressure behaviors of alkaline earth halides and searching for novel high temperature superconductors.

Predicted stable Li5P2 and Li4P at ambient pressure: novel high-performance anodes for lithium-ion batteries.

Lithium-rich phosphides have recently attracted considerable attention due to their potential application as high-capacity and high-rate anodes for lithium-ion batteries (LIBs). However, there is still short of the promising candidate thus far because of the poor electrical conductivity or huge volume change in the already known Li-P compounds. In this work, we report two novel Li-P states, Li5P2 and Li4P, stabilized under high pressures that are predicted to be quenchable down to ambient conditions by first-principles swarm structure calculations. The predicted P3m1 Li5P2 shows interesting features as a p-type semiconductor with an indirect band gap of 0.787 eV, possessing significant anisotropy properties in electrical transport, while R3[combining macron]m Li4P acts as a typical electride with metallic behavior at pressures of 0-82 GPa. More importantly, our calculations reveal that the theoretical capacities of Li5P2 and Li4P are predicted to reach 2164 and 3462 mA h g-1, respectively. Combined with the good electrical transport properties, the calculated volume expansion of Li5P2 (130%) is found to be much smaller than those of the previously reported Li-P compounds, indicating its potential as a high performance anode material for LIBs.

Identification of breast cancer associated variants that modulate transcription factor binding.

Genome-wide association studies (GWAS) have discovered thousands loci associated with disease risk and quantitative traits, yet most of the variants responsible for risk remain uncharacterized. The majority of GWAS-identified loci are enriched for non-coding single-nucleotide polymorphisms (SNPs) and defining the molecular mechanism of risk is challenging. Many non-coding causal SNPs are hypothesized to alter transcription factor (TF) binding sites as the mechanism by which they affect organismal phenotypes. We employed an integrative genomics approach to identify candidate TF binding motifs that confer breast cancer-specific phenotypes identified by GWAS. We performed de novo motif analysis of regulatory elements, analyzed evolutionary conservation of identified motifs, and assayed TF footprinting data to identify sequence elements that recruit TFs and maintain chromatin landscape in breast cancer-relevant tissue and cell lines. We identified candidate causal SNPs that are predicted to alter TF binding within breast cancer-relevant regulatory regions that are in strong linkage disequilibrium with significantly associated GWAS SNPs. We confirm that the TFs bind with predicted allele-specific preferences using CTCF ChIP-seq data. We used The Cancer Genome Atlas breast cancer patient data to identify ANKLE1 and ZNF404 as the target genes of candidate TF binding site SNPs in the 19p13.11 and 19q13.31 GWAS-identified loci. These SNPs are associated with the expression of ZNF404 and ANKLE1 in breast tissue. This integrative analysis pipeline is a general framework to identify candidate causal variants within regulatory regions and TF binding sites that confer phenotypic variation and disease risk.

Pressure-Induced Stable Binary Compounds of Magnesium and Germanium.

Motivated by the possibility to obtain unusual stoichiometric compounds (e.g., Na-Cl and Mg-O systems) with exotic properties at high pressures, we systematically investigated the high-pressure structures and chemical bonding of Mg-Ge systems by using a structure-searching method and first-principles calculations. Compared with the stable composition of Mg2 Ge at ambient pressure, several stoichiometries (e.g., Mg3 Ge, MgGe, and MgGe2 ) were predicted to be stable under high pressures. The Pm 3 ‾ m Mg3 Ge structure consists of a 12-fold-coordinated face-sharing GeMg12 cuboctahedron, whereas the P4/mmm MgGe and Cmcm MgGe2 phases form MgGe8 hexahedrons and MgGe4 polygons, respectively. All the stable phases of Mg-Ge compounds under high pressures exhibit metallic features owing to overlap between the conduction and valence bands. For Cmcm MgGe2 , the projected density of states near the Fermi energy mainly derive from Ge s, Ge p, and Ge d, which are responsible for its metallicity. The calculated superconducting critical temperature values of Cmcm Mg2 Ge and P4/mmm MgGe reach 10.3 and 9.07 K at 5 GPa, respectively.

The Structure and Properties of Magnesium-Phosphorus Compounds Under Pressure.

Inspired by the emergence of compounds with novel structures and unique properties (i.e., superconductivity and hardness) under high pressure, we systematically explored a binary Mg-P system under pressure, combining first-principles calculations with structure prediction. Several stoichiometries (Mg3 P, Mg2 P, MgP, MgP2 , and MgP3 ) were predicted to be stable under pressure. Especially, the P-P bonding patterns are different in the P-rich compounds and the Mg-rich compounds: in the former, the P-P bonding patterns form P2 , P3 , quadrilateral units, P-P⋅⋅⋅P chains or disordered "graphene-like" sublattice, while in the latter, the P-P bonding patterns eventually evolve isolated P ions. The analysis of integrated-crystal orbital Hamilton populations reveals that the P-P interactions are mainly responsible for the structural stability. The P-rich compounds with stoichiometries of MgP, MgP2 and MgP3 exhibit superconductive behaviors, and these phases show Tc in the range of 4.3-20 K. Our study provides useful information for understanding the Mg-P binary compounds at high pressure.

Stability and Superconductivity of K-P Compounds under Pressure.

We explore the phase diagram, structures, electron properties, and potential superconductivity of the K-P system at pressures of up to 200 GPa through unbiased structure searching techniques and first-principles calculations. Five stable chemical stoichiometries (K4P, K3P, K2P, KP, and KP2) have been theoretically predicted. In particular, P2 units or P-chains are uncovered in K2P, KP, and KP2 compounds with the existence of covalent bonds by analyzing the electron localization functions. And the Bader analysis demonstrates that charges transfer from K atoms to P atoms. Electron-phonon calculations show that the Tc of metallic I4/mmm-KP2 is 22.01 K at 5 GPa. The investigating of the K-P system is in favor of understanding the crystal structures and corresponding properties of potassium phosphides, which also give a strong motivation to search and design new superconductor materials in other phosphides.

Stability and properties of the Ru-H system at high pressure.

We report on a first-principles study of the phase diagram, structures and properties of the Ru-H system in the H-rich regime over a wide range of pressures. The results show that RuH is thermodynamically stable and can coexist with RuH3 and RuH6 under pressure. RuH and RuH3 stoichiometries exhibit metallic character as a result of notable band structures, while RuH6 is a semiconductor. Strikingly, some hydrogen atoms pairwise couple into H2 units in the RuH6 compound. An estimation of superconducting transition temperature Tc is carried out by applying the Allen-Dynes modified McMillan equation for Fm3[combining macron]m (RuH), Pm3[combining macron]m (RuH3), and Pm3[combining macron]n (RuH3) structures and the resulting Tc reaches 0.41, 3.57 and 1.25 K at different pressures, respectively.

Pressure-Induced Structures and Properties in Indium Hydrides.

The structures, electron properties, and potential superconductivity of indium hydrides are systematically studied under high pressure by first-principles density functional calculations. Upon compression, two stable stoichiometries (InH3 and InH5) are predicted to be thermodynamically stable. Particularly, in the two compounds, all hydrogen atoms exist in the form of H2 or H3 units. The stable phases present metallic features with the overlap between the conduction and the valence bands. The Bader analysis indicates that charges transfer from In atoms to H atoms. Electron-phonon calculations show that the estimated transition temperatures (Tc) of InH3 and InH5 are 34.1-40.5 and 22.4-27.1 K at 200 and 150 GPa, respectively.

Enhancement of T(c) in the atomic phase of iodine-doped hydrogen at high pressures.

The high-pressure structures and superconductivity of iodine-doped hydrogen have been studied by ab initio calculations. Above 100 GPa, we discover a stable phase with Pnma symmetry in the H2I stoichiometry that consists of a monatomic iodine tube trapping hydrogen molecular units. Interestingly, H2 molecular units dissociate and form a novel atomic phase with R3̄m symmetry at 246 GPa. Further electron-phonon coupling calculations predict the critical temperature of superconductivity T(c) to be 3.8 K for the Pnma phase and 33 K for the R3̄m phase at 240 GPa. Significantly, the T(c) of the R3̄m phase is enhanced approximately 8 times that of the Pnma phase, which is mainly attributed to the reason that H2 molecules are broken exhibiting an atomic character in the R3̄m phase.

The low coordination number of nitrogen in hard tungsten nitrides: a first-principles study.

Tungsten-nitrogen (W-N) compounds are studied via a combination of first-principles calculations and variable-composition evolutionary structure searches. New candidate ground states and high-pressure phases at 3 : 2, 1 : 1, and 5 : 6 compositions are uncovered and established for possible synthesis. We found that the structures in 4/5-fold N coordination (i.e., NbO-WN and W5N6) are more favoured for the W-N system at low-pressures compared with the conventional 6-fold phases (rs-WN and δ-WN). We attribute the low N coordination feature of W-N ground states to the enhanced W 5d-N 2p orbital hybridization and strong covalent W-N bonding, which involves the full-filling of W-N bonding and antibonding states and can remarkably improve the mechanical strength and hardness. These findings not only clarify the phase diagram of the W-N system, but also shed light on the correlations of hardness with microscopic crystal and electronic structures.

Investigation of stable germane structures under high-pressure.

The evolutionary structure-searching method discovers that the energetically preferred compounds of germane can be synthesized at a pressure of 190 GPa. New structures with the space groups Ama2 and C2/c proposed here contain semimolecular H2 and V-type H3 units, respectively. Electronic structure analysis shows the metallic character and charge transfer from Ge to H. The conductivity of the two structures originates from the electrons around the hydrogen atoms. Further electron-phonon coupling calculations predict that the two phases are superconductors with a high Tc of 47-57 K for Ama2 at 250 GPa and 70-84 K for C2/c at 500 GPa from quasi-harmonic approximation calculations, which may be higher than under actual conditions.

Predicted Formation of H3(+) in Solid Halogen Polyhydrides at High Pressures.

The structures of compressed halogen polyhydrides HnX (X = F, Cl and n > 1) and their evolution under pressure are studied using ab initio calculation based on density functional theory. HnF (n > 1) are metastable up to 300 GPa, whereas for HnCl (n > 1), four new stoichiometries (H2Cl, H3Cl, H5Cl, and H7Cl) are predicted to be stable at high pressures. Interestingly, triangular H3(+) species are unexpectedly found in stoichiometries H2F with [H3](+)[HF2](-), H3F with [H3](+)[F](-), H5F with [H3](+)[HF2](-)[H2]3, and H5Cl with [H3](+)[Cl](-)[H2] above 100 GPa. Importantly, formation processes of H3(+) species are clearly seen on the basis of comparing bond lengths, bond overlap populations, electron localization functions, and Bader charges as a functions of pressure. Further analysis reveals that the formation of H3(+) species is attributed to the pressure-induced charge transfer from hydrogen atoms to halogen atoms.