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

Manipulating the onset of lambing season in communal ewes through hormonal intervention

The study was conducted to evaluate the effectiveness of using long-acting medroxyprogesterone acetate (MPA) to delay the lambing season in communal wool sheep ewes. The study was conducted in three phases. In phase 1, a random assessment was made to determine whether the hormone had any effect on delaying the onset of the lambing season. In the second phase, the administration of the hormone at different times during the perceived mating season was assessed. In the third phase, it was investigated whether the use of the hormone had residual effects in the subsequent lambing season after the treatment was discontinued. From the results it is evident that the administration of 150 mg MPA before conception could delay lambing between two and three months. November seems to be the optimum month for hormone administration. However, administration of the hormone did not guarantee effective prevention of conception in all treated ewes and discontinuation of treatment resulted in ewes reverting to pre-treatment lambing patterns. In conclusion, long-acting MPA can be used selectively as an effective method to delay the lambing season in communal ewes and to manipulate it towards more favourable environmental conditions for ewes and lambs. There can be a seasonal effect on time of conception in communal ewes and this should be considered when timing a hormonal treatment protocol. Keywords: communal sheep farming, lambing season, manipulation, medroxyprogesterone acetat

Communication and re-use of chemical information in bioscience.

The current methods of publishing chemical information in bioscience articles are analysed. Using 3 papers as use-cases, it is shown that conventional methods using human procedures, including cut-and-paste are time-consuming and introduce errors. The meaning of chemical terms and the identity of compounds is often ambiguous. valuable experimental data such as spectra and computational results are almost always omitted. We describe an Open XML architecture at proof-of-concept which addresses these concerns. Compounds are identified through explicit connection tables or links to persistent Open resources such as PubChem. It is argued that if publishers adopt these tools and protocols, then the quality and quantity of chemical information available to bioscientists will increase and the authors, publishers and readers will find the process cost-effective.An article submitted to BiomedCentral Bioinformatics, created on request with their Publicon system. The transformed manuscript is archived as PDF. Although it has been through the publishers system this is purely automatic and the contents are those of a pre-refereed preprint. The formatting is provided by the system and tables and figures appear at the end. An accommpanying submission, http://www.dspace.cam.ac.uk/handle/1810/34580, describes the rationale and cultural aspects of publishing , abstracting and aggregating chemical information. BMC is an Open Access publisher and we emphasize that all content is re-usable under Creative Commons Licens

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

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

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

Suzuki Coupling Catalyzed by (8-(dimesitylboryl)quinoline)palladium(0) Species: A Theoretical Analysis

The Suzuki reaction is a catalyzed cross-coupling reaction which is of upmost importance in the formation of carbon-carbon (C-C) bonds in modern organic synthesis. Recently a new catalyst including an 8-(dimesitylboryl)quinoline for the coupling of aryl halides with phenylboronic acids was synthetized. We synthesized ligand that includes a frustrated Lewis pair, (quinolin-8-yl)dimesitylborane (DMBQ), complexed it with group X metals (nickel (Ni), palladium (Pd), and platinum (Pt)), and studied the process of oxidative addition with carbon-fluorine (C-F) bonds and activation towards Suzuki coupling. Mayer bond analysis and electron localization function maps showed a bond between the boron center in the ligand and the palladium center, but electron density, gradient and Laplacian maps showed no interaction. Thus, an elaborate extended transition state method involving natural chemical valence (ETS-NOCV) theory was performed to further characterize this interaction

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

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

The Resonance Peak in Sr2_2RuO4_4: Signature of Spin Triplet Pairing

We study the dynamical spin susceptibility, $\chi({\bf q}, \omega)$, in the normal and superconducting state of Sr$_2$RuO$_4$. In the normal state, we find a peak in the vicinity of ${\bf Q}_i\simeq (0.72\pi,0.72\pi)$ in agreement with recent inelastic neutron scattering (INS) experiments. We predict that for spin triplet pairing in the superconducting state a {\it resonance peak} appears in the out-of-plane component of $\chi$, but is absent in the in-plane component. In contrast, no resonance peak is expected for spin singlet pairing.Comment: 4 pages, 4 figures, final versio