51 research outputs found
The MIGenAS integrated bioinformatics toolkit for web-based sequence analysis
We describe a versatile and extensible integrated bioinformatics toolkit for the analysis of biological sequences over the Internet. The web portal offers convenient interactive access to a growing pool of chainable bioinformatics software tools and databases that are centrally installed and maintained by the RZG. Currently, supported tasks comprise sequence similarity searches in public or user-supplied databases, computation and validation of multiple sequence alignments, phylogenetic analysis and protein–structure prediction. Individual tools can be seamlessly chained into pipelines allowing the user to conveniently process complex workflows without the necessity to take care of any format conversions or tedious parsing of intermediate results. The toolkit is part of the Max-Planck Integrated Gene Analysis System (MIGenAS) of the Max Planck Society available at (click ‘Start Toolkit’)
All-electron periodic implementation with numerical atomic orbital basis functions: algorithm and benchmarks
We present an all-electron, periodic {\GnWn} implementation within the
numerical atomic orbital (NAO) basis framework. A localized variant of the
resolution-of-the-identity (RI) approximation is employed to significantly
reduce the computational cost of evaluating and storing the two-electron
Coulomb repulsion integrals. We demonstrate that the error arising from
localized RI approximation can be reduced to an insignificant level by
enhancing the set of auxiliary basis functions, used to expand the products of
two single-particle NAOs. An efficient algorithm is introduced to deal with the
Coulomb singularity in the Brillouin zone sampling that is suitable for the NAO
framework. We perform systematic convergence tests and identify a set of
computational parameters, which can serve as the default choice for most
practical purposes. Benchmark calculations are carried out for a set of
prototypical semiconductors and insulators, and compared to independent
reference values obtained from an independent implementation based on
linearized augmented plane waves (LAPW) plus high-energy localized orbitals
(HLOs) basis set, as well as experimental results. With a moderate (FHI-aims
\textit{tier} 2) NAO basis set, our calculations produce band gaps
that typically lie in between the standard LAPW and the LAPW+HLO results.
Complementing \textit{tier} 2 with highly localized Slater-type orbitals
(STOs), we find that the obtained band gaps show an overall convergence towards
the LAPW+HLO results. The algorithms and techniques developed in this work pave
the way for efficient implementations of correlated methods within the NAO
framework.Comment: 23 pages, 7 figure
Benefits from using mixed precision computations in the ELPA-AEO and ESSEX-II eigensolver projects
We first briefly report on the status and recent achievements of the ELPA-AEO
(Eigenvalue Solvers for Petaflop Applications - Algorithmic Extensions and
Optimizations) and ESSEX II (Equipping Sparse Solvers for Exascale) projects.
In both collaboratory efforts, scientists from the application areas,
mathematicians, and computer scientists work together to develop and make
available efficient highly parallel methods for the solution of eigenvalue
problems. Then we focus on a topic addressed in both projects, the use of mixed
precision computations to enhance efficiency. We give a more detailed
description of our approaches for benefiting from either lower or higher
precision in three selected contexts and of the results thus obtained
A Novel CCR5 Mutation Common in Sooty Mangabeys Reveals SIVsmm Infection of CCR5-Null Natural Hosts and Efficient Alternative Coreceptor Use In Vivo
In contrast to HIV infection in humans and SIV in macaques, SIV infection of natural hosts including sooty mangabeys (SM) is non-pathogenic despite robust virus replication. We identified a novel SM CCR5 allele containing a two base pair deletion (Δ2) encoding a truncated molecule that is not expressed on the cell surface and does not support SIV entry in vitro. The allele was present at a 26% frequency in a large SM colony, along with 3% for a CCR5Δ24 deletion allele that also abrogates surface expression. Overall, 8% of animals were homozygous for defective CCR5 alleles and 41% were heterozygous. The mutant allele was also present in wild SM in West Africa. CD8+ and CD4+ T cells displayed a gradient of CCR5 expression across genotype groups, which was highly significant for CD8+ cells. Remarkably, the prevalence of natural SIVsmm infection was not significantly different in animals lacking functional CCR5 compared to heterozygous and homozygous wild-type animals. Furthermore, animals lacking functional CCR5 had robust plasma viral loads, which were only modestly lower than wild-type animals. SIVsmm primary isolates infected both homozygous mutant and wild-type PBMC in a CCR5-independent manner in vitro, and Envs from both CCR5-null and wild-type infected animals used CXCR6, GPR15 and GPR1 in addition to CCR5 in transfected cells. These data clearly indicate that SIVsmm relies on CCR5-independent entry pathways in SM that are homozygous for defective CCR5 alleles and, while the extent of alternative coreceptor use in SM with CCR5 wild type alleles is uncertain, strongly suggest that SIVsmm tropism and host cell targeting in vivo is defined by the distribution and use of alternative entry pathways in addition to CCR5. SIVsmm entry through alternative pathways in vivo raises the possibility of novel CCR5-negative target cells that may be more expendable than CCR5+ cells and enable the virus to replicate efficiently without causing disease in the face of extremely restricted CCR5 expression seen in SM and several other natural host species
Chapitre VI. Le « texte strasbourgeois » de la littérature russe du xviiie siècle
1. Strasbourg dans les récits de voyages russes du xviiie siècle Comme l’a justement noté Wladimir Berelowitch, Karamzine faisait une entorse à la vérité en déclarant, dans l’article du Spectateur du Nord, avoir été le premier Russe à voyager « sa (sic) plume à la main ». De fait, si très peu de récits de voyage originaux avaient été publiés avant les Lettres, un certain nombre de voyageurs russes avaient déjà consigné par écrit leurs impressions de voyage, sous les formes diverses de l’écrit..
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