A Computer Algebra System for R: Macaulay2 and the m2r Package

Algebraic methods have a long history in statistics. Apart from the ubiquitous applications of linear algebra, the most visible manifestations of modern algebra in statistics are found in the young field of algebraic statistics, which brings tools from commutative algebra and algebraic geometry to bear on statistical problems. Now over two decades old, algebraic statistics has applications in a wide range of theoretical and applied statistical domains. Nevertheless, algebraic statistical methods are still not mainstream, mostly due to a lack of easy off-the-shelf implementations. In this article we debut m2r, an R package that connects R to Macaulay2 through a persistent back-end socket connection running locally or on a cloud server. Topics range from basic use of m2r to applications and design philosophy

Kawa|compiling dynamic languages to the Java VM

Many are interested in Java for its portable bytecodes and extensive libraries, but prefer a different language, especially for scripting. People have implemented other languages using an interpreter (which is slow), or by translating into Java source (with poor responsiveness for eval). Kawa uses an interpreter only for “simple” expressions; all non-trivial expressions (such as function definitions) are compiled into Java bytecodes, which are emitted into an in-memory byte array. This can be saved for later, or quickly loaded using the Java ClassLoader. Kawa is intended to be a framework that supports multiple source languages. Currently, it only supports Scheme, which is a lexically-scoped language in the Lisp family. The Kawa dialect of Scheme implements almost all of the current Scheme standard (R5RS), with a number of extensions, and is written in a efficient objectoriented style. It includes the full “numeric tower”, with complex numbers, exact infinite-precision rational arithmetic, and units. A number of extensions provide access to Java primitives, and some Java methods provide convenient access to Scheme. Since all Java objects are Scheme values and vice versa, this makes for a very powerful hybrid Java/Scheme environment. An implementation of ECMAScript (the standardized “core ” of JavaScript) is under construction. Other languages, including Emacs Lisp, are also being considered

Open-source software in medical imaging: development of OsiriX

Purpose Open source software (oss) development for medical imaging enables collaboration of individuals and groups to produce high-quality tools that meet user needs. This process is reviewed and illustrated with OsiriX, a fast DICOM viewer program for the Apple Macintosh. Materials and methods OsiriX is an oss for the Apple Macintosh under Mac OS X v10.4 or higher specifically designed for navigation and visualization of multimodality and multidimensional images: 2D Viewer, 3D Viewer, 4D Viewer (3D series with temporal dimension, for example: Cardiac-CT) and 5D Viewer (3D series with temporal and functional dimensions, for example: Cardiac-PET-CT). The 3D Viewer offers all modern rendering modes: multiplanar reconstruction, surface rendering, volume rendering and maximum Intensity projection. All these modes support 4D data and are able to produce image fusion between two different series (for example: PET-CT). OsiriX was developed using the Apple Xcode development environment and Cocoa framework as both a DICOM PACS workstation for medical imaging and an image processing software package for medical research (radiology and nuclear imaging), functional imaging, 3D imaging, confocal microscopy and molecular imaging. Results OsiriX is an open source program by Antoine Rosset, a radiologist and software developer, was designed specifically for the needs of advanced imaging modalities. The software program turns an Apple Macintosh into a DICOM PACS workstation for medical imaging and image processing. OsiriX is distributed free of charge under the GNU General Public License and its source code is available to anyone. This system illustrates how open software development for medical imaging tools can be successfully designed, implemented and disseminated. Conclusion oss development can provide useful cost effective tools tailored to specific needs and clinical tasks. The integrity and quality assurance of open software developed by a community of users does not follow the traditional conformance and certification required for commercial medical software programs. However, open software can lead to innovative solutions designed by users better suited for specific task

A moonlighting enzyme imposes second messenger bistability to drive lifestyle decisions in E. coli.

Bacteria preferentially colonize surfaces and air-liquid interfaces as matrix embedded communities called biofilms. Biofilms exhibit specific physiological properties, including general stress tolerance, increased antibiotic recalcitrance and tolerance against phagocytic clearance. Together this largely accounts for increased biofilm persistence, chronic infections and infection relapses. One of the principle regulators of biofilm formation is c-di-GMP, a bacterial second messenger controlling various cellular processes. Cellular levels of c-di-GMP are controlled by two antagonistic enzyme families, diguanylate cyclases and phosphodiesterases. But despite the identification and characterization of an increasing number of components of the c-di-GMP network in different bacterial model organisms, details of c-di- GMP mediated decision-making have remained unclear. In particular, how cells shuttle between specific c-di-GMP regimes at the population and single cell level is largely unknown and moreover how these transitions are deterministically made in time and space, given that bacterial networks of diguanylate cyclases and phosphodiesterases show a high degree of complexity. Here we describe a novel mechanism regulating c-di-GMP mediated biofilm formation in E. coli. This mechanism relies on the bistable expression of a key phosphodiesterase that acts both as catalyst for c- di-GMP degradation and as a transcription factor promoting its own production. Bistability results from two interconnected positive feedback loops operating on the catalytic and gene expression level. Based on genetic, structural and biochemical analyses we postulate a simple substrate-induced switch mechanism through which this enzyme can sense changing concentration of c-di-GMP and convert this information into a bistable c-di-GMP response. This mechanism may explain how cellular heterogeneity of small signaling molecules is generated in bacteria and used as a bet hedging strategy for important lifestyle transitions

Role of the PAS2 domain of the NifL regulatory protein in redox signal transduction

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Minkowski Sum Construction and other Applications of Arrangements of Geodesic Arcs on the Sphere

We present two exact implementations of efficient output-sensitive algorithms that compute Minkowski sums of two convex polyhedra in 3D. We do not assume general position. Namely, we handle degenerate input, and produce exact results. We provide a tight bound on the exact maximum complexity of Minkowski sums of polytopes in 3D in terms of the number of facets of the summand polytopes. The algorithms employ variants of a data structure that represents arrangements embedded on two-dimensional parametric surfaces in 3D, and they make use of many operations applied to arrangements in these representations. We have developed software components that support the arrangement data-structure variants and the operations applied to them. These software components are generic, as they can be instantiated with any number type. However, our algorithms require only (exact) rational arithmetic. These software components together with exact rational-arithmetic enable a robust, efficient, and elegant implementation of the Minkowski-sum constructions and the related applications. These software components are provided through a package of the Computational Geometry Algorithm Library (CGAL) called Arrangement_on_surface_2. We also present exact implementations of other applications that exploit arrangements of arcs of great circles embedded on the sphere. We use them as basic blocks in an exact implementation of an efficient algorithm that partitions an assembly of polyhedra in 3D with two hands using infinite translations. This application distinctly shows the importance of exact computation, as imprecise computation might result with dismissal of valid partitioning-motions.Comment: A Ph.D. thesis carried out at the Tel-Aviv university. 134 pages long. The advisor was Prof. Dan Halperi

Pathophysiologic correlates of exercise intolerance in adults with pulmonary hypertension and congenital heart disease

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