Observation of a molecular muonium polaron and its application to probing magnetic and electronic states

We thank the Engineering and Physical Sciences Research Council (EPSRC UK) for support via Grants No. EP/M000923/1, No. EP/K036408/1, No. EP/I004483/1, No. EP/S031081/1, and No. EP/S030263/1. L.L., S.S., D.J. and G.T. acknowledge also support from STFC-ISIS Neutron and Muon Source and Ada Lovelace Centre at STFC-SCD. We acknowledge use of the ARCHER (via the U.K. Car–Parrinello Consortium, EP/P022618/1 and EP/P022189/2), U.K. Materials and Molecular Modelling Hub (EP/P020194/1), and STFC Scientific Computing Department's SCARF HCP facilities. We acknowledge support from the Henry Royce Institute. This work was also supported financially through the EPSRC Grant Nos. EP/ P022464/1, and EP/R00661X/1.Muonium is a combination of first- and second-generation matter formed by the electrostatic interaction between an electron and an antimuon (μ+). Although a well-known physical system, their ability to form collective excitations in molecules had not been observed. Here, we give evidence for the detection of a muonium state that propagates in a molecular semiconductor lattice via thermally activated dynamics: a muonium polaron. By measuring the temperature dependence of the depolarization of the muonium state in C60, we observe a thermal narrowing of the hyperfine distribution that we attribute to the dynamics of the muonium between molecular sites. As a result of the time scale for muonium decay, the energies involved, charge and spin selectivity, this quasiparticle is a widely applicable experimental tool. It is an excellent probe of emerging electronic, dynamic, and magnetic states at interfaces and in low dimensional systems, where direct spatial probing is an experimental challenge owing to the buried interface, nanoscale elements providing the functionality localization and small magnitude of the effects.Publisher PDFPeer reviewe

T-Cell Memory Responses Elicited by Yellow Fever Vaccine are Targeted to Overlapping Epitopes Containing Multiple HLA-I and -II Binding Motifs

The yellow fever vaccines (YF-17D-204 and 17DD) are considered to be among the safest vaccines and the presence of neutralizing antibodies is correlated with protection, although other immune effector mechanisms are known to be involved. T-cell responses are known to play an important role modulating antibody production and the killing of infected cells. However, little is known about the repertoire of T-cell responses elicited by the YF-17DD vaccine in humans. In this report, a library of 653 partially overlapping 15-mer peptides covering the envelope (Env) and nonstructural (NS) proteins 1 to 5 of the vaccine was utilized to perform a comprehensive analysis of the virus-specific CD4+ and CD8+ T-cell responses. The T-cell responses were screened ex-vivo by IFN-γ ELISPOT assays using blood samples from 220 YF-17DD vaccinees collected two months to four years after immunization. Each peptide was tested in 75 to 208 separate individuals of the cohort. The screening identified sixteen immunodominant antigens that elicited activation of circulating memory T-cells in 10% to 33% of the individuals. Biochemical in-vitro binding assays and immunogenetic and immunogenicity studies indicated that each of the sixteen immunogenic 15-mer peptides contained two or more partially overlapping epitopes that could bind with high affinity to molecules of different HLAs. The prevalence of the immunogenicity of a peptide in the cohort was correlated with the diversity of HLA-II alleles that they could bind. These findings suggest that overlapping of HLA binding motifs within a peptide enhances its T-cell immunogenicity and the prevalence of the response in the population. In summary, the results suggests that in addition to factors of the innate immunity, "promiscuous" T-cell antigens might contribute to the high efficacy of the yellow fever vaccines. © 2013 de Melo et al

Acquisition of pneumococci specific effector and regulatory Cd4+ T cells localising within human upper respiratory-tract mucosal lymphoid tissue

The upper respiratory tract mucosa is the location for commensal Streptococcus (S.) pneumoniae colonization and therefore represents a major site of contact between host and bacteria. The CD4(+) T cell response to pneumococcus is increasingly recognised as an important mediator of immunity that protects against invasive disease, with data suggesting a critical role for Th17 cells in mucosal clearance. By assessing CD4 T cell proliferative responses we demonstrate age-related sequestration of Th1 and Th17 CD4(+) T cells reactive to pneumococcal protein antigens within mucosal lymphoid tissue. CD25(hi) T cell depletion and utilisation of pneumococcal specific MHCII tetramers revealed the presence of antigen specific Tregs that utilised CTLA-4 and PDL-1 surface molecules to suppress these responses. The balance between mucosal effector and regulatory CD4(+) T cell immunity is likely to be critical to pneumococcal commensalism and the prevention of unwanted pathology associated with carriage. However, if dysregulated, such responses may render the host more susceptible to invasive pneumococcal infection and adversely affect the successful implementation of both polysaccharide-conjugate and novel protein-based pneumococcal vaccines

Modelling the Health and Economic Impacts of Population-Wide Testing, Contact Tracing and Isolation (PTTI) Strategies for COVID-19 in the UK

Background: The COVID-19 epidemic in the UK has resulted in over 280,000 reported cases and over 40,000 deaths as of 5th June 2020. In the context of a slower increase in reported cases and deaths associated with COVID-19 over the last few weeks compared to earlier in the epidemic, the UK is starting to relax the physical restrictions (‘lockdown’) that have been imposed since 23 March 2020. This has been accompanied by the announcement of a strategy to test people for infection, trace contacts of those tested positive, and isolate positive diagnoses. While such policies are expected to be impactful, there is no conclusive evidence of which approach to this is likely to achieve the most appropriate balance between benefits and costs. This study combines mathematical and economic modelling to estimate the impact, costs, feasibility, and health and economic effects of different strategies. / Methods: We provide detailed description, impact, costing, and feasibility assessment of population-scale testing, tracing, and isolation strategies (PTTI). We estimate the impact of different PTTI strategies with a deterministic mathematical model for SARS-CoV-2 transmission that accurately captures tracing and isolation of contacts of individuals exposed, infectious, and diagnosed with the virus. We combine this with an economic model to project the mortality, intensive care, hospital, and non-hospital case outcomes, costs to the UK National Health Service, reduction in GDP, and intervention costs of each strategy. Model parameters are derived from publicly available data, and the model is calibrated to reported deaths associated with COVID-19. We modelled 31 scenarios in total (Panel 2). The first 18 comprised nine with ‘triggers’ (labelled with the -Trig suffix) for subsequent lockdown periods (>40,000 new infections per day) and lockdown releases (<10,000 new infections per day), and nine corresponding scenarios without triggers, namely: no large-scale PTTI (scenario 1); scale-up of PTTI to testing the whole population every week, with May–July 2020 lockdown release (scenario 2b), or delayed lockdown release until scale-up complete on 31 August 2020 (scenario 2a); these two scenarios with mandatory use of face coverings (scenarios 3a and 3b); and scenarios 2a, 2b, 3a, 3b replacing untargeted PTTI with testing of symptomatic people only (scenarios 4a, 4b, 4c, 4d). The final 13 scenarios looked at: whole population weekly testing to suppress the epidemic with lower tracing success (scenarios 3b-Trig00, 3b-Trig10, 3b-Trig20, 3b-Trig30) and switched to targeted testing after two months when it may suppress the epidemic (scenarios 3b-Trig00-2mo and 3b-Trig30-2mo), and targeted testing with lower tracing success (scenarios 4d-Trig10, 4dTrig20, 4d-Trig30, 4d-Trig40, 4d-Trig50, 4d-Trig60, 4d-Trig70). / Findings: Given that physical distancing measures have already been relaxed in the UK, scenario 4d-Trig (targeted testing of symptomatic people only, with a mandatory face coverings policy and subsequent lockdown triggered to enable PTTI to suppress the epidemic), is a strategy that will result in the fewest deaths (~52,000) and has the lowest intervention costs (~£8bn). The additional lockdown results in total reduction in GDP of ~£503bn, less than half the cost to the economy of subsequent lockdowns triggered in a scenario without PTTI (scenario 1-Trig, ~£1180bn reduction in GDP, ~105,000 deaths). In summer months, with lower cold and flu prevalence, approximately 75,000 symptomatic people per day need to be tested for this strategy to work, assuming 64% of their contacts are effectively traced (~80% traced with 80% success) within the infectious period (most within the first two days and nearly all by seven days) and all are isolated – including those without any symptoms – for 14 days. Untargeted testing of everyone every week, if it were feasible, may work without tracing, but at a higher cost (scenario 3b-Trig00). This cost could be reduced by switching to targeted testing after the epidemic is suppressed (scenario 3b-Trig30-2mo), though we note the epidemic could be suppressed with targeted testing itself providing tracing and isolation has at least a 32% success rate (scenario 4dTrig40). / Interpretation: PTTI strategies to suppress the COVID-19 epidemic within the context of a relaxation of lockdown will necessitate subsequent lockdowns to keep the epidemic suppressed during PTTI scale-up. Targeted testing of symptomatic people only can suppress the epidemic if accompanied by mandated use of face coverings. The feasibility of PTTI depends on sufficient capacity, capabilities, infrastructure and integrated systems to deliver it. The political and public acceptability of alternative scenarios for subsequent lockdowns needs to take account of crucial implications for employment, personal and national debt, education, population mental health and non-COVID-19 disease. Our model is able to incorporate additional scenarios as the situation evolves

A genetic approach for building different alphabets for peptide and protein classification

<p>Abstract</p> <p>Background</p> <p>In this paper, it is proposed an optimization approach for producing reduced alphabets for peptide classification, using a Genetic Algorithm. The classification task is performed by a multi-classifier system where each classifier (Linear or Radial Basis function Support Vector Machines) is trained using features extracted by different reduced alphabets. Each alphabet is constructed by a Genetic Algorithm whose objective function is the maximization of the area under the ROC-curve obtained in several classification problems.</p> <p>Results</p> <p>The new approach has been tested in three peptide classification problems: HIV-protease, recognition of T-cell epitopes and prediction of peptides that bind human leukocyte antigens. The tests demonstrate that the idea of training a pool classifiers by reduced alphabets, created using a Genetic Algorithm, allows an improvement over other state-of-the-art feature extraction methods.</p> <p>Conclusion</p> <p>The validity of the novel strategy for creating reduced alphabets is demonstrated by the performance improvement obtained by the proposed approach with respect to other reduced alphabets-based methods in the tested problems.</p

DOP011 A genome wide association study identifying association of the MHC region with 5-aminosalicylate (5-ASA) induced nephrotoxicity in inflammatory bowel disease

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Structural Properties of MHC Class II Ligands, Implications for the Prediction of MHC Class II Epitopes

Major Histocompatibility class II (MHC-II) molecules sample peptides from the extracellular space allowing the immune system to detect the presence of foreign microbes from this compartment. Prediction of MHC class II ligands is complicated by the open binding cleft of the MHC class II molecule, allowing binding of peptides extending out of the binding groove. Furthermore, only a few HLA-DR alleles have been characterized with a sufficient number of peptides (100–200 peptides per allele) to derive accurate description of their binding motif. Little work has been performed characterizing structural properties of MHC class II ligands. Here, we perform one such large-scale analysis. A large set of SYFPEITHI MHC class II ligands covering more than 20 different HLA-DR molecules was analyzed in terms of their secondary structure and surface exposure characteristics in the context of the native structure of the corresponding source protein. We demonstrated that MHC class II ligands are significantly more exposed and have significantly more coil content than other peptides in the same protein with similar predicted binding affinity. We next exploited this observation to derive an improved prediction method for MHC class II ligands by integrating prediction of MHC- peptide binding with prediction of surface exposure and protein secondary structure. This combined prediction method was shown to significantly outperform the state-of-the-art MHC class II peptide binding prediction method when used to identify MHC class II ligands. We also tried to integrate N- and O-glycosylation in our prediction methods but this additional information was found not to improve prediction performance. In summary, these findings strongly suggest that local structural properties influence antigen processing and/or the accessibility of peptides to the MHC class II molecule

Low-temperature magnetic crossover in the topological kagome magnet TbMn6Sn6

Magnetic topological phases of quantum matter are an emerging frontier in physics and materials science, of which kagome magnets appear as a highly promising platform. Here, we explore magnetic correlations in the recently identified topological kagome system TbMn$_{6}$Sn$_{6}$using muon spin rotation, combined with local field analysis and neutron diffraction. Our studies identify an out-of-plane ferrimagnetic structure with slow magnetic fluctuations which exhibit a critical slowing down below$${T}_{{{{{{{{\rm{C1}}}}}}}}}^{* }$$ ≃ 120 K and finally freeze into static patches with ideal out-of-plane order belowT$_{C1}$ ≃ 20 K. We further show that hydrostatic pressure of 2.1 GPa stabilises the static out-of-plane topological ferrimagnetic ground state in the whole volume of the sample. Therefore the exciting perspective arises of a magnetically-induced topological system whose magnetism can be controlled through external parameters. The present results will stimulate theoretical investigations to obtain a microscopic understanding of the relation between the low-temperature volume-wise magnetic evolution of the staticc-axis ferrimagnetic patches and the topological electronic properties in TbMn$_{6}$Sn$_{6}$