Risks associated with endotoxins in feed additives produced by fermentation

Acknowledgements We thank Jordi Tarrés Call, who recorded the discussions and offered advice about procedures, and Nicole Reisinger and Gerd Schatzmayr, who provided valuable information about endotoxins in animal feeds. The Rowett Institute of Nutrition and Health is funded by the Rural and Environment Science and Analytical Services Division (RESAS) of the Scottish Government.Peer reviewedPublisher PD

Beyond XSPEC: Towards Highly Configurable Analysis

We present a quantitative comparison between software features of the defacto standard X-ray spectral analysis tool, XSPEC, and ISIS, the Interactive Spectral Interpretation System. Our emphasis is on customized analysis, with ISIS offered as a strong example of configurable software. While noting that XSPEC has been of immense value to astronomers, and that its scientific core is moderately extensible--most commonly via the inclusion of user contributed "local models"--we identify a series of limitations with its use beyond conventional spectral modeling. We argue that from the viewpoint of the astronomical user, the XSPEC internal structure presents a Black Box Problem, with many of its important features hidden from the top-level interface, thus discouraging user customization. Drawing from examples in custom modeling, numerical analysis, parallel computation, visualization, data management, and automated code generation, we show how a numerically scriptable, modular, and extensible analysis platform such as ISIS facilitates many forms of advanced astrophysical inquiry.Comment: Accepted by PASP, for July 2008 (15 pages

Quantum Monte Carlo Study of Strongly Correlated Electrons: Cellular Dynamical Mean-Field Theory

We study the Hubbard model using the Cellular Dynamical Mean-Field Theory (CDMFT) with quantum Monte Carlo (QMC) simulations. We present the algorithmic details of CDMFT with the Hirsch-Fye QMC method for the solution of the self-consistently embedded quantum cluster problem. We use the one- and two-dimensional half-filled Hubbard model to gauge the performance of CDMFT+QMC particularly for small clusters by comparing with the exact results and also with other quantum cluster methods. We calculate single-particle Green's functions and self-energies on small clusters to study their size dependence in one- and two-dimensions.Comment: 14 pages, 18 figure

Session-Based Programming for Parallel Algorithms: Expressiveness and Performance

This paper investigates session programming and typing of benchmark examples to compare productivity, safety and performance with other communications programming languages. Parallel algorithms are used to examine the above aspects due to their extensive use of message passing for interaction, and their increasing prominence in algorithmic research with the rising availability of hardware resources such as multicore machines and clusters. We contribute new benchmark results for SJ, an extension of Java for type-safe, binary session programming, against MPJ Express, a Java messaging system based on the MPI standard. In conclusion, we observe that (1) despite rich libraries and functionality, MPI remains a low-level API, and can suffer from commonly perceived disadvantages of explicit message passing such as deadlocks and unexpected message types, and (2) the benefits of high-level session abstraction, which has significant impact on program structure to improve readability and reliability, and session type-safety can greatly facilitate the task of communications programming whilst retaining competitive performance

Passage time distributions in large Markov chains

Accepted versio

Design and evaluation of Nemesis, a scalable, low-latency, message-passing communication subsystem

This paper presents a new low-level communication subsystem called Nemesis. Nemesis has been designed and implemented to be scalable and efficient both in the intranode communication context using shared-memory and in the internode communication case using high-performance networks and is natively multimethod-enabled. Nemesis has been integrated in MPICH2 as a CH3 channel and delivers better performance than other dedicated communication channels in MPICH2. Furthermore, the resulting MPICH2 architecture outperforms other MPI implementations in point-to-point benchmarks

Finding apparent horizons and other two-surfaces of constant expansion

Apparent horizons are structures of spacelike hypersurfaces that can be determined locally in time. Closed surfaces of constant expansion (CE surfaces) are a generalisation of apparent horizons. I present an efficient method for locating CE surfaces. This method uses an explicit representation of the surface, allowing for arbitrary resolutions and, in principle, shapes. The CE surface equation is then solved as a nonlinear elliptic equation. It is reasonable to assume that CE surfaces foliate a spacelike hypersurface outside of some interior region, thus defining an invariant (but still slicing-dependent) radial coordinate. This can be used to determine gauge modes and to compare time evolutions with different gauge conditions. CE surfaces also provide an efficient way to find new apparent horizons as they appear e.g. in binary black hole simulations.Comment: 21 pages, 8 figures; two references adde

R.A.Fisher, design theory, and the Indian connection

Design Theory, a branch of mathematics, was born out of the experimental statistics research of the population geneticist R. A. Fisher and of Indian mathematical statisticians in the 1930s. The field combines elements of combinatorics, finite projective geometries, Latin squares, and a variety of further mathematical structures, brought together in surprising ways. This essay will present these structures and ideas as well as how the field came together, in itself an interesting story.Comment: 11 pages, 3 figure