ConSole: using modularity of contact maps to locate solenoid domains in protein structures.

BackgroundPeriodic proteins, characterized by the presence of multiple repeats of short motifs, form an interesting and seldom-studied group. Due to often extreme divergence in sequence, detection and analysis of such motifs is performed more reliably on the structural level. Yet, few algorithms have been developed for the detection and analysis of structures of periodic proteins.ResultsConSole recognizes modularity in protein contact maps, allowing for precise identification of repeats in solenoid protein structures, an important subgroup of periodic proteins. Tests on benchmarks show that ConSole has higher recognition accuracy as compared to Raphael, the only other publicly available solenoid structure detection tool. As a next step of ConSole analysis, we show how detection of solenoid repeats in structures can be used to improve sequence recognition of these motifs and to detect subtle irregularities of repeat lengths in three solenoid protein families.ConclusionsThe ConSole algorithm provides a fast and accurate tool to recognize solenoid protein structures as a whole and to identify individual solenoid repeat units from a structure. ConSole is available as a web-based, interactive server and is available for download at http://console.sanfordburnham.org

Cutting tool tracking and recognition based on infrared and visual imaging systems using principal component analysis (PCA) and discrete wavelet transform (DWT) combined with neural networks

The implementation of computerised condition monitoring systems for the detection cutting tools’ correct installation and fault diagnosis is of a high importance in modern manufacturing industries. The primary function of a condition monitoring system is to check the existence of the tool before starting any machining process and ensure its health during operation. The aim of this study is to assess the detection of the existence of the tool in the spindle and its health (i.e. normal or broken) using infrared and vision systems as a non-contact methodology. The application of Principal Component Analysis (PCA) and Discrete Wavelet Transform (DWT) combined with neural networks are investigated using both types of data in order to establish an effective and reliable novel software program for tool tracking and health recognition. Infrared and visual cameras are used to locate and track the cutting tool during the machining process using a suitable analysis and image processing algorithms. The capabilities of PCA and Discrete Wavelet Transform (DWT) combined with neural networks are investigated in recognising the tool’s condition by comparing the characteristics of the tool to those of known conditions in the training set. The experimental results have shown high performance when using the infrared data in comparison to visual images for the selected image and signal processing algorithms

Overlapping Community Detection in Networks: the State of the Art and Comparative Study

This paper reviews the state of the art in overlapping community detection algorithms, quality measures, and benchmarks. A thorough comparison of different algorithms (a total of fourteen) is provided. In addition to community level evaluation, we propose a framework for evaluating algorithms' ability to detect overlapping nodes, which helps to assess over-detection and under-detection. After considering community level detection performance measured by Normalized Mutual Information, the Omega index, and node level detection performance measured by F-score, we reached the following conclusions. For low overlapping density networks, SLPA, OSLOM, Game and COPRA offer better performance than the other tested algorithms. For networks with high overlapping density and high overlapping diversity, both SLPA and Game provide relatively stable performance. However, test results also suggest that the detection in such networks is still not yet fully resolved. A common feature observed by various algorithms in real-world networks is the relatively small fraction of overlapping nodes (typically less than 30%), each of which belongs to only 2 or 3 communities.Comment: This paper (final version) is accepted in 2012. ACM Computing Surveys, vol. 45, no. 4, 2013 (In press) Contact: [email protected]

Spatial Algorithms for Geometric Contact Detection in Multibody System Dynamics

This article belongs to the Topic Dynamical Systems: Theory and Applications.In the present work, different algorithms for contact detection in multibody systems based on smooth contact modelling approaches are presented. Beginning with the simplest ones, some difficult interactions are subsequently introduced. In addition, a brief overview on the different kinds of contact/impact modelling is provided and an underlining of the advantages and the drawbacks of each of them is determined. Finally, some practical examples of each interaction are presented and analyzed and an outline of the issues arisen during the design process and how they have been solved in order to obtain stable and accurate results is given. The main goal of this paper is to provide a resource for the early-stage researchers in the field that serves as an introduction to the modelling of simple contact/impact events in the context of multibody system dynamics.The authors would like to acknowledge the Spanish Government through the MCYT Project "RETOS2015: sistema de monitorización integral de conjuntos mecánicos críticos para la mejora del mantenimiento en el transporte-maqstatus". The authors would also like to acknowledge the financial support received by the Community of Madrid through its multi-year agreement with University Carlos III focused on its policy "Excelencia para el Profesorado Universitario"