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Automated Approach (automate + approach)
Selected AbstractsAutolabo: an automated system for ligand-soaking experiments with protein crystalsJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 4 2010Michihiro Sugahara Ligand soaking of protein crystals is important for the preparation of heavy-atom derivative crystals for experimental phasing as well as for large-scale ligand screening in pharmaceutical developments. To facilitate laborious large-scale ligand screening, to reduce the risk of human contact with hazardous ligand reagents and to increase the success rate of the soaking experiments, a protein crystallization robot `Autolabo' has been developed and implemented in the high-throughput crystallization-to-structure pipeline at RIKEN SPring-8 Center. The main functions of this robotic system are the production of protein crystals for experiments, the ligand soaking of these crystals and the observation of soaked crystals. The separate eight-channel dispensers of Autolabo eliminate the cross-contamination of reagents which should be strictly avoided in the ligand-soaking experiment. Furthermore, the automated approach reduces physical damage to crystals during experiments when compared with the conventional manual approach, and thereby has the potential to yield better quality diffraction data. Autolabo's performance as a ligand-soaking system was evaluated with a crystallization experiment on ten proteins from different sources and a heavy-atom derivatization experiment on three proteins using a versatile cryoprotectant containing heavy-atom reagents as ligands. The crystallization test confirmed reliable crystal reproduction in a single condition and the capability for crystallization with nucleants to improve crystal quality. Finally, Autolabo reproducibly derivatized the test protein crystals with sufficient diffraction quality for experimental phasing and model building, indicating a high potentiality of this automated approach in ligand-soaking experiments. [source] Discrimination of cyanobacterial strains isolated from saline soils in Nakhon Ratchasima, Thailand using attenuated total reflectance FTIR spectroscopyJOURNAL OF BIOPHOTONICS, Issue 8-9 2010Somchanh Bounphanmy Abstract A method was developed whereby high quality FTIR spectra could be rapidly acquired from soil-borne filamentous cyanobacteria using ATR FTIR spectroscopy. Spectra of all strains displayed bands typical of those previously reported for microalgae and water-borne cyanobacteria, with each strain having a unique spectral profile. Most variation between strains occurred in the C,O stretching and the amide regions. Soft Independent Modelling by Class Analogy (SIMCA) was used to classify the strains with an accuracy of better than 93%, with best classification results using the spectral region from 1800,950 cm,1. Despite this spectral region undergoing substantial changes, particularly in amide and C,O stretching bands, as cultures progressed through the early-, mid- to late-exponential growth phases, classification accuracy was still good (,80%) with data from all growth phases combined. These results indicate that ATR/FTIR spectroscopy combined with chemometric classification methods constitute a rapid, reproducible, and potentially automated approach to classifying soil-borne filamentous cyanobacteria. (© 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] An automated approach for abstracting execution logs to execution eventsJOURNAL OF SOFTWARE MAINTENANCE AND EVOLUTION: RESEARCH AND PRACTICE, Issue 4 2008Zhen Ming Jiang Abstract Execution logs are generated by output statements that developers insert into the source code. Execution logs are widely available and are helpful in monitoring, remote issue resolution, and system understanding of complex enterprise applications. There are many proposals for standardized log formats such as the W3C and SNMP formats. However, most applications use ad hoc non-standardized logging formats. Automated analysis of such logs is complex due to the loosely defined structure and a large non-fixed vocabulary of words. The large volume of logs, produced by enterprise applications, limits the usefulness of manual analysis techniques. Automated techniques are needed to uncover the structure of execution logs. Using the uncovered structure, sophisticated analysis of logs can be performed. In this paper, we propose a log abstraction technique that recognizes the internal structure of each log line. Using the recovered structure, log lines can be easily summarized and categorized to help comprehend and investigate the complex behavior of large software applications. Our proposed approach handles free-form log lines with minimal requirements on the format of a log line. Through a case study using log files from four enterprise applications, we demonstrate that our approach abstracts log files of different complexities with high precision and recall. Copyright © 2008 John Wiley & Sons, Ltd. [source] Automated Layer-by-Layer Deposition of Polyelectrolytes in Flow ModeMACROMOLECULAR MATERIALS & ENGINEERING, Issue 6-7 2009Svetlozar Ivanov Abstract Multilayer structures of conducting polymers were fabricated by a simply automated approach in flow mode. Polyaniline and poly(styrene sulfonate) were used as a model system, allowing a fast electrochemical and spectroscopic determination of the amount of deposited material. The technology was applied for layer-by-layer deposition of up to 100 bilayers. The results demonstrate a well reproducible and almost constant amount of the adsorbed polymer at each deposition cycle. The method can be applied for deposition of other conducting or non-conducting polymers, biological macromolecules and composites of polyelectrolytes and nanoparticles. [source] When a graph is poorer than 100 words: A comparison of computerised natural language generation, human generated descriptions and graphical displays in neonatal intensive careAPPLIED COGNITIVE PSYCHOLOGY, Issue 1 2010Marian van der Meulen Volunteer staff from a Neonatal Intensive Care Unit (NICU) were presented with sets of anonymised physiological data recorded over approximately 45,minute periods from former patients. Staff were asked to select medical/nursing actions appropriate for each of the patients whose data were displayed. Data were shown in one of three conditions (a) as multiple line graphs similar to those commonly shown on the ward, or as textual descriptions generated by (b) expert medical/nursing staff or (c) computerised natural language generation (NLG). An overall advantage was found for the human generated text, but NLG resulted in decisions that were at least as good as those for the graphical displays with which staff were familiar. It is suggested that NLG might offer a viable automated approach to removing noise and artefacts in real, complex and dynamic data sets, thereby reducing visual complexity and mental workload, and enhancing decision-making particularly for inexperienced staff. Copyright © 2008 John Wiley & Sons, Ltd. [source] 3133: Planar patch-clamping in human corneal endothelial cells: a new tool for clinical application?ACTA OPHTHALMOLOGICA, Issue 2010S MERGLER Purpose Identification of apoptotic or damaged human corneal endothelial cells (HCECs) is limited to morphological evaluation such as phase contrast microscopy and vital staining. The molecular mechanisms of corneal endothelial cell loss are not fully understood. Special investigations in cellular signalling and ion channel research are necessary to elucidate the mechanisms of corneal cell loss. In this context, it is known that this cell loss is often caused by apoptosis in oxidative stress. Methods Automated planar patch-clamp has become common in drug development and safety programs because it enables efficient and systematic testing of compounds against ion channels during voltage-clamp. A particularly successful automated approach is based on planar patch-clamp chips and this is the basis for the technology used here. Routine intracellular or extracellular perfusion opens possibilities for studying the regulation and pharmacology of ion channels. Previously, these studies were available only to highly skilled and dedicated experimenters. Results Notable, definite ion channel activities could be demonstrated by conventional as well as by planar patch-clamp in HCECs for the first time. In particular, temperature-sensing transient receptor potential (TRP)-like non-selective cation channel currents as well as capsaicin-sensitive ion channel currents could be detected. The expression of TRPV1-3 ion channels in HCEC could also be confirmed by RT-PCR, Western blot analysis and fluorescence cell imaging. Conclusion The administration of this novel measuring technology opens new perspectives in the investigation of the physiology of HCEC. The findings may have direct clinical implication (eye banking procedures, keratoplasty). [source] Approaches for semantic interoperability between domain ontologiesEXPERT SYSTEMS, Issue 3 2008Bhavna Orgun Abstract: Domain ontologies and knowledge-based systems have become very important in the agent and semantic web communities. As their use has increased, providing means of resolving semantic differences has also become very important. In this paper we survey the approaches that have been proposed for providing interoperability among domain ontologies. We also discuss some key issues that still need to be addressed if we are to move from semi-automated to fully automated approaches to providing consensus among heterogeneous ontologies. [source] Quantitive evaluation of macromolecular crystallization experiments using 1,8-ANS fluorescenceACTA CRYSTALLOGRAPHICA SECTION D, Issue 8 2010David Watts Modern X-ray structure analysis and advances in high-throughput robotics have allowed a significant increase in the number of conditions screened for a given sample volume. An efficient evaluation of the increased amount of crystallization trials in order to identify successful experiments is now urgently required. A novel approach is presented for the visualization of crystallization experiments using fluorescence from trace amounts of a nonspecific dye. The fluorescence images obtained strongly contrast protein crystals against other phenomena, such as precipitation and phase separation. Novel software has been developed to quantitatively evaluate the crystallization outcome based on a biophysical metric correlated with voxel protein concentration. In >1500 trials, 85.6% of the successful crystallization experiments were correctly identified, yielding a 50% reduction in the number of `missed hits' compared with current automated approaches. The use of the method in the crystallization of three previously uncharacterized proteins from the malarial parasite Plasmodium falciparum is further demonstrated. [source] | |||||||||||||