A5056067513- Biomedical Text Mining and Ontologies
- Semantic Web and Ontologies
- Chemical Synthesis and Analysis
- Supramolecular Chemistry and Complexes
- Fluid Dynamics and Turbulent Flows
- Molecular Sensors and Ion Detection
- Topic Modeling
- Natural Language Processing Techniques
- Mass Spectrometry Techniques and Applications
- Advanced Text Analysis Techniques
- Bioinformatics and Genomic Networks
- Academic Writing and Publishing
- Plant Water Relations and Carbon Dynamics
- scientometrics and bibliometrics research
- History and advancements in chemistry
- Analytical Chemistry and Chromatography
- Receptor Mechanisms and Signaling
- Molecular Junctions and Nanostructures
- Computational Drug Discovery Methods
- Legal Issues in South Africa
- Computational Fluid Dynamics and Aerodynamics
- linguistics and terminology studies
- Quantum chaos and dynamical systems
- Metabolomics and Mass Spectrometry Studies
- Aerodynamics and Acoustics in Jet Flows
Royal Society of Chemistry
2017-2020
University of Cambridge
2004-2011
Linguamatics (United Kingdom)
2010-2011
Unilever (United Kingdom)
2011
University of Groningen
2008
University of Strathclyde
2008
Unilever (India)
2006
Institut de Mécanique des Fluides de Toulouse
2001-2003
Airbus (Germany)
2003
École Polytechnique Fédérale de Lausanne
2000-2001
We have produced an open source, freely available, algorithm (Open Parser for Systematic IUPAC Nomenclature, OPSIN) that interprets the majority of organic chemical nomenclature in a fast and precise manner. This has been achieved using approach based on regular grammar. grammar is used to guide tokenization, potentially difficult problem names. From parsed name, XML parse tree constructed operated stepwise manner until structure reconstructed from name. Results OPSIN various computer...
Configurations of perturbation velocity which optimally excite an algebraic growth mechanism in the Falkner–Skan boundary layer are studied using a direct–adjoint technique. The largest transient amplification is obtained by stream-wise oriented vortices, agreement with previous results for Blasius layer. Adverse pressure gradient found to increase resulting growth, reverse true accelerated flows. It shown that excited mechanisms capable competition Tollmien–Schlichting waves super-critical...
A high-affinity, induced-fit receptor for NMe4I was discovered using dynamic combinatorial chemistry. The addition of the guest to a library made racemic mixture chiral building blocks caused strong and highly diastereoselective amplification at expense other components. its mode binding were characterized by NMR, ITC, re-equilibration experiments, from which it deduced that probably forms folded four-stave barrel shape on guest.
The CALBC initiative aims to provide a large-scale biomedical text corpus that contains semantic annotations for named entities of different kinds. generation this requires the from automatic annotation systems be harmonized. In first phase, five participants (EMBL-EBI, EMC Rotterdam, NLM, JULIE Lab Jena, and Linguamatics) were gathered. All delivered in common format included concept identifiers boundary assignments enabled comparison alignment results. During harmonization results produced...
Characterisation of gender differences throughout peer-review publication process as revealed by thorough analysis Royal Society Chemistry submissions, publications and citation data.
We present a versatile computer model of diverse dynamic combinatorial libraries, and examine how molecular recognition between library members template can be used to amplify the best binders. The correlation host-guest binding amplification was examined for set 50 libraries with >300 components each over wide range building block concentrations. Depending on these concentrations correlations vary from poor (when using large excess template) good (for very dilute and/or substoichiometric...
The Orr–Sommerfeld operator's eigenvalues determine the stability of exponentially growing disturbances in parallel and quasi-parallel flows. This work assesses sensitivity these to modifications base flow, which need not be infinitesimally small. Such flow variations may represent differences between laboratory its ideal, theoretical counterpart. worst case, i.e. change with most destabilizing effect on eigenvalues, is found using variational techniques for plane Couette flow. Relatively...
Dynamic combinatorial chemistry is a powerful tool for the discovery of strong binders (synthetic receptors or ligands) because binding causes shift in equilibrium library members toward those that bind well. Ideally, best are selectively amplified. However, theoretical studies predict this not always case. This paper describes first quantitative experimental evidence proving that, under special circumstances, preferential amplification suboptimal synthetic can indeed occur. Our results also...
Herein we describe an extensive study of the response a set closely related dynamic combinatorial libraries (DCLs) macrocyclic receptors to introduction focused range guest molecules. We have determined amplification two sets diastereomeric induced by series neutral and cationic guests, including biologically relevant compounds such as acetylcholine morphine. The host-guest binding affinities were investigated using isothermal titration calorimetry. resulting dataset enabled detailed...
A simple water-soluble naphthalenedithiol building block is converted quantitatively into a series of octameric [2]-catenanes, composed two interlocked molecular squares. When this mixture re-equilibrated in the presence an adamantyl ammonium guest, catenanes disassemble their macrocyclic components that bind guest with nanomolar affinity water.
Competitions in text mining have been used to measure the performance of automatic processing solutions against a manually annotated gold standard corpus (GSC). The preparation GSC is time-consuming and costly final consists at most few thousand documents with limited set semantic groups. To overcome these shortcomings, CALBC project partners (PPs) produced large-scale biomedical four different groups through harmonisation annotations from solutions, first version Silver Standard Corpus...
Chemical named entities represent an important facet of biomedical text. We have developed a system to use character-based n-grams, Maximum Entropy Markov Models and rescoring recognise chemical names other such entities, make confidence estimates for the extracted entities. An adjustable threshold allows be tuned high precision or recall. At set balanced recall, we were able extract at F score 80.7% from chemistry papers 83.2% PubMed abstracts. Furthermore, achieve 57.6% 60.3% recall 95%...
Chemical named entity recognition (NER) has traditionally been dominated by conditional random fields (CRF)-based approaches but given the success of artificial neural network techniques known as "deep learning" we decided to examine them an alternative CRFs. We present here several chemical systems. The first system translates traditional CRF-based idioms into a deep learning framework, using rich per-token features and word embeddings, producing sequence tags bidirectional long short term...
Optimal perturbations for the family of three-dimensional boundary layers described by Falkner–Skan–Cooke similarity solution are obtained using a variational technique in temporal framework. The disturbances experiencing most growth take form vortices almost aligned with external streamline at inception and evolve into streaks. In subcritical flows these can attain about twice transient amplification observed comparably forced two-dimensional flows. Possible connections between optimal...
We describe the annotation of chemical named entities in scientific text. A set guidelines defines 5 types entities, and provides instructions for resolution special cases. corpus fulltext chemistry papers was annotated, with an inter-annotator agreement F score 93%. An investigation entity recognition using LingPipe suggests that scores 63% are possible without customisation, 74% addition custom tokenisation use dictionaries.
Small talk: Molecular recognition events involving a small subset of members dynamic combinatorial library (DCL) can affect all other species in the mixture. For example, patterns emerge calculated 322-component DCL (see picture), depending on random distribution binding constants. These provide an intriguing means for transmitting information between molecules. Supporting this article is available WWW under http://www.wiley-vch.de/contents/jc_2002/2007/z702460_s.pdf or from author. Please...
Using simple computer simulations of model dynamic combinatorial libraries, we show that the best binders can be amplified to useful concentrations in libraries containing 10-10(6) compounds. [structure: see text]
Abstract ChemInform is a weekly Abstracting Service, delivering concise information at glance that was extracted from about 200 leading journals. To access Abstract, please click on HTML or PDF.
We describe the semantic enrichment of journal articles with chemical structures and biomedical ontology terms using Oscar, a program for named entity recognition (NER). how Oscar works it can been adapted general NER. discuss its implementation in real publishing workflow possible applications enriched articles.