Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles)

Policies supporting the rapid and open sharing of proteomic data are being implemented by the leading journals in the field. The proteomics community is taking steps to ensure that data are made publicly accessible and are of high quality, a challenging task that requires the development and deployment of methods for measuring and documenting data quality metrics. On September 18, 2010, the U.S. National Cancer Institute (NCI) convened the "International Workshop on Proteomic Data Quality Metrics" in Sydney, Australia, to identify and address issues facing the development and use of such methods for open access proteomics data. The stakeholders at the workshop enumerated the key principles underlying a framework for data quality assessment in mass spectrometry data that will meet the needs of the research community, journals, funding agencies, and data repositories. Attendees discussed and agreed up on two primary needs for the wide use of quality metrics: (i) an evolving list of comprehensive quality metrics and (ii) standards accompanied by software analytics. Attendees stressed the importance of increased education and training programs to promote reliable protocols in proteomics. This workshop report explores the historic precedents, key discussions, and necessary next steps to enhance the quality of open access data. By agreement, this article is published simultaneously in Proteomics, Proteomics Clinical Applications, Journal of Proteome Research, and Molecular and Cellular Proteomics, as a public service to the research community. The peer review process was a coordinated effort conducted by a panel of referees selected by the journals.     

64-Bit and 128-bit DX random number generators

Extending 32-bit DX generators introduced by Deng and Xu (ACM Trans Model Comput Simul 13:299–309, 2003), we perform an extensive computer search for classes of 64-bit and 128-bit DX generators of large orders. The period lengths of these high resolution DX generators are ranging from 10¹⁹¹⁵ to 10⁵⁸²²¹. The software implementation of these generators can be developed for 64-bit or 128-bit hardware. The great empirical performances of DX generators have been confirmed by an extensive battery of tests in the TestU01 package. These high resolution DX generators can be useful to perform large scale simulations in scientific investigations for various computer systems.     

Providing Architectural Languages and Tools Interoperability through Model Transformation Technologies

Many architectural languages have been proposed in the last 15 years, each one with the chief aim of becoming the ideal language for specifying software architectures. What is evident nowadays, instead, is that architectural languages are defined by stakeholder concerns. Capturing all such concerns within a single, narrowly focused notation is impossible. At the same time, it is also impractical to define and use a “universal” notation, such as UML. As a result, many domain-specific notations for architectural modeling have been proposed, each one focusing on a specific application domain, analysis type, or modeling environment. As a drawback, a proliferation of languages exists, each one with its own specific notation, tools, and domain specificity. No effective interoperability is possible to date. Therefore, if a software architect has to model a concern not supported by his own language/tool, he has to manually transform (and, eventually, keep aligned) the available architectural specification into the required language/tool. This paper presents DUALLy, an automated framework that allows architectural languages and tools interoperability. Given a number of architectural languages and tools, they can all interoperate thanks to automated model transformation techniques. DUALLy is implemented as an Eclipse plugin. Putting it in practice, we apply the DUALLy approach to the Darwin/FSP ADL and to a UML2.0 profile for software architectures. By making use of an industrial complex system, we transform a UML software architecture specification in Darwin/FSP, make some verifications by using LTSA, and reflect changes required by the verifications back to the UML specification.     

Fast indirect illumination using Layered Depth Images

We present a novel hybrid rendering method for diffuse and glossy indirect illumination. A scene is rendered using standard rasterization on a GPU. In a shader, secondary ray queries are used to sample incident light and to compute indirect lighting. We observe that it is more important to cast many rays than to have precise results for each ray. Thus, we approximate secondary rays by intersecting them with precomputed layered depth images of the scene. We achieve interactive to real-time frame rates including indirect diffuse and glossy effects.     

Microfluidic mixing via transverse electrokinetic effects in a planar microchannel

A new micromixer incorporating integrated electrodes deposited on the bottom surface of a glass/PDMS microchannel is used to induce a localized, perpendicular electric field within pressure driven axial flow. The presence of the electric field drives electro-osmotic flow in the transverse direction along the channel walls, creating helical motion that serves to mix the fluid. A numerical model is used to describe the three-dimensional flow field, where characterization is performed via particle tracking of passive tracer particles, and the conditional entropy (S _lc) is utilized to approximate the extent of mixing along cross-sectional planes. The geometrical parameters and operating conditions of the numerical model are used to fabricate an experimental device, and fluorescence microscopy measurements are used to verify mixing of rhodamine B across the width of the microchannel for a wide range of fluid flow rates. The results demonstrate that under certain operating conditions and selective placement of the electrode gaps along the width of the microchannel, efficient mixing can be achieved within 6 mm of the inlet.

Automated magnification calibration in transmission electron microscopy using Fourier analysis of replica images

The magnification factor in transmission electron microscopy is not very precise, hampering for instance quantitative analysis of specimens. Calibration of the magnification is usually performed interactively using replica specimens, containing line or grating patterns with known spacing. In the present study, a procedure is described for automated magnification calibration using digital images of a line replica. This procedure is based on analysis of the power spectrum of Fourier transformed replica images, and is compared to interactive measurement in the same images. Images were used with magnification ranging from 1,000 x to 200,000 x. The automated procedure deviated on average 0.10% from interactive measurements. Especially for catalase replicas, the coefficient of variation of automated measurement was considerably smaller (average 0.28%) compared to that of interactive measurement (average 3.5%). In conclusion, calibration of the magnification in digital images from transmission electron microscopy may be performed automatically, using the procedure presented here, with high precision and accuracy.     

Flow-Based Image Abstraction

We present a non-photorealistic rendering technique that automatically delivers a stylized abstraction of a photograph. Our approach is based on shape/color filtering guided by a vector field that describes the flow of salient features in the image. This flow-based filtering significantly improves the abstraction performance in terms of feature enhancement and stylization. Our method is simple, fast, and easy to implement. Experimental results demonstrate the effectiveness of our method in producing stylistic and feature-enhancing illustrations from photographs.     

A Link-Node Discrete-Time Dynamic Second Best Toll Pricing Model with a Relaxation Solution Algorithm

Dynamic congestion pricing has become an important research topic because of its practical implications. In this paper, we formulate dynamic second-best toll pricing (DSBTP) on general networks as a bilevel problem: the upper level is to minimize the total weighted system travel time and the lower level is to capture motorists’ route choice behavior. Different from most of existing DSBTP models, our formulation is in discrete-time, which has very distinct properties comparing with its continuous-time counterpart. Solution existence condition of the proposed model is established independent of the actual formulation of the underlying dynamic user equilibrium (DUE). To solve the bilevel DSBTP model, we adopt a relaxation scheme. For this purpose, we convert the bilevel formulation into a single level nonlinear programming problem by applying a link-node based nonlinear complementarity formulation for DUE. The single level problem is solved iteratively by first relaxing the strick complementarity by a relaxation parameter, which is then progressively reduced. Numerical results are also provided in this paper to illustrate the proposed model and algorithm. In particular, we show that by varying travel time weights on different links, DSBTP can help traffic management agencies better achieve certain system objectives. Examples are given on how changes of the weights impact the optimal tolls and associated objective function values.

MatrixExplorer: a dual-representation system to explore social networks

MatrixExplorer is a network visualization system that uses two representations: node-link diagrams and matrices. Its design comes from a list of requirements formalized after several interviews and a participatory design session conducted with social science researchers. Although matrices are commonly used in social networks analysis, very few systems support the matrix-based representations to visualize and analyze networks. MatrixExplorer provides several novel features to support the exploration of social networks with a matrix-based representation, in addition to the standard interactive filtering and clustering functions. It provides tools to reorder (layout) matrices, to annotate and compare findings across different layouts and find consensus among several clusterings. MatrixExplorer also supports node-link diagram views which are familiar to most users and remain a convenient way to publish or communicate exploration results. Matrix and node-link representations are kept synchronized at all stages of the exploration process     

Simultaneous registration and fusion of multiple dissimilar sensors for cooperative driving

The fusion of multiple sensory information plays a key role in cooperative driving for flexible platooning of automated vehicles over a couple of lanes within a short intervehicle distance. In this paper, the problem of online sensor fusion with spatially and temporally misaligned dissimilar sensors is considered. A spatial-temporal registration model for the popular intelligent vehicular sensors including radar, global positioning system, inertial navigation system, and camera is first developed for sensor alignment. An unscented Kalman filter (UKF) is proposed here to fuse and register these sensors that are installed on a platoon of vehicles simultaneously. When the road geometry information is available from a digital map database, a constrained UKF is further developed to improve the fusion accuracy. The effect of spatial-temporal sensor misalignment upon the vehicle-state estimation is also analyzed theoretically. Simulations show that the proposed UKF method not only can align the dissimilar vehicular sensors properly with both spatial and temporal biases, but can also obtain accurate fused tracks of vehicles in a platoon.