The crystal structure of methane B at 8 GPa-An alpha-Mn arrangement of molecules

From a combination of powder and single-crystal synchrotron x-ray diffraction data we have determined the carbon substructure of phase B of methane at a pressure of ∼8 GPa. We find this substructure to be cubic with space group I4 ¯ 3m I4¯3m and 58 molecules in the unit cell. The unit cell has a lattice parameter a = 11.911(1) Å at 8.3(2) GPa, which is a factor of √2 larger than had previously been proposed by Umemoto et al. [J. Phys.: Condens. Matter14, 10675 (2002)]. The substructure as now solved is not related to any close-packed arrangement, contrary to previous proposals. Surprisingly, the arrangement of the carbon atoms is isostructural with that of α-manganese at ambient conditions. © 2014, AIP Publishing LLC

NetCTLpan: pan-specific MHC class I pathway epitope predictions

Reliable predictions of immunogenic peptides are essential in rational vaccine design and can minimize the experimental effort needed to identify epitopes. In this work, we describe a pan-specific major histocompatibility complex (MHC) class I epitope predictor, NetCTLpan. The method integrates predictions of proteasomal cleavage, transporter associated with antigen processing (TAP) transport efficiency, and MHC class I binding affinity into a MHC class I pathway likelihood score and is an improved and extended version of NetCTL. The NetCTLpan method performs predictions for all MHC class I molecules with known protein sequence and allows predictions for 8-, 9-, 10-, and 11-mer peptides. In order to meet the need for a low false positive rate, the method is optimized to achieve high specificity. The method was trained and validated on large datasets of experimentally identified MHC class I ligands and cytotoxic T lymphocyte (CTL) epitopes. It has been reported that MHC molecules are differentially dependent on TAP transport and proteasomal cleavage. Here, we did not find any consistent signs of such MHC dependencies, and the NetCTLpan method is implemented with fixed weights for proteasomal cleavage and TAP transport for all MHC molecules. The predictive performance of the NetCTLpan method was shown to outperform other state-of-the-art CTL epitope prediction methods. Our results further confirm the importance of using full-type human leukocyte antigen restriction information when identifying MHC class I epitopes. Using the NetCTLpan method, the experimental effort to identify 90% of new epitopes can be reduced by 15% and 40%, respectively, when compared to the NetMHCpan and NetCTL methods. The method and benchmark datasets are available at http://www.cbs.dtu.dk/services/NetCTLpan/

Quantitative predictions of peptide binding to any HLA-DR molecule of known sequence: NetMHCIIpan

CD4 positive T helper cells control many aspects of specific immunity. These cells are specific for peptides derived from protein antigens and presented by molecules of the extremely polymorphic major histocompatibility complex (MHC) class II system. The identification of peptides that bind to MHC class II molecules is therefore of pivotal importance for rational discovery of immune epitopes. HLA-DR is a prominent example of a human MHC class II. Here, we present a method, NetMHCIIpan, that allows for pan-specific predictions of peptide binding to any HLA-DR molecule of known sequence. The method is derived from a large compilation of quantitative HLA-DR binding events covering 14 of the more than 500 known HLA-DR alleles. Taking both peptide and HLA sequence information into account, the method can generalize and predict peptide binding also for HLA-DR molecules where experimental data is absent. Validation of the method includes identification of endogenously derived HLA class II ligands, cross-validation, leave-one-molecule-out, and binding motif identification for hitherto uncharacterized HLA-DR molecules. The validation shows that the method can successfully predict binding for HLA-DR molecules-even in the absence of specific data for the particular molecule in question. Moreover, when compared to TEPITOPE, currently the only other publicly available prediction method aiming at providing broad HLA-DR allelic coverage, NetMHCIIpan performs equivalently for alleles included in the training of TEPITOPE while outperforming TEPITOPE on novel alleles. We propose that the method can be used to identify those hitherto uncharacterized alleles, which should be addressed experimentally in future updates of the method to cover the polymorphism of HLA-DR most efficiently. We thus conclude that the presented method meets the challenge of keeping up with the MHC polymorphism discovery rate and that it can be used to sample the MHC "space," enabling a highly efficient iterative process for improving MHC class II binding predictions

Isostructural second-order phase transition of b-Bi2O3 at high pressures: an experimental and theoretical study

This document is the Accepted Manuscript version of a Published Work that appeared in final form in Journal of Physical Chemistry C, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see http://dx.doi.org/10.1021/jp507826jWe report a joint experimental and theoretical study of the structural and vibrational properties of synthetic sphaerobismoite (beta-Bi2O3) at high pressures in which room-temperature angle-dispersive X-ray diffraction (XRD) and Raman scattering measurements have been complemented with ab initio total energy and lattice dynamics calculations. Striking changes in Raman spectra were observed around 2 GPa, whereas X-ray diffraction measurements evidence no change in the tetragonal symmetry of the compound up to 20 GPa; however, a significant change exists in the compressibility when increasing pressure above 2 GPa. These features have been understood by means of theoretical calculations, which show that beta-Bi2O3 undergoes a pressure-induced isostructural phase transition near 2 GPa. In the new isostructural beta' phase, the Bi3+ and O2- environments become more regular than those in the original beta phase because of the strong decrease in the activity of the lone electron pair of Bi above 2 GPa. Raman measurements and theoretical calculations provide evidence of the second-order nature of the pressure-induced isostructural transition. Above 20 GPa, XRD measurements suggest a partial amorphization of the sample despite Raman measurements still show weak peaks, probably related to a new unknown phase which remains up to 27 GPa. On pressure release, XRD patterns and Raman spectra below 2 GPa correspond to elemental Bi-I, thus evidencing a pressure-induced decomposition of the sample during downstroke.Financial support from the Spanish Consolider Ingenio 2010 Program (MALTA Project CSD2007-00045) is acknowledged. This work was also supported by Brazilian Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq) under Project 201050/2012-9, Spanish MICINN under Projects MAT2010-21270-004-01/03/04 and MAT2013-46649-C4-2/3/4-P, Spanish MINECO under Project CTQ2012-36253-C03-02, and from Vicerrectorado de Investigacion de la Universitat Politecnica de Valencia under Projects UPV2011-0914 PAID-05-11 and UPV2011-0966 PAID-06-11. Supercomputer time has been provided by the Red Espanola de Supercomputacion (RES) and the MALTA cluster. JAS. acknowledges Juan de la Cierva fellowship program for financial support.Pereira, ALJ.; Sans Tresserras, JÁ.; Vilaplana Cerda, RI.; Gomis, O.; Manjón Herrera, FJ.; Rodriguez-Hernandez, P.; Muñoz, A.... (2014). Isostructural second-order phase transition of b-Bi2O3 at high pressures: an experimental and theoretical study. Journal of Physical Chemistry C. 118(40):23189-23201. https://doi.org/10.1021/jp507826jS23189232011184