Motivation: Gene set enrichment (GSE) analysis allows researchers to efficiently extract biological insight from long lists of differentially expressed genes by interrogating them at a systems level. In recent years, there has been a proliferation of GSE analysis methods and hence it has become increasingly difficult for researchers to select an optimal GSE tool based on their particular dataset. Moreover, the majority of GSE analysis methods do not allow researchers to simultaneously compare gene set level results between multiple experimental conditions. Results: The ensemble of genes set enrichment analyses (EGSEA) is a method developed for RNA-sequencing data that combines results from twelve algorithms and calculates collective gene set scores to improve the biological relevance of the highest ranked gene sets. EGSEA's gene set database contains around 25 000 gene sets from sixteen collections. It has multiple visualization capabilities that allow researchers to view gene sets at various levels of granularity. EGSEA has been tested on simulated data and on a number of human and mouse datasets and, based on biologists' feedback, consistently outperforms the individual tools that have been combined. Our evaluation demonstrates the superiority of the ensemble approach for GSE analysis, and its utility to effectively and efficiently extrapolate biological functions and potential involvement in disease processes from lists of differentially regulated genes. Availability and Implementation: EGSEA is available as an R package at http://www.bioconductor.org/packages/EGSEA/ . The gene sets collections are available in the R package EGSEAdata from http://www.bioconductor.org/packages/EGSEAdata/ . Contacts: [email protected] [email protected]. Supplementary information: Supplementary data are available at Bioinformatics online.

The upcoming Landsat Data Continuity Mission (LDCM) will include new channels centered around 1.38$\mu\hbox{m}$and 12$\mu \hbox{m}$. This work studies the potential impact of these new channels on LDCM's cloud detection capabilities by using MODerate resolution Imaging Spectroradiometer (MODIS) data as a proxy. Thresholds for the 1.38$\mu\hbox{m}$band and the so-called “split window” technique (using the brightness temperature difference of bands centered at 11$ \mu\hbox{m}$and 12$\mu\hbox{m}$) are derived using atmospheric profiles from the ECMWF ERA-40 reanalysis and a MODIS-band radiance simulator. The thresholds are incorporated into a previously published cloud mask scheme and applied on low- and mid-latitude (60$^{\circ}$S to 60$^{\circ}\ \hbox{N}$) MODIS radiance data from two different days, six months apart. While the previous scheme yields agreement rates to the MODIS cloud mask just below 80$\%$, the addition of the 1.38$\mu\hbox{m}$and split window tests increases the agreement by 7–9%. The earlier scheme is still appropriate for cloud masking of historical Landsat images and for carrying consistent cloud detection into the future. The enhanced scheme of this paper, on the other hand, with its improved masking of primarily high thin clouds, can be either used independently or combined with other masking techniques for generating reliable LDCM cloud mask products that can potentially include confidence indicators based on the degree of agreement between multiple cloud masks.

This letter assesses the performance on Landsat-7 images of a modified version of a cloud-masking algorithm originally developed for clear-sky compositing of Moderate Resolution Imaging Spectroradiometer images at northern midlatitudes. While most historical Landsat data include measurements at thermal wavelengths and such measurements are also planned for the next mission, thermal tests are not included in the suggested algorithm in order to maintain greater versatility and ease of use. The evaluation of the masking algorithm takes advantage of the availability of manual (visual) cloud masks developed at the U.S. Geological Survey for a collection of Landsat scenes. As part of the evaluation, we also include the automated cloud cover assessment (ACCA) algorithm which does include thermal tests and is used operationally by the Landsat-7 mission to provide scene cloud fractions but no cloud masks. We show that the proposed algorithm performs on par with the ACCA both in terms of scene cloud fraction and pixel-level mask agreement. Specifically, the algorithm gives an error of 0.8% for the scene cloud fraction of 156 scenes and a root-mean-square error of 7.1%, while it agrees with the manual mask for 93.1% of the pixels. These performance indicators are very similar to those of the ACCA (1.2%, 7.1%, and 93.7%).

Dedicated, spatially configured FPGA interconnect is efficient for applications that require high throughput connections between processing elements (PEs) but with a limited degree of PE interconnectivity (e.g. wiring up gates and datapaths). Applications which virtualize PEs may require a large number of distinct PE-to-PE connections (e.g. using one PE to simulate 100s of operators, each requiring input data from thousands of other operators), but with each connection having low throughput compared with the PE's operating cycle time. In these highly interconnected conditions, dedicating spatial interconnect resources for all possible connections is costly and inefficient. Alternatively, we can time share physical network resources by virtualizing interconnect links, either by statically scheduling the sharing of resources prior to runtime or by dynamically negotiating resources at runtime. We explore the tradeoffs (e.g. area, route latency, route quality) between time-multiplexed and packet-switched networks overlayed on top of commodity FPGAs. We demonstrate modular and scalable networks which operate on a Xilinx XC2V6000-4 at 166MHz. For our applications, time-multiplexed, offline scheduling offers up to a 63% performance increase over online, packet-switched scheduling for equivalent topologies. When applying designs to equivalent area, packet-switching is up to 2times faster for small area designs while time-multiplexing is up to 5times faster for larger area designs. When limited to the capacity of a XC2V6000, if all communication is known, time-multiplexed routing outperforms packet-switching; however when the active set of links drops below 40% of the potential links, packet-switched routing can outperform time-multiplexing

How can Programmable Logic Arrays (PLAs) be built without relying on lithography to pattern their smallest features? In this paper, we detail designs which exploit emerging, bottom-up material synthesis techniques to build PLAs using molecular-scale nanowires. Our new designs accommodate technologies where the only post-fabrication programmable element is a non-restoring diode. We introduce stochastic techniques which allow us to restore the diode logic at the nanoscale so that it can be cascaded and interconnected for general logic evaluation. Under conservative assumptions using 10nm nanowires and 90nm lithographic support, we project yielded logic density around 500,000nm2/or term for a 60 or-term array; a complete 60-term, two-level PLA is roughly the same size as a single 4-LUT logic block in 22nm lithography. Each or term is comparable in area to a 4-transistor hardwired gate at 22nm. Mapping sample datapaths and conventional programmable logic benchmarks, we estimate that each 60-or-term PLA plane will provide equivalent logic to 5--10 4-input LUTs.

Satellites measure radiance, and inspection of data from the Multi-angle Imaging SpectroRadiometer (MISR) reveals that cloud cover does have an effect on the measured radiances over bright surfaces. MISR observations by employing a radiative transfer model to examine the effects of cloud micro- and macrophysical properties, surface albedo, sun and view angle on the top-of-atmosphere (TOA) measured bidirectional reflectance factor (BRF). In this paper, the effects of cloud optical depth and solar zenith angle on the transition surface albedo, defined here as the Lambertian surface albedo at which an atmosphere with a specified cloud cover has the same TOA BRF as an atmosphere without cloud cover, are presented. Above this transition surface albedo, cloudy regions are darker than clear regions, while below this albedo, the cloudy regions appear brighter than clear regions. This transition albedo varies dramatically with cloud optical depth solar zenith angle

We present the first observational study on the potential of band-differenced angular signatures for cloud detection. A band-differenced angular signature is the reflectance difference between the blue and near-infrared channels examined as a function of view angle, and it is observed in this study from the Multi-angle Imaging SpectroRadiometer (MISR). The observed band-differenced angular signatures over a variety of scene types qualitatively compare well with previously published theoretical predictions. Examples of cloud detection in polar and desert regions using band-differenced angular signatures from MISR are shown to highlight its contribution to cloud detection in areas where traditional spectral techniques tend to perform poorly.

A method is presented for generating a time-dependent parametric surface. The application on which this paper concentrates is that of producing a parametric surface description of the surfaces of the left and right ventricles of the human heart. The model is generated from two-dimensional section data obtained from MRI images of the heart. The method views surface generation as a boundary-value problem and produces surfaces as the solutions to elliptic partial differential equations. Shape parameters controlling the geometry of the surface model are introduced through the boundary conditions on the solution of the partial differential equation. These parameters are functions of time, and the surface model can be used to produce an animation of the heart during the cardiac cycle.

Interactive design of practical surfaces using the partial differential equation (PDE) method is considered. The PDE method treats surface design as a boundary value problem (ensuring that surfaces can be defined using a small set of design parameters). Owing to the elliptic nature of the PDE operator, the boundary conditions imposed around the edges of the surface control the internal shape of the surface. Moreover, surfaces obtained in this manner tend to be smooth and fair. The PDE chosen has a closed form solution allowing the interactive manipulation of the surfaces in real time. Thus we present efficient techniques by which we show how surfaces of practical significance can be constructed interactively in real time.