A 3-D diamondoid MOF catalyst based on in situ generated [Cu(L)2] N-heterocyclic carbene (NHC) linkers: hydroboration of CO(2)

Includes supplementary informationA new MOF, [Zn4O{Cu(L)2}2] (1), with a 4-fold interpenetrated 3D diamondoid structure was synthesised from in situ generated [Cu(L)2] NHC linkers. MOF 1 possesses tetrahedral Zn4O nodes, which are unusually coordinated by four pairs of carboxylates from four [Cu(L)2] linkers, and 14 A 1-D pore channels lined with [Cu(L)2] moieties that catalyse the hydroboration of CO2.Alexandre Burgun, Rachel S. Crees, Marcus L. Cole, Christian J. Doonan and Christopher J. Sumb

Production of cascade hypernuclei via the (K-,K+) reaction within a quark-meson coupling model

We study the production of bound cascade hypernuclei via the (K-,K+) reaction on 12C and 28Si targets within a covariant effective Lagrangian model, employing the cascade bound state spinors derived from the latest quark-meson coupling model as well as Dirac single particle wave functions. The K+-cascade production vertex is described by excitation, propagation and decay of Lambda and Sigma resonance states in the initial collision of a K- meson with a target proton in the incident channel. The parameters of the resonance vertices are fixed by describing the available data on total and differential cross sections for the cascade production in elementary (K-,K+) reaction. We find that both the elementary and hypernuclear production cross sections are dominated by the contributions from the Lambda(1520) intermediate resonant state. The 0 degree differential cross sections for the formation of simple s-state cascade particle-hole states peak at a beam momentum around 1.0 GeV/c, with a value in excess of 1 mub.Comment: 17 pages, 8 figures, version accepted for publication in Nucl. Phys.

Measurements of KL Branching Fractions and the CP Violation Parameter |eta+-|

We present new measurements of the six largest branching fractions of the KL using data collected in 1997 by the KTeV experiment (E832) at Fermilab. The results are B(KL -> pi e nu) = 0.4067 +- 0.0011 B(KL -> pi mu nu) = 0.2701 +- 0.0009 B(KL -> pi+ pi- pi0) = 0.1252 +- 0.0007 B(KL -> pi0 pi0 pi0) = 0.1945 +- 0.0018 B(KL -> pi+ pi-) = (1.975 +- 0.012)E-3, and B(KL -> pi0 pi0) = (0.865 +- 0.010)E-3, where statistical and systematic errors have been summed in quadrature. We also determine the CP violation parameter |eta+-| to be (2.228 +- 0.010)E-3. Several of these results are not in good agreement with averages of previous measurements.Comment: Submitted to Phys. Rev. D; 20 pages, 22 figure

Mapping data elements to terminological resources for integrating biomedical data sources

BACKGROUND: Data integration is a crucial task in the biomedical domain and integrating data sources is one approach to integrating data. Data elements (DEs) in particular play an important role in data integration. We combine schema- and instance-based approaches to mapping DEs to terminological resources in order to facilitate data sources integration. METHODS: We extracted DEs from eleven disparate biomedical sources. We compared these DEs to concepts and/or terms in biomedical controlled vocabularies and to reference DEs. We also exploited DE values to disambiguate underspecified DEs and to identify additional mappings. RESULTS: 82.5% of the 474 DEs studied are mapped to entries of a terminological resource and 74.7% of the whole set can be associated with reference DEs. Only 6.6% of the DEs had values that could be semantically typed. CONCLUSION: Our study suggests that the integration of biomedical sources can be achieved automatically with limited precision and largely facilitated by mapping DEs to terminological resources

War of Ontology Worlds: Mathematics, Computer Code, or Esperanto?

The use of structured knowledge representations—ontologies and terminologies—has become standard in biomedicine. Definitions of ontologies vary widely, as do the values and philosophies that underlie them. In seeking to make these views explicit, we conducted and summarized interviews with a dozen leading ontologists. Their views clustered into three broad perspectives that we summarize as mathematics, computer code, and Esperanto. Ontology as mathematics puts the ultimate premium on rigor and logic, symmetry and consistency of representation across scientific subfields, and the inclusion of only established, non-contradictory knowledge. Ontology as computer code focuses on utility and cultivates diversity, fitting ontologies to their purpose. Like computer languages C++, Prolog, and HTML, the code perspective holds that diverse applications warrant custom designed ontologies. Ontology as Esperanto focuses on facilitating cross-disciplinary communication, knowledge cross-referencing, and computation across datasets from diverse communities. We show how these views align with classical divides in science and suggest how a synthesis of their concerns could strengthen the next generation of biomedical ontologies

Protecting-group-free site-selective reactions in a metal–organic framework reaction vessel

Site-selective organic transformations are commonly required in the synthesis of complex molecules. By employing a bespoke metal-organic framework (MOF, 1·[Mn(CO)3N3]), in which coordinated azide anions are precisely positioned within 1D channels, we present a strategy for the site-selective transformation of dialkynes into alkyne-functionalized triazoles. As an illustration of this approach, 1,7-octadiyne-3,6-dione stoichiometrically furnishes the mono-“click” product N-methyl-4-hex-5’-ynl-1’,4’dione-1,2,3-triazole with only trace bis-triazole side-product. Stepwise insights into conversions of the MOF reaction vessel were obtained by X-ray crystallography, demonstrating that the reactive sites are “isolated” from one another. Single-crystal to singlecrystal transformations of the Mn(I)-metalated material 1·[Mn(CO)3(H2O)]Br to the corresponding azide species 1·[Mn(CO)3N3] with sodium azide, followed by a series of [3+2] azide-alkyne cycloaddition reactions, are reported. The final liberation of the “click” products from the porous material is achieved by N-alkylation with MeBr, regenerating starting MOF 1·[Mn(CO)3(H2O)]Br, and the organic products characterized by NMR spectroscopy and mass spectrometry. Once the dialkyne length exceeds the azide separation, site selectivity is lost, confirming the critical importance of isolated azide moieties for this strategy. We postulate that carefully designed MOFs can act as physical protecting groups to facilitate other site-selective and chemoselective transformations

A transversal approach to predict gene product networks from ontology-based similarity

<p>Abstract</p> <p>Background</p> <p>Interpretation of transcriptomic data is usually made through a "standard" approach which consists in clustering the genes according to their expression patterns and exploiting Gene Ontology (GO) annotations within each expression cluster. This approach makes it difficult to underline functional relationships between gene products that belong to different expression clusters. To address this issue, we propose a transversal analysis that aims to predict functional networks based on a combination of GO processes and data expression.</p> <p>Results</p> <p>The transversal approach presented in this paper consists in computing the semantic similarity between gene products in a Vector Space Model. Through a weighting scheme over the annotations, we take into account the representativity of the terms that annotate a gene product. Comparing annotation vectors results in a matrix of gene product similarities. Combined with expression data, the matrix is displayed as a set of functional gene networks. The transversal approach was applied to 186 genes related to the enterocyte differentiation stages. This approach resulted in 18 functional networks proved to be biologically relevant. These results were compared with those obtained through a standard approach and with an approach based on information content similarity.</p> <p>Conclusion</p> <p>Complementary to the standard approach, the transversal approach offers new insight into the cellular mechanisms and reveals new research hypotheses by combining gene product networks based on semantic similarity, and data expression.</p

TargetMine, an Integrated Data Warehouse for Candidate Gene Prioritisation and Target Discovery

Prioritising candidate genes for further experimental characterisation is a non-trivial challenge in drug discovery and biomedical research in general. An integrated approach that combines results from multiple data types is best suited for optimal target selection. We developed TargetMine, a data warehouse for efficient target prioritisation. TargetMine utilises the InterMine framework, with new data models such as protein-DNA interactions integrated in a novel way. It enables complicated searches that are difficult to perform with existing tools and it also offers integration of custom annotations and in-house experimental data. We proposed an objective protocol for target prioritisation using TargetMine and set up a benchmarking procedure to evaluate its performance. The results show that the protocol can identify known disease-associated genes with high precision and coverage. A demonstration version of TargetMine is available at http://targetmine.nibio.go.jp/