329,771 research outputs found

    Automated protein structure calculation from NMR data

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    Current software is almost at the stage to permit completely automatic structure determination of small proteins of < 15 kDa, from NMR spectra to structure validation with minimal user interaction. This goal is welcome, as it makes structure calculation more objective and therefore more easily validated, without any loss in the quality of the structures generated. Moreover, it releases expert spectroscopists to carry out research that cannot be automated. It should not take much further effort to extend automation to ca 20 kDa. However, there are technological barriers to further automation, of which the biggest are identified as: routines for peak picking; adoption and sharing of a common framework for structure calculation, including the assembly of an automated and trusted package for structure validation; and sample preparation, particularly for larger proteins. These barriers should be the main target for development of methodology for protein structure determination, particularly by structural genomics consortia

    Modelling the influence of the process inputs on the removal of surface contaminants from Ti-6Al-4V linear friction welds

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    The linear friction welding (LFW) process is finding increasing interest from industry for the fabrication of near-net-shape, titanium alloy Ti–6Al–4V, aerospace components. Currently, the removal of surface contaminants, such as oxides and foreign particles, from the weld interface into the flash is not fully understood. To address this problem, two-dimensional (2D) computational models were developed using the finite element analysis (FEA) software DEFORM and validated with experiments. The key findings showed that the welds made with higher applied forces required less burn-off to completely remove the surface contaminants from the interface into the flash; the interface temperature increased as the applied force was decreased or the rubbing velocity increased; and the boundary temperature between the rapid flash formation and negligible material flow was approximately 970 °C. An understanding of these phenomena is of particular interest for the industrialisation of near-net-shape titanium alloy aerospace components.EPSRC, Boeing Company, Welding Institut

    A Novel Gaussian Extrapolation Approach for 2D Gel Electrophoresis Saturated Protein Spots

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    Analysis of images obtained from two-dimensional gel electrophoresis (2D-GE) is a topic of utmost importance in bioinformatics research, since commercial and academic software available currently has proven to be neither completely effective nor fully automatic, often requiring manual revision and refinement of computer generated matches. In this work, we present an effective technique for the detection and the reconstruction of over-saturated protein spots. Firstly, the algorithm reveals overexposed areas, where spots may be truncated, and plateau regions caused by smeared and overlapping spots. Next, it reconstructs the correct distribution of pixel values in these overexposed areas and plateau regions, using a two-dimensional least-squares fitting based on a generalized Gaussian distribution. Pixel correction in saturated and smeared spots allows more accurate quantification, providing more reliable image analysis results. The method is validated for processing highly exposed 2D-GE images, comparing reconstructed spots with the corresponding non-saturated image, demonstrating that the algorithm enables correct spot quantificatio

    A Novel Generic Framework for Track Fitting in Complex Detector Systems

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    This paper presents a novel framework for track fitting which is usable in a wide range of experiments, independent of the specific event topology, detector setup, or magnetic field arrangement. This goal is achieved through a completely modular design. Fitting algorithms are implemented as interchangeable modules. At present, the framework contains a validated Kalman filter. Track parameterizations and the routines required to extrapolate the track parameters and their covariance matrices through the experiment are also implemented as interchangeable modules. Different track parameterizations and extrapolation routines can be used simultaneously for fitting of the same physical track. Representations of detector hits are the third modular ingredient to the framework. The hit dimensionality and orientation of planar tracking detectors are not restricted. Tracking information from detectors which do not measure the passage of particles in a fixed physical detector plane, e.g. drift chambers or TPCs, is used without any simplifications. The concept is implemented in a light-weight C++ library called GENFIT, which is available as free software

    Miniature exoplanet radial velocity array I: design, commissioning, and early photometric results

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    The MINiature Exoplanet Radial Velocity Array (MINERVA) is a US-based observational facility dedicated to the discovery and characterization of exoplanets around a nearby sample of bright stars. MINERVA employs a robotic array of four 0.7 m telescopes outfitted for both high-resolution spec- troscopy and photometry, and is designed for completely autonomous operation. The primary science program is a dedicated radial velocity survey and the secondary science objective is to obtain high precision transit light curves. The modular design of the facility and the flexibility of our hardware allows for both science programs to be pursued simultaneously, while the robotic control software provides a robust and efficient means to carry out nightly observations. In this article, we describe the design of MINERVA including major hardware components, software, and science goals. The telescopes and photometry cameras are characterized at our test facility on the Caltech campus in Pasadena, CA, and their on-sky performance is validated. New observations from our test facility demonstrate sub-mmag photometric precision of one of our radial velocity survey targets, and we present new transit observations and fits of WASP-52b—a known hot-Jupiter with an inflated radius and misaligned orbit. The process of relocating the MINERVA hardware to its final destination at the Fred Lawrence Whipple Observatory in southern Arizona has begun, and science operations are expected to commence within 2015

    A Survey of Agent-Based Modeling Practices (January 1998 to July 2008)

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    In the 1990s, Agent-Based Modeling (ABM) began gaining popularity and represents a departure from the more classical simulation approaches. This departure, its recent development and its increasing application by non-traditional simulation disciplines indicates the need to continuously assess the current state of ABM and identify opportunities for improvement. To begin to satisfy this need, we surveyed and collected data from 279 articles from 92 unique publication outlets in which the authors had constructed and analyzed an agent-based model. From this large data set we establish the current practice of ABM in terms of year of publication, field of study, simulation software used, purpose of the simulation, acceptable validation criteria, validation techniques and complete description of the simulation. Based on the current practice we discuss six improvements needed to advance ABM as an analysis tool. These improvements include the development of ABM specific tools that are independent of software, the development of ABM as an independent discipline with a common language that extends across domains, the establishment of expectations for ABM that match their intended purposes, the requirement of complete descriptions of the simulation so others can independently replicate the results, the requirement that all models be completely validated and the development and application of statistical and non-statistical validation techniques specifically for ABM.Agent-Based Modeling, Survey, Current Practices, Simulation Validation, Simulation Purpose

    Prevalence of smoking among the students resided at dormitories in Golestan university of medical sciences, Iran

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    Introduction: Cigarette smoking leads to harmful physical and emotional problems and also is a predisposed factor for the addiction. The aim of this study was an attempt to determine the rate of prevalence and causes of smoking among the students of Golestan University of Medical Sciences who resided in the dormitories. Material & Methods: A cross-sectional analytical study conducted among the resident students of dormitories in 2010. The sample size consisted of all the university dormitory students. The data gathered using a validated and reliable questionnaire. The data analyzed using SPSS software and statistical tests including Chi-square, Logistic regression and Independent t-test. Results: Of 669 students, 538 (80%) of them filled out the questionnaires completely. 67.3% (362 subjects) were female. 6.1% (33 students) were smoker and 83.5% of them had experiences of cigarette smoking. The most important reasons for the smoking tendency were “having a smoker friend in 33%, a personal interest 27% and as hobby in 24% of the cases”. There were significant relation between “age, sex, region and year of education” with smoking (P0.05). Conclusion: The results indicated low prevalence of cigarette smoking among the students. However, preventive measures should be taken to conduit youth toward healthier behaviors. It seems parental control and monitoring children’s friend finding are crucial issue. © 2014, Bangladesh Journal of Medical Science. All rights reserved

    SpreadCluster: Recovering Versioned Spreadsheets through Similarity-Based Clustering

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    Version information plays an important role in spreadsheet understanding, maintaining and quality improving. However, end users rarely use version control tools to document spreadsheet version information. Thus, the spreadsheet version information is missing, and different versions of a spreadsheet coexist as individual and similar spreadsheets. Existing approaches try to recover spreadsheet version information through clustering these similar spreadsheets based on spreadsheet filenames or related email conversation. However, the applicability and accuracy of existing clustering approaches are limited due to the necessary information (e.g., filenames and email conversation) is usually missing. We inspected the versioned spreadsheets in VEnron, which is extracted from the Enron Corporation. In VEnron, the different versions of a spreadsheet are clustered into an evolution group. We observed that the versioned spreadsheets in each evolution group exhibit certain common features (e.g., similar table headers and worksheet names). Based on this observation, we proposed an automatic clustering algorithm, SpreadCluster. SpreadCluster learns the criteria of features from the versioned spreadsheets in VEnron, and then automatically clusters spreadsheets with the similar features into the same evolution group. We applied SpreadCluster on all spreadsheets in the Enron corpus. The evaluation result shows that SpreadCluster could cluster spreadsheets with higher precision and recall rate than the filename-based approach used by VEnron. Based on the clustering result by SpreadCluster, we further created a new versioned spreadsheet corpus VEnron2, which is much bigger than VEnron. We also applied SpreadCluster on the other two spreadsheet corpora FUSE and EUSES. The results show that SpreadCluster can cluster the versioned spreadsheets in these two corpora with high precision.Comment: 12 pages, MSR 201

    SFDL: MVC Applied to Workflow Design

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    Process management based on workflow systems is a growing trend in collaborative environments. One of the most notorious areas of improvement is that of user interfaces, especially since business process definition languages do not address efficiently the point of contact between workflow engines and human interactions. With that in focus, we propose the MVC pattern design to workflow systems. To accomplish this, we have designed a new dynamic view definition language called SFDL, oriented towards the easy interoperability with the different workflow definition languages, while maintaining enough flexibility to be represented in different formats and being adaptable to several environments. To validate our approach, we have carried out an implementation in a real banking scenario, which has provided continuous feedback and enabled us to refine the proposal. The work is fully based on widely accepted and used web standards (XML, YAML, JSON, Atom and REST). Some guidelines are given to facilitate the adoption of our solution
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