Geometrization of metric boundary data for Einstein's equations

The principle part of Einstein equations in the harmonic gauge consists of a constrained system of 10 curved space wave equations for the components of the space-time metric. A well-posed initial boundary value problem based upon a new formulation of constraint-preserving boundary conditions of the Sommerfeld type has recently been established for such systems. In this paper these boundary conditions are recast in a geometric form. This serves as a first step toward their application to other metric formulations of Einstein's equations.Comment: Article to appear in Gen. Rel. Grav. volume in memory of Juergen Ehler

The Chemical Translation Service—a web-based tool to improve standardization of metabolomic reports

Summary: Metabolomic publications and databases use different database identifiers or even trivial names which disable queries across databases or between studies. The best way to annotate metabolites is by chemical structures, encoded by the International Chemical Identifier code (InChI) or InChIKey. We have implemented a web-based Chemical Translation Service that performs batch conversions of the most common compound identifiers, including CAS, CHEBI, compound formulas, Human Metabolome Database HMDB, InChI, InChIKey, IUPAC name, KEGG, LipidMaps, PubChem CID+SID, SMILES and chemical synonym names. Batch conversion downloads of 1410 CIDs are performed in 2.5 min. Structures are automatically displayed

Identifying metabolites by integrating metabolome databases with mass spectrometry cheminformatics.

Novel metabolites distinct from canonical pathways can be identified through the integration of three cheminformatics tools: BinVestigate, which queries the BinBase gas chromatography-mass spectrometry (GC-MS) metabolome database to match unknowns with biological metadata across over 110,000 samples; MS-DIAL 2.0, a software tool for chromatographic deconvolution of high-resolution GC-MS or liquid chromatography-mass spectrometry (LC-MS); and MS-FINDER 2.0, a structure-elucidation program that uses a combination of 14 metabolome databases in addition to an enzyme promiscuity library. We showcase our workflow by annotating N-methyl-uridine monophosphate (UMP), lysomonogalactosyl-monopalmitin, N-methylalanine, and two propofol derivatives

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Initial data for fluid bodies in general relativity

We show that there exist asymptotically flat almost-smooth initial data for Einstein-perfect fluid's equation that represent an isolated liquid-type body. By liquid-type body we mean that the fluid energy density has compact support and takes a strictly positive constant value at its boundary. By almost-smooth we mean that all initial data fields are smooth everywhere on the initial hypersurface except at the body boundary, where tangential derivatives of any order are continuous at that boundary. PACS: 04.20.Ex, 04.40.Nr, 02.30.JrComment: 38 pages, LaTeX 2e, no figures. Accepted for publication in Phys. Rev.

How Large Is the Metabolome? A Critical Analysis of Data Exchange Practices in Chemistry

Calculating the metabolome size of species by genome-guided reconstruction of metabolic pathways misses all products from orphan genes and from enzymes lacking annotated genes. Hence, metabolomes need to be determined experimentally. Annotations by mass spectrometry would greatly benefit if peer-reviewed public databases could be queried to compile target lists of structures that already have been reported for a given species. We detail current obstacles to compile such a knowledge base of metabolites.As an example, results are presented for rice. Two rice (oryza sativa) subspecies have been fully sequenced, oryza japonica and oryza indica. Several major small molecule databases were compared for listing known rice metabolites comprising PubChem, Chemical Abstracts, Beilstein, Patent databases, Dictionary of Natural Products, SetupX/BinBase, KNApSAcK DB, and finally those databases which were obtained by computational approaches, i.e. RiceCyc, KEGG, and Reactome. More than 5,000 small molecules were retrieved when searching these databases. Unfortunately, most often, genuine rice metabolites were retrieved together with non-metabolite database entries such as pesticides. Overlaps from database compound lists were very difficult to compare because structures were either not encoded in machine-readable format or because compound identifiers were not cross-referenced between databases.We conclude that present databases are not capable of comprehensively retrieving all known metabolites. Metabolome lists are yet mostly restricted to genome-reconstructed pathways. We suggest that providers of (bio)chemical databases enrich their database identifiers to PubChem IDs and InChIKeys to enable cross-database queries. In addition, peer-reviewed journal repositories need to mandate submission of structures and spectra in machine readable format to allow automated semantic annotation of articles containing chemical structures. Such changes in publication standards and database architectures will enable researchers to compile current knowledge about the metabolome of species, which may extend to derived information such as spectral libraries, organ-specific metabolites, and cross-study comparisons

Collective modes in the electronic polarization of double-layer systems in the superconducting state

Standard weak coupling methods are used to study collective modes in the superconducting state of a double-layer system with intralayer and interlayer interaction, as well as a Josephson-type coupling and single particle hopping between the layers by calculating the electronic polarization function perpendicular to the layers. New analytical results are derived for the mode frequencies corresponding to fluctuations of the relative phase and amplitude of the layer order parameters in the case of interlayer pairing and finite hopping $t$. A new effect is found for finite $k$-dependent hopping: then the amplitude and phase fluctuations are coupled. Therefore two collective modes may appear in the dynamical c-axis conductivity below the threshold energy for breaking Cooper pairs. With help of numerical calculations we investigate the temperature dependence of the collective modes and show how a plasmon corresponding to charge fluctuations between the layers evolves in the normal state.Comment: 17 pages, latex, 8 ps figure