FACTA: a text search engine for finding associated biomedical concepts

FACTA is a text search engine for MEDLINE abstracts, which is designed particularly to help users browse biomedical concepts (e.g. genes/proteins, diseases, enzymes and chemical compounds) appearing in the documents retrieved by the query. The concepts are presented to the user in a tabular format and ranked based on the co-occurrence statistics. Unlike existing systems that provide similar functionality, FACTA pre-indexes not only the words but also the concepts mentioned in the documents, which enables the user to issue a flexible query (e.g. free keywords or Boolean combinations of keywords/concepts) and receive the results immediately even when the number of the documents that match the query is very large. The user can also view snippets from MEDLINE to get textual evidence of associations between the query terms and the concepts. The concept IDs and their names/synonyms for building the indexes were collected from several biomedical databases and thesauri, such as UniProt, BioThesaurus, UMLS, KEGG and DrugBank. AVAILABILITY: The system is available at http://www.nactem.ac.uk/software/facta/     

Query Chem: a Google-powered web search combining text and chemical structures

Query Chem (www.QueryChem.com) is a Web program that integrates chemical structure and text-based searching using publicly available chemical databases and Google's Web Application Program Interface (API). Query Chem makes it possible to search the Web for information about chemical structures without knowing their common names or identifiers. Furthermore, a structure can be combined with textual query terms to further restrict searches. Query Chem's search results can retrieve many interesting structure-property relationships of biomolecules on the Web.     

Building a protein name dictionary from full text: a machine learning term extraction approach

Background  

The majority of information in the biological literature resides in full text articles, instead of abstracts. Yet, abstracts remain the focus of many publicly available literature data mining tools. Most literature mining tools rely on pre-existing lexicons of biological names, often extracted from curated gene or protein databases. This is a limitation, because such databases have low coverage of the many name variants which are used to refer to biological entities in the literature.     

Environmental issues in the planned release of genetically-engineered organisms

This paper examines issues concerned with the environmental release of genetically-engineered micro-organisms. Besides the obvious social and economic benefits from the technology, genetically-engineered micro-organisms can have considerable beneficial effects on environmental concerns, such as the degradation of pollutants and toxic chemical wastes, and less use of hazardous pesticides and chemicals. There may be uncertain negative effects arising from the technology. The hazards of the technology and possible policy approaches are discussed. It is concluded that, overall, the applications arising from this technology are likely to be benign, because its effects on the environment can largely be anticipated by an increase in scientific knowledge gained from field trials and greater experience with releases.     

Key issues in the deliberate release of genetically-manipulated bacteria

Abstract The deliberate release of a genetically engineered bacterium often requires that a complex pathway be travelled through scientific and regulatory questions. It is important to consider the scientific aim of the release and the nature of the modification (deletion or insertion, site of insertion, level of expression) and its likely effect on survival of the organism and the possibility of gene transfer. In Australia, the Genetic Manipulation Advisory Committee assesses applications and makes recommendations about pre-release testing and procedures for conducting field release. Two examples of field release of genetically manipulated bacteria in Australia are considered. Firstly, the commercial product Agrobacterium strain K1026 (‘NoGall’^TM), a genetically engineered biological control agent for crown gall disease of stone fruits and roses. Secondly, a lacZY -marked derivative of a strain of Pseudomonas corrugata , that can act as a biological control agent against take-all disease of wheat. Prior to release, bacterial survival and competition was tested in soil microcosms. The distribution and survival of the organism were monitored after field release. Since 1992 the marked bacteria have been recovered only after enrichment. Assessment of risk should consider the survival and spread of the genetically manipulated bacterium and its foreign DNA and the impact of the inoculated bacteria on other (‘non-target’) organisms.     

Investigating a back door mechanism of actin phosphate release by steered molecular dynamics

In actin-based cell motility, phosphate (Pi) release after ATP hydrolysis is an essential biochemical process, but the actual pathway of Pi separation from actin is not well understood. We report a series of molecular dynamics simulations that induce the dissociation of Pi from actin. After cleavage from ATP, the singly protonated phosphate (HPO4(2-)) rotates about the ADP-associated Ca2+ ion, turning away from the negatively charged ADP towards the putative exit near His73. To reveal the microscopic processes underlying the release of Pi, adhesion forces were measured when pulling the substrate out of its binding pocket. The results suggest that the separation from the divalent cation is the rate-limiting step in Pi release. Protonation of HPO4(2-) to H2PO4- lowers the electrostatic barrier during Pi liberation from the ion. The simulations revealed a propensity of charged His73+ to form a salt bridge with HPO4(2-), but not with H2PO4-. His73 stabilizes HPO4(2-) and, thereby, inhibits rapid Pi release from actin. Arg177 remains attached to Pi along the putative back door pathway, suggesting a shuttle function that facilitates the transport of Pi to a binding site on the protein surface.     

The structural and content aspects of abstracts versus bodies of full text journal articles are different

Background  

An increase in work on the full text of journal articles and the growth of PubMedCentral have the opportunity to create a major paradigm shift in how biomedical text mining is done. However, until now there has been no comprehensive characterization of how the bodies of full text journal articles differ from the abstracts that until now have been the subject of most biomedical text mining research.     

On the search for the electrical synapse: a glimpse at the future

The traditional concept of electrotonic synapses suggests that they synchronize outputs from coupled neurons and provide rapid impulse propagation between pre- and postsynaptic elements. These properties have provided an evolutionary advantage in certain behavioral repertoires, for example, in the rapid impulse propagation between axonal segments in the crayfish and in electrotonic synapses on motoneurons. Recent theoretical and experimental evidence, in particular with regard to neuronal synchronization, ultrastructure and molecular biology, shows that this concept has new relevance. In particular, computer simulations demonstrated that neurons synchronize and alter their firing patterns depending on gap-junctional communication. The cloning of neuronal gap-junction proteins and the ablation of the neuronal connexin36 (Cx36) provided novel insights into the extent and functional significance of electrotonic coupling between paired interneurons. Furthermore, electrophysiological recording of gap-junctional communication supports its importance in network behavior. Hence, in addition to chemical transmission, direct coupling by electrotonic synapses is now accepted to provide a second major pathway contributing to normal and abnormal physiological rhythms.     

On the manifestations of memory in visual search

Evidence is presented supporting the thesis that performance in visual search tasks is affected by the contribution of memory processes. Three levels of analysis, corresponding to the various time scales present in a typical search experiment, are discussed. Perceptual learning involves the task and stimulus specific improvement seen across blocks of training. Trial-to-trial priming has an influence which extends over 5-8 trials and lasts on the order of 30 s. Within-trial tagging prevents the re-inspection of already attended (or fixated) items. Also at the within-trial level of analysis, parallel accumulation of evidence for target presence/absence or target location inherently involves memory mechanisms. Organizing the various phenomena in this way makes it apparent that the various mechanisms may interact in a causal way. Within-trial tagging may contribute to priming which may contribute to perceptual learning. Recent proposals that visual search is memoryless (amnesic) are discussed and dismissed.     

Marine protected area strategies: issues,divergences and the search for middle ground

Reviews in Fish Biology and Fisheries - There has been a dramatic increase in recentyears in the number of papers, reports, etc.,which have been published concerning MarineProtected Areas (MPAs)....     

On the meanings of nestedness: back to the basics

The ecological concepts of nestedness and β‐diversity first appeared more than five decades ago, but there is still controversy over their precise meaning and application. Here, we focus on the concept of nestedness, the ordered loss of species along environmental or ecological gradients. Because there is no species replacement if the distribution of species among a number of sites is perfectly nested, some studies have defined nestedness as the inverse of species turnover. We argue that such a redefinition relies on a misinterpretation of the original concept of nestedness as the inverse of species replacement. Such a narrow interpretation might result in misleading conclusions about the mechanisms regulating species distribution patterns. We argue, in particular, that any quantification of nestedness must be as explicit as possible about the gradient to be analyzed.