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Expanding the question-answering potential of single-cell microbeams at RARAF, USA.

ABSTRACT: Charged-particle microbeams, developed to provide targeted irradiation of individual cells, and then of sub-cellular components, and then of 3-D tissues and now organisms, have been instrumental in challenging and changing long accepted paradigms of radiation action. However the potential of these valuable tools can be enhanced by integrating additional components with the direct ability to measure biological responses in real time, or to manipulate the cell, tissue or organism of interest under conditions where information gained can be optimized. The RARAF microbeam has recently undergone an accelerator upgrade, and been modified to allow for multiple microbeam irradiation laboratories. Researchers with divergent interests have expressed desires for particular modalities to be made available and ongoing developments reflect these desires. The focus of this review is on the design, incorporation and use of multiphoton and other imaging, micro-manipulation and single cell biosensor capabilities at RARAF. Additionally, an update on the status of the other biology oriented microbeams in the Americas is provided.

SUBMITTER: Bigelow A

PROVIDER: S-EPMC2924733 | biostudies-literature | 2009 Mar

REPOSITORIES: biostudies-literature

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Expanding the question-answering potential of single-cell microbeams at RARAF, USA.

Bigelow Alan A Garty Guy G Funayama Tomoo T Randers-Pehrson Gerhard G Brenner David D Geard Charles C

Journal of radiation research 20090301

Charged-particle microbeams, developed to provide targeted irradiation of individual cells, and then of sub-cellular components, and then of 3-D tissues and now organisms, have been instrumental in challenging and changing long accepted paradigms of radiation action. However the potential of these valuable tools can be enhanced by integrating additional components with the direct ability to measure biological responses in real time, or to manipulate the cell, tissue or organism of interest under ...[more]

PMID: 19346682

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Project description:The proliferation of the scientific literature in the field of biomedicine makes it difficult to keep abreast of current knowledge, even for domain experts. While general Web search engines and specialized information retrieval (IR) systems have made important strides in recent decades, the problem of accurate knowledge extraction from the biomedical literature is far from solved. Classical IR systems usually return a list of documents that have to be read by the user to extract relevant information. This tedious and time-consuming work can be lessened with automatic Question Answering (QA) systems, which aim to provide users with direct and precise answers to their questions. In this work we propose a novel methodology for QA based on semantic relations extracted from the biomedical literature.We extracted semantic relations with the SemRep natural language processing system from 122,421,765 sentences, which came from 21,014,382 MEDLINE citations (i.e., the complete MEDLINE distribution up to the end of 2012). A total of 58,879,300 semantic relation instances were extracted and organized in a relational database. The QA process is implemented as a search in this database, which is accessed through a Web-based application, called SemBT (available at http://sembt.mf.uni-lj.si ). We conducted an extensive evaluation of the proposed methodology in order to estimate the accuracy of extracting a particular semantic relation from a particular sentence. Evaluation was performed by 80 domain experts. In total 7,510 semantic relation instances belonging to 2,675 distinct relations were evaluated 12,083 times. The instances were evaluated as correct 8,228 times (68%).In this work we propose an innovative methodology for biomedical QA. The system is implemented as a Web-based application that is able to provide precise answers to a wide range of questions. A typical question is answered within a few seconds. The tool has some extensions that make it especially useful for interpretation of DNA microarray results.

Dataset Information

Expanding the question-answering potential of single-cell microbeams at RARAF, USA.

Publications

Expanding the question-answering potential of single-cell microbeams at RARAF, USA.

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