Primers‐4‐Yeast: a comprehensive web tool for planning primers for Saccharomyces cerevisiae

The budding yeast Saccharomyces cerevisiae is a key model organism of functional genomics, due to its ease and speed of genetic manipulations. In fact, in this yeast, the requirement for homologous sequences for recombination purposes is so small that 40 base pairs (bp) are sufficient. Hence, an enormous variety of genetic manipulations can be performed by simply planning primers with the correct homology, using a defined set of transformation plasmids. Although designing primers for yeast transformations and for the verification of their correct insertion is a common task in all yeast laboratories, primer planning is usually done manually and a tool that would enable easy, automated primer planning for the yeast research community is still lacking. Here we introduce Primers‐4‐Yeast, a web tool that allows primers to be designed in batches for S. cerevisiae gene‐targeting transformations, and for the validation of correct insertions. This novel tool enables fast, automated, accurate primer planning for large sets of genes, introduces consistency in primer planning and is therefore suggested to serve as a standard in yeast research. Primers‐4‐Yeast is available at: http://www.weizmann.ac.il/Primers‐4‐Yeast Copyright © 2013 John Wiley & Sons, Ltd.     

Gabor feature based nonlocal means filter for textured image denoising

The nonlocal means (NLM) filter has distinct advantages over traditional image denoising techniques. However, in spite of its simplicity, the pixel value-based self-similarity measure used by the NLM filter is intrinsically less robust when applied to images with non-stationary contents. In this paper, we use Gabor-based texture features to measure the self-similarity, and thus propose the Gabor feature based NLM (GFNLM) filter for textured image denoising. This filter recovers noise-corrupted images by replacing each pixel value with the weighted sum of pixel values in its search window, where each weight is defined based on the Gabor-based texture similarity measure. The GFNLM filter has been compared to the classical NLM filter and four other state-of-the-art image denoising algorithms in textured images degraded by additive Gaussian noise. Our results show that the proposed GFNLM filter can denoise textured images more effectively and robustly while preserving the texture information.     

SparkMed: a framework for dynamic integration of multimedia medical data into distributed m-Health systems

With the advent of 4G and other long-term evolution (LTE) wireless networks, the traditional boundaries of patient record propagation are diminishing as networking technologies extend the reach of hospital infrastructure and provide on-demand mobile access to medical multimedia data. However, due to legacy and proprietary software, storage and decommissioning costs, and the price of centralization and redevelopment, it remains complex, expensive, and often unfeasible for hospitals to deploy their infrastructure for online and mobile use. This paper proposes the SparkMed data integration framework for mobile healthcare (m-Health), which significantly benefits from the enhanced network capabilities of LTE wireless technologies, by enabling a wide range of heterogeneous medical software and database systems (such as the picture archiving and communication systems, hospital information system, and reporting systems) to be dynamically integrated into a cloud-like peer-to-peer multimedia data store. Our framework allows medical data applications to share data with mobile hosts over a wireless network (such as WiFi and 3G), by binding to existing software systems and deploying them as m-Health applications. SparkMed integrates techniques from multimedia streaming, rich Internet applications (RIA), and remote procedure call (RPC) frameworks to construct a Self-managing, Pervasive Automated netwoRK for Medical Enterprise Data (SparkMed). Further, it is resilient to failure, and able to use mobile and handheld devices to maintain its network, even in the absence of dedicated server devices. We have developed a prototype of the SparkMed framework for evaluation on a radiological workflow simulation, which uses SparkMed to deploy a radiological image viewer as an m-Health application for telemedical use by radiologists and stakeholders. We have evaluated our prototype using ten devices over WiFi and 3G, verifying that our framework meets its two main objectives: 1) interactive delivery of medical multimedia data to mobile devices; and 2) attaching to non-networked medical software processes without significantly impacting their performance. Consistent response times of under 500 ms and graphical frame rates of over 5 frames per second were observed under intended usage conditions. Further, overhead measurements displayed linear scalability and low resource requirements.     

Stability of shallow karstic caverns in blocky rock masses

The limiting relationship is explored between underground opening span and required cover height for stability in blocky rock masses characterized by a network of horizontal bedding planes and vertical joints. Understanding this relationship is crucial for the design of mining excavations in karstic terrain as typically encountered in carbonate rock masses. We perform numerical analysis of multiple roof spans vs. cover height geometries using the DDA method to obtain the boundary curve between stable and unstable opening geometries. Our results indicate that for cavern spans of up to 18 m a low cover height vs. opening span ratio of h/B=0.33 is sufficient for stability. For spans greater than 18 m the demand for cover height rapidly increases and it appears to stabilize at h/B=1.0 for B=26 m and above.To validate our numerical analysis results, a unique case study is analyzed wherein a 40 m span karstic cavern, the Ayalon cave, has been preserved below an active open pit mine in central Israel with cover height of only 30 m, thus rendering the cave marginally stable according to our model prediction. Indeed there is ample evidence of partial collapse of the roof in the cave. The predictive capability of our model is further confirmed using two additional case studies in blocky rock masses, each of which possesses very different mechanical parameters such as intact rock strength, density, and deformability, suggesting that our model predictions remain valid as long the rock mass maintains a “blocky” structural configuration.