Chemistry in Bioinformatics

A preprint of an invited submission to BioMedCentral Bioinformatics. This short manuscript is an overview or the current problems and opportunities in publishing chemical information. Full details of technology are given in the sibling manuscript http://www.dspace.cam.ac.uk/handle/1810/34579 The manuscript is the authors' preprint although it has been automatically transformed into this archived PDF by the submission system. The authors are not responsible for the formattingChemical information is now seen as critical for most areas of life sciences. But unlike Bioinformatics, where data is Openly available and freely re−usable, most chemical information is closed and cannot be re−distributed without permission. This has led to a failure to adopt modern informatics and software techniques and therefore paucity of chemistry in bioinformatics. New technology, however, offers the hope of making chemical data (compounds and properties) Free during the authoring process. We argue that the technology is already available; we require a collective agreement to enhance publication protocols

Representation and use of chemistry in the global electronic age.

We present an overview of the current state of public semantic chemistry and propose new approaches at a strategic and a detailed level. We show by example how a model for a Chemical Semantic Web can be constructed using machine-processed data and information from journal articles.This manuscript addresses questions of robotic access to data and its automatic re-use, including the role of Open Access archival of data. This is a pre-refereed preprint allowed by the publisher's (Royal Soc. Chemistry) Green policy. The author's preferred manuscript is an HTML hyperdocument with ca. 20 links to images, some of which are JPEgs and some of which are SVG (scalable vector graphics) including animations. There are also links to molecules in CML, for which the Jmol viewer is recommended. We susgeest that readers who wish to see the full glory of the manuscript, download the Zipped version and unpack on their machine. We also supply a PDF and DOC (Word) version which obviously cannot show the animations, but which may be the best palce to start, particularly for those more interested in the text

Molecular self-organisation in a developmental model for the evolution of large-scale artificial neural networks

We argue that molecular self-organisation during embryonic development allows evolution to perform highly nonlinear combinatorial optimisation. A structured approach to architectural optimisation of large-scale Artificial Neural Networks using this principle is presented. We also present simulation results demonstrating the evolution of an edge detecting retina using the proposed methodology

Semantic physical science.

The articles in this special issue arise from a workshop and symposium held in January 2012 (Semantic Physical Science'). We invited people who shared our vision for the potential of the web to support chemical and related subjects. Other than the initial invitations, we have not exercised any control over the content of the contributed articles.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Tauroursodeoxycholic acid exerts anticholestatic effects by a cooperative cPKC alpha-/PKA-dependent mechanism in rat liver.

Objective: Ursodeoxycholic acid (UDCA) exerts anticholestatic effects in part by protein kinase C (PKC)-dependent mechanisms. Its taurine conjugate, TUDCA, is a cPKCa agonist. We tested whether protein kinase A (PKA) might contribute to the anticholestatic action of TUDCA via cooperative cPKCa-/PKA-dependent mechanisms in taurolithocholic acid (TLCA)-induced cholestasis. Methods: In perfused rat liver, bile flow was determined gravimetrically, organic anion secretion spectrophotometrically, lactate dehydrogenase (LDH) release enzymatically, cAMP response-element binding protein (CREB) phosphorylation by immunoblotting, and cAMP by immunoassay. PKC/PKA inhibitors were tested radiochemically. In vitro phosphorylation of the conjugate export pump, Mrp2/Abcc2, was studied in rat hepatocytes and human Hep-G2 hepatoma cells. Results: In livers treated with TLCA (10 mmol/l)+TUDCA (25 mmol/l), combined inhibition of cPKC by the cPKCselective inhibitor Go¨6976 (100 nmol/l) or the nonselective PKC inhibitor staurosporine (10 nmol/l) and of PKA by H89 (100 nmol/l) reduced bile flow by 36% (p,0.05) and 48% (p,0.01), and secretion of the Mrp2/ Abcc2 substrate, 2,4-dinitrophenyl-S-glutathione, by 31% (p,0.05) and 41% (p,0.01), respectively; bile flow was unaffected in control livers or livers treated with TUDCA only or TLCA+taurocholic acid. Inhibition of cPKC or PKA alone did not affect the anticholestatic action of TUDCA. Hepatic cAMP levels and CREB phosphorylation as readout of PKA activity were unaffected by the bile acids tested, suggesting a permissive effect of PKA for the anticholestatic action of TUDCA. Rat and human hepatocellular Mrp2 were phosphorylated by phorbol ester pretreatment and recombinant cPKCa, nPKCe, and PKA, respectively, in a staurosporine-sensitive manner. Conclusion: UDCA conjugates exert their anticholestatic action in bile acid-induced cholestasis in part via cooperative post-translational cPKCa-/PKA-dependent mechanisms. Hepatocellular Mrp2 may be one target of bile acid-induced kinase activation

Knowledge and the artefact

This paper discusses ways that knowledge may be found in or through artefacts. One purpose is to suggest situations where artefacts might be central to a narrative, rather than secondary to a text. A second purpose is to suggest ways that design and production of artefacts might be instrumental in eliciting knowledge. Four general situations are proposed: (1) Simple Forms - an artefact demonstrates or describes a principle or technique. (2) Communication of Process - artefacts arising from a process make the process explicit. (3) Artefacts Within the Research - artefacts are instrumental in advancing the research by communicating ideas or information. (4) Knowledge Elicited by Artefacts - artefacts provide a stimulus or context which enables information to be uncovered. .</p

Microscopic resolution broadband dielectric spectroscopy

Results are presented for a non-contact measurement system capable of micron level spatial resolution. It utilises the novel electric potential sensor (EPS) technology, invented at Sussex, to image the electric field above a simple composite dielectric material. EP sensors may be regarded as analogous to a magnetometer and require no adjustments or offsets during either setup or use. The sample consists of a standard glass/epoxy FR4 circuit board, with linear defects machined into the surface by a PCB milling machine. The sample is excited with an a.c. signal over a range of frequencies from 10 kHz to 10 MHz, from the reverse side, by placing it on a conducting sheet connected to the source. The single sensor is raster scanned over the surface at a constant working distance, consistent with the spatial resolution, in order to build up an image of the electric field, with respect to the reference potential. The results demonstrate that both the surface defects and the internal dielectric variations within the composite may be imaged in this way, with good contrast being observed between the glass mat and the epoxy resin

National Evaluation of the Capacity Building Programme in English Local Government: Evaluation of the National Programmes: Annex 2: Evaluation of the National Programmes

The report is one of a series of outputs from the national evaluation of the CBP, being undertaken by a team of researchers at the Policy Research Institute (PRI) at Leeds Metropolitan University and the Cities Research Unit at the University of West of England. The Capacity Building Programme for local government was launched in 2003 as a joint Department for Communities and Local Government (DCLG) / Local Government Association (LGA) initiative to support capacity building and improvement activities within local authorities in England. The evaluation of the Capacity Building Programme has been underway since late 2004. A scoping phase was conducted until May 2005, including a short evaluation of the Pilot Programmes. The main phase of the evaluation commenced in September 2005 and encompassed four main phases (see Section 1.3: p10)

Evolution of helicity in NOAA 10923 over three consecutive solar rotations

We have studied the evolution of magnetic helicity and chirality in an active region over three consecutive solar rotations. The region when it first appeared was named NOAA10923 and in subsequent rotations it was numbered NOAA 10930, 10935 and 10941. We compare the chirality of these regions at photospheric, chromospheric and coronal heights. The observations used for photospheric and chromospheric heights are taken from Solar Vector Magnetograph (SVM) and H_alpha imaging telescope of Udaipur Solar Observatory (USO), respectively. We discuss the chirality of the sunspots and associated H_alpha filaments in these regions. We find that the twistedness of superpenumbral filaments is maintained in the photospheric transverse field vectors also. We also compare the chirality at photospheric and chromospheric heights with the chirality of the associated coronal loops, as observed from the HINODE X-Ray Telescope.Comment: 8 pages, 4 figure

Statistical characteristics of surrogate data based on geophysical measurements

In this study, the statistical properties of a range of measurements are compared with those of their surrogate time series. Seven different records are studied, amongst others, historical time series of mean daily temperature, daily rain sums and runoff from two rivers, and cloud measurements. Seven different algorithms are used to generate the surrogate time series. The best-known method is the iterative amplitude adjusted Fourier transform (IAAFT) algorithm, which is able to reproduce the measured distribution as well as the power spectrum. Using this setup, the measurements and their surrogates are compared with respect to their power spectrum, increment distribution, structure functions, annual percentiles and return values. It is found that the surrogates that reproduce the power spectrum and the distribution of the measurements are able to closely match the increment distributions and the structure functions of the measurements, but this often does not hold for surrogates that only mimic the power spectrum of the measurement. However, even the best performing surrogates do not have asymmetric increment distributions, i.e., they cannot reproduce nonlinear dynamical processes that are asymmetric in time. Furthermore, we have found deviations of the structure functions on small scales