PubMed | Hubei University, Beijing Forestry University, University of Lisbon, Manchester Institute of Biotechnology and 27 more.
Type: Journal Article | Journal: Journal of cheminformatics | Year: 2015
The automatic extraction of chemical information from text requires the recognition of chemical entity mentions as one of its key steps. When developing supervised named entity recognition (NER) systems, the availability of a large, manually annotated text corpus is desirable. Furthermore, large corpora permit the robust evaluation and comparison of different approaches that detect chemicals in documents. We present the CHEMDNER corpus, a collection of 10,000 PubMed abstracts that contain a total of 84,355 chemical entity mentions labeled manually by expert chemistry literature curators, following annotation guidelines specifically defined for this task. The abstracts of the CHEMDNER corpus were selected to be representative for all major chemical disciplines. Each of the chemical entity mentions was manually labeled according to its structure-associated chemical entity mention (SACEM) class: abbreviation, family, formula, identifier, multiple, systematic and trivial. The difficulty and consistency of tagging chemicals in text was measured using an agreement study between annotators, obtaining a percentage agreement of 91. For a subset of the CHEMDNER corpus (the test set of 3,000 abstracts) we provide not only the Gold Standard manual annotations, but also mentions automatically detected by the 26 teams that participated in the BioCreative IV CHEMDNER chemical mention recognition task. In addition, we release the CHEMDNER silver standard corpus of automatically extracted mentions from 17,000 randomly selected PubMed abstracts. A version of the CHEMDNER corpus in the BioC format has been generated as well. We propose a standard for required minimum information about entity annotations for the construction of domain specific corpora on chemical and drug entities. The CHEMDNER corpus and annotation guidelines are available at: http://www.biocreative.org/resources/biocreative-iv/chemdner-corpus/.
News Article | March 2, 2017
Catalysis will play a major role in tackling the grand challenges of the 21st Century, such as climate change, growing demands and subsequent environmental issues stemming from the predicted rise in global population. It already plays a leading role in many processes that contribute to human well-being: including energy generation, food production, transportation, healthcare and well-being, and water (in the form of wastewater treatment). The contribution of catalysis to manufacturing adds up to almost 40% of global GDP--and the demand for such catalysts will only increase. Catalysts make existing processes greener. In other words, they produce less waste, consume less energy and use fewer raw materials to make the same mass of products. This will also mean new pathways to existing materials and products from renewable feedstocks, for example, and also routes to entirely new classes of materials with as yet unimagined properties. Catalysts make processes more efficient and effective and each of these challenges will require advances in catalytic technology in diverse sectors from energy, to water, food production, functional materials, bulk and intermediate materials and pharmaceuticals/fine chemicals. In order to maximise the benefits from research and create the greatest contribution to all these areas and more, improved understanding and targeted research programmes with collaboration between academia and industry are required to deepen understanding and develop new catalytic processes by using a design led approach. Edited by Graham Hutchings (Cardiff University, UK), Matthew Davidson (University of Bath, UK), Richard Catlow (University College London, UK & Cardiff University, UK), Christopher Hardacre (University of Manchester, UK), Nicholas Turner (University of Manchester, UK) and Paul Collier (Johnson Matthey Technology Centre, UK), Modern Developments in Catalysis provides a review of current research and practise on catalysis, focussing on five main themes: catalysis design, environmental catalysis, catalysis and energy, chemical transformation and biocatalysis and biotransformations. This book highlights many powerful examples of how catalysis can impact society and also how catalysis science is making use of the most advanced capabilities and techniques to shed light on how catalytic processes work. Topics range from complex reactions to the intricacies of catalyst preparation for supported nanoparticles, while chapters illustrate the challenges facing catalytic science and the directions in which the field is developing. Modern Developments in Catalysis provides a unique learning opportunity for students and professionals studying and working towards speeding-up, improving and increasing the rate of catalytic reactions in science and industry. This book is sold at major bookstores at US$139 / £115 (hardcover). To know more about the book, or to place and order, visit http://www. . C. Richard A. Catlow has long standing experience in the development and application of both experimental and computer modelling techniques in catalysis and molecular sciences. He holds approximately £2.5M of current EPSRC funding and has extensive experience in the field of HPC simulation techniques. He has been PI of the EPSRC funded Materials Chemistry HPC consortium for 15 years and has wide experience in managing large flexible consortium grants including a portfolio partnership grant (2005-2010), a High Performance Computing Consortium grant (2008-2013), and is currently the PI of the Centre for Catalytic Science (2011-2016). Graham J. Hutchings is the Director of the Cardiff Catalysis Institute and is the inaugural Director of the UK Catalysis Hub. The UK Catalysis Hub will coordinate and strengthen research efforts in catalytic science, allowing the UK to remain a world-leader in the field and tackle major global challenges. There will be a strong emphasis on energy sustainability, environmental protection and innovative catalytic processes to support the UK chemical industry. One of Prof Graham Hutchings' major scientific achievements is the pioneering work of using gold as an active catalyst, which still remains today as an important area of research. Christopher Hardacre's research is focused on the understanding of heterogeneously catalysed reactions including water gas shift catalysis, the use of transients to determine gas phase mechanisms, liquid phase hydrogenation and oxidation of pharmaceuticals, low temperature fuel cells and clean energy production. Of particular interest is the development of techniques to probe reaction mechanisms at short time scales in the gas phase and the understanding of solvent effects in liquid phase reactions. Strong interactions exist between his group and the theory group of Prof Peijun Hu (QUB) in order to develop DFT methods to predict new catalysts and validate the proposals made. He has also developed a strong research group in ionic liquids within the Queen's University Ionic Liquids Laboratory (QUILL) University-Industry research centre with interests in heterogeneously catalysed reactions, structural determination of ionic liquids, and species dissolved therein, analytical aspects, electrochemistry and prediction of physical properties of ionic liquids. Matthew G. Davidson is Whorrod Professor of Sustainable Chemical Technologies and director of the Centre for Sustainable Chemical Technologies at the University of Bath. His research interests are in the application of catalysis to the sustainable manufacture of fuels, materials and chemicals. Following a PhD and Research Fellowship at Cambridge, he held lectureships in Cambridge and Durham before being appointed to a Chair at the University of Bath. He is a Fellow of the Royal Society of Chemistry and a recipient of the Harrison Memorial Prize of the Royal Society of Chemistry and a Royal Society Industry Fellowship. He currently serves on the REF 2014 Chemistry Panel and holds over £13M of funding from research councils and industry. Nicholas J. Turner obtained his DPhil in 1985 with Prof Sir Jack Baldwin and from 1985-1987 was a Royal Society Junior Research Fellow, spending time at Harvard University with Prof George Whitesides. He was appointed lecturer in 1987 at Exeter University and moved to Edinburgh in 1995, initially as a Reader and subsequently Professor in 1998. In October 2004 he joined Manchester University as Professor of Chemical Biology where his research group is located in the Manchester Institute of Biotechnology Biocentre (MIB: http://www. ). He is Director of the Centre of Excellence in Biocatalysis (CoEBio3) (http://www. ) and also a cofounder and Scientific Director of Ingenza (http://www. ), a spin-out biocatalysis company based in Edinburgh and more recently Discovery Biocatalysts. He is a member of the Editorial Board of ChemCatChem and Advanced Synthesis and Catalysis. His research interests are in the area of biocatalysis with particular emphasis on the discovery and development of novel enzyme catalysed reactions for applications in organic synthesis. His group are also interested in the application of directed evolution technologies for the development of biocatalysts with tailored functions. Paul Collier is a Senior Research Scientist at the Johnson Matthey Technology Centre, Sonning Common, UK. He is interested in all aspects of heterogeneous catalysis, especially gas phase catalysis. Dr Paul collier spends approximately one day a week at the Harwell Campus interacting with the UK Catalysis Hub and Diamond Light source. Paul completed his PhD at Liverpool University in 1996 before undertaking a postdoctoral research position at Cardiff University focusing on the direct synthesis of Hydrogen peroxide, as well as investigating other catalytic systems. Following this he went to work for Johnson Matthey. World Scientific Publishing is a leading independent publisher of books and journals for the scholarly, research, professional and educational communities. The company publishes about 600 books annually and about 130 journals in various fields. World Scientific collaborates with prestigious organizations like the Nobel Foundation, US National Academies Press, as well as its subsidiary, the Imperial College Press, amongst others, to bring high quality academic and professional content to researchers and academics worldwide. To find out more about World Scientific, please visit http://www. . For more information, contact Amanda Yun at email@example.com
PubMed | University Institute of Health Sciences, Manchester Institute of Biotechnology, Matrix and University of Manchester
Type: Journal Article | Journal: Journal of the American Society of Nephrology : JASN | Year: 2015
Phospholipase A2 receptor 1 (PLA2R) is a target autoantigen in 70% of patients with idiopathic membranous nephropathy. We describe the location of a major epitope in the N-terminal cysteine-rich ricin domain of PLA2R that is recognized by 90% of human anti-PLA2R autoantibodies. The epitope was sensitive to reduction and SDS denaturation in the isolated ricin domain and the larger fragment containing the ricin, fibronectin type II, first and second C-type lectin domains (CTLD). However, in nondenaturing conditions the epitope was protected against reduction in larger fragments, including the full-length extracellular region of PLA2R. To determine the composition of the epitope, we isolated immunoreactive tryptic fragments by Western blotting and analyzed them by mass spectrometry. The identified peptides were tested as inhibitors of autoantibody binding to PLA2R by surface plasmon resonance. Two peptides from the ricin domain showed strong inhibition, with a longer sequence covering both peptides (31-mer) producing 85% inhibition of autoantibody binding to PLA2R. Anti-PLA2R antibody directly bound this 31-mer peptide under nondenaturing conditions and binding was sensitive to reduction. Analysis of PLA2R and the PLA2R-anti-PLA2R complex using electron microscopy and homology-based representations allowed us to generate a structural model of this major epitope and its antibody binding site, which is independent of pH-induced conformational change in PLA2R. Identification of this major PLA2R epitope will enable further therapeutic advances for patients with idiopathic membranous nephropathy, including antibody inhibition therapy and immunoadsorption of circulating autoantibodies.
PubMed | Manchester Institute of Biotechnology, Unilever and University of Manchester
Type: Journal Article | Journal: Journal of biomedical semantics | Year: 2016
The motivation for the BioHub project is to create an Integrated Knowledge Management System (IKMS) that will enable chemists to source ingredients from bio-renewables, rather than from non-sustainable sources such as fossil oil and its derivatives.The BioHubKB is the data repository of the IKMS; it employs Semantic Web technologies, especially OWL, to host data about chemical transformations, bio-renewable feedstocks, co-product streams and their chemical components. Access to this knowledge base is provided to other modules within the IKMS through a set of RESTful web services, driven by SPARQL queries to a Sesame back-end. The BioHubKB re-uses several bio-ontologies and bespoke extensions, primarily for chemical feedstocks and products, to form its knowledge organisation schema.Parts of plants form feedstocks, while various processes generate co-product streams that contain certain chemicals. Both chemicals and transformations are associated with certain qualities, which the BioHubKB also attempts to capture. Of immediate commercial and industrial importance is to estimate the cost of particular sets of chemical transformations (leading to candidate surfactants) performed in sequence, and these costs too are captured. Data are sourced from companies internal knowledge and document stores, and from the publicly available literature. Both text analytics and manual curation play their part in populating the ontology. We describe the prototype IKMS, the BioHubKB and the services that it supports for the IKMS.The BioHubKB can be found via http://biohub.cs.manchester.ac.uk/ontology/biohub-kb.owl .
PubMed | Manchester Institute of Biotechnology and University of Manchester
Type: Journal Article | Journal: Chemical communications (Cambridge, England) | Year: 2016
We report here the first experimental evidence of a self-assembling three-dimensional (3D) peptide hydrogel, with recognition motifs immobilized on the surface of fibres capable of sequence-specific oligonucleotide detection. These systems have the potential to be further developed into diagnostic and prognostic tools in human pathophysiology.
PubMed | University of the Philippines at Diliman and Manchester Institute of Biotechnology
Type: Journal Article | Journal: Journal of cheminformatics | Year: 2015
The development of robust methods for chemical named entity recognition, a challenging natural language processing task, was previously hindered by the lack of publicly available, large-scale, gold standard corpora. The recent public release of a large chemical entity-annotated corpus as a resource for the CHEMDNER track of the Fourth BioCreative Challenge Evaluation (BioCreative IV) workshop greatly alleviated this problem and allowed us to develop a conditional random fields-based chemical entity recogniser. In order to optimise its performance, we introduced customisations in various aspects of our solution. These include the selection of specialised pre-processing analytics, the incorporation of chemistry knowledge-rich features in the training and application of the statistical model, and the addition of post-processing rules.Our evaluation shows that optimal performance is obtained when our customisations are integrated into the chemical entity recogniser. When its performance is compared with that of state-of-the-art methods, under comparable experimental settings, our solution achieves competitive advantage. We also show that our recogniser that uses a model trained on the CHEMDNER corpus is suitable for recognising names in a wide range of corpora, consistently outperforming two popular chemical NER tools.The contributions resulting from this work are two-fold. Firstly, we present the details of a chemical entity recognition methodology that has demonstrated performance at a competitive, if not superior, level as that of state-of-the-art methods. Secondly, the developed suite of solutions has been made publicly available as a configurable workflow in the interoperable text mining workbench Argo. This allows interested users to conveniently apply and evaluate our solutions in the context of other chemical text mining tasks.
PubMed | Manchester Institute of Biotechnology
Type: Journal Article | Journal: Environmental science and pollution research international | Year: 2015
Predictive toxicology using chemometric tools can be very useful in order to fill the data gaps for ionic liquids (ILs) with limited available experimental toxicity information, in view of their growing industrial uses. Though originally promoted as green chemicals, ILs have now been shown to possess considerable toxicity against different ecological endpoints. Against this background, quantitative structure-activity relationship (QSAR) models have been developed here for the toxicity of ILs against the green algae Scenedesmus vacuolatus using computed descriptors with definite physicochemical meaning. The final models emerged from E-state indices, extended topochemical atom (ETA) indices and quantum topological molecular similarity (QTMS) indices. The developed partial least squares models support the established mechanism of toxicity of ionic liquids in terms of a surfactant action of cations and chaotropic action of anions. The models have been developed within the guidelines of the Organization of Economic Co-operation and Development (OECD) for regulatory QSAR models, and they have been validated both internally and externally using multiple strategies and also tested for applicability domain. A preliminary attempt has also been made, for the first time, to develop interspecies quantitative toxicity-toxicity relationship (QTTR) models for the algal toxicity of ILs with Daphnia toxicity, which should be interesting while predicting toxicity of ILs for an endpoint when the data for the other are available.
PubMed | Manchester Institute of Biotechnology and University of Manchester
Type: | Journal: Methods in molecular biology (Clifton, N.J.) | Year: 2016
Protein crystallography is the most powerful method to obtain atomic resolution information on the three-dimensional structure of proteins. An essential step towards determining the crystallographic structure of a protein is to produce good quality crystals from a concentrated sample of purified protein. These crystals are then used to obtain X-ray diffraction data necessary to determine the 3D structure by direct phasing or molecular replacement if the model of a homologous protein is available. Here, we describe the main approaches and techniques to obtain suitable crystals for X-ray diffraction. We include tools and guidance on how to evaluate and design the protein construct, how to prepare Se-methionine derivatized protein, how to assess the stability and quality of the sample, and how to crystallize and prepare crystals for diffraction experiments. While general strategies for protein crystallization are summarized, specific examples of the application of these strategies to the crystallization of PTP domains are discussed.
PubMed | Manchester Institute of Biotechnology, York St John University, University of Manchester and Andrews University
Type: | Journal: Phytochemistry | Year: 2015
The control and interaction between nitrogen and carbon assimilatory pathways is essential in both photosynthetic and non-photosynthetic tissue in order to support metabolic processes without compromising growth. Physiological differences between the basal and mature region of wheat (Triticum aestivum) primary leaves confirmed that there was a change from heterotrophic to autotrophic metabolism. Fourier Transform Infrared (FT-IR) spectroscopy confirmed the suitability and phenotypic reproducibility of the leaf growth conditions. Principal Component-Discriminant Function Analysis (PC-DFA) revealed distinct clustering between base, and tip sections of the developing wheat leaf, and from plants grown in the presence or absence of nitrate. Gas Chromatography-Time of Flight/Mass Spectrometry (GC-TOF/MS) combined with multivariate and univariate analyses, and Bayesian network (BN) analysis, distinguished different tissues and confirmed the physiological switch from high rates of respiration to photosynthesis along the leaf. The operation of nitrogen metabolism impacted on the levels and distribution of amino acids, organic acids and carbohydrates within the wheat leaf. In plants grown in the presence of nitrate there was reduced levels of a number of sugar metabolites in the leaf base and an increase in maltose levels, possibly reflecting an increase in starch turnover. The value of using this combined metabolomics analysis for further functional investigations in the future are discussed.
PubMed | Manchester Institute of Biotechnology
Type: Journal Article | Journal: Proceedings. Biological sciences | Year: 2015
Since the late eighteenth century, fossils of bizarre extinct creatures have been described from the Americas, revealing a previously unimagined chapter in the history of mammals. The most bizarre of these are the native South American ungulates thought to represent a group of mammals that evolved in relative isolation on South America, but with an uncertain affinity to any particular placental lineage. Many authors have considered them descended from Laurasian condylarths, which also includes the probable ancestors of perissodactyls and artiodactyls, whereas others have placed them either closer to the uniquely South American xenarthrans (anteaters, armadillos and sloths) or the basal afrotherians (e.g. elephants and hyraxes). These hypotheses have been debated owing to conflicting morphological characteristics and the hitherto inability to retrieve molecular information. Of the native South American mammals, only the toxodonts and litopterns persisted until the Late Pleistocene-Early Holocene. Owing to known difficulties in retrieving ancient DNA (aDNA) from specimens from warm climates, this research presents a molecular phylogeny for both Macrauchenia patachonica (Litopterna) and Toxodon platensis (Notoungulata) recovered using proteomics-based (liquid chromatography-tandem mass spectrometry) sequencing analyses of bone collagen. The results place both taxa in a clade that is monophyletic with the perissodactyls, which today are represented by horses, rhinoceroses and tapirs.