Making Fedora easier to implement with Fez: A free open source content model and workflow management front-end to Fedora

The University of Queensland, Australia has developed Fez, a world-leading user-interface and management system for Fedora-based institutional repositories, which bridges the gap between a repository and users. Christiaan Kortekaas, Andrew Bennett and Keith Webster will review this open source software that gives institutions the power to create a comprehensive repository solution without the hassle..

Expokit: A software package for computing matrix exponentials

Expokit provides a set of routines aimed at computing matrix exponentials. More precisely, it computes either a small matrix exponential in full, the action of a large sparse matrix exponential on an operand vector, or the solution of a system of linear ODEs with constant inhomogeneity. The backbone of the sparse routines consists of matrix-free Krylov subspace projection methods (Arnoldi and Lanczos processes), and that is why the toolkit is capable of coping with sparse matrices of large dimension. The software handles real and complex matrices and provides specific routines for symmetric and Hermitian matrices. The computation of matrix exponentials is a numerical issue of critical importance in the area of Markov chains and furthermore, the computed solution is subject to probabilistic constraints. In addition to addressing general matrix exponentials, a distinct attention is assigned to the computation of transient states of Markov chains.

Sources of variation in larval quality for free-spawning marine invertebrates: Egg size and the local sperm environment

There has been growing interest in the effects of variation in larval quality on the post-larval performance of adult marine invertebrates. Variation in egg/larval size is an obvious source of variation in larval quality but sources of variation have received little attention. For broadcast spawners, larval size may vary according to the local sperm environment but the generality of this result is unclear. Here, we show that, for a solitary ascidian, a polychaete and an echinoid, larval size is affected by the concentration of sperm present during fertilization. Larvae that are produced at high sperm concentrations are smaller than larvae that are produced from eggs exposed to low sperm concentrations. We also show that for three ascidians and an asteroid, egg size increases with maternal body size. These differences in larval size are likely to affect larval and subsequent adult performance in the field. Given that sperm concentrations in the field can fluctuate widely, it is likely that larval quality in free-spawning marine invertebrates will also vary widely.

The benefits of polyandry in the free-spawning polychaete Galeolaria caespitosa

In many species, females are thought to benefit from polyandry due to the reduced risks of fertilization by genetically incompatible sperm. However, few studies that have reported such benefits have directly attributed variation in female reproductive success to the interacting effects of males and females at fertilization. In this paper, we determine whether male x female interactions influence fertilization in vitro in the free-spawning, sessile polychaete Galeolaria caespitosa. Furthermore, we determined whether polyandry results in direct fertilization benefits for females by experimentally manipulating the number of males contributing towards staged spawning events. To test for male x female interaction effects we performed an initial experiment that crossed seven males with six females (in all 42 combinations), enabling us to assess fertilization rates for each specific male-female pairing and attribute variation in fertilization success to males, females and their interaction. This initial experiment revealed a strong interaction between males and females at fertilization, confirming that certain male-female combinations were more compatible than others. A second experiment tested the hypothesis that polyandry enhances female reproductive success by exposing each female's eggs to either a single male's sperm (monandry) or the sperm from three males simultaneously (polyandry). We performed this second experiment at two ecologically relevant sperm concentrations. This latter experiment revealed a strong fertilization benefit of polyandry, independent of the effects of sperm concentration (which were also significant). We suggest that these direct fertilization gains arising from polyandry will constitute an important source of selection on females to mate multiply in nature.

Intracellular free Ca2+ and basal Mn2+ influx in cultured aortic smooth muscle cells from spontaneously hypertensive and normotensive Wistar-Kyoto rats.

Numerous studies investigating the possible role of altered Ca2+ homeostasis in hypertension have compared resting and agonist-stimulated intracellular free Ca2+ ([Ca2+](i)) in cultured aortic smooth muscle cells from spontaneously hypertensive (SHR) and normotensive Wistar-Kyoto (WKY) rats. However, such studies have not given consistent results. Differences in the method used to load cells with the Ca2+-sensitive indicator fura-2 have been investigated here as a possible source of variability between studies. We also describe the adaptation of a fluorescence technique for the assessment of basal Ca2+ permeability in SHR and WKY through the measurement of Mn2+ influx. The results are consistent with the hypothesis that basal Ca2+ influx is elevated in cultured aortic smooth muscle cells from SHR compared to those from WKY. However, this was not reflected as a significant difference between the two strains in basal or angiotensin II (200 nmol/L)stimulated [Ca2+](i). Furthermore, this result was not dependent on the protocol used to load cells with fura-2. Hence, measurement of bulk [Ca2+](i) does not appear to be the most sensitive parameter for altered Ca2+ homeostasis in SHR. Other compartments of the cell may better reflect altered Ca2+ fluxes in hypertension and are discussed in this work.

A review on the role of duckweed in nutrient reclamation and as a source of animal feed

The family of lemnacae colloquially known as duckweed contains the world's smallest species of flowering plants (macrophytes). Aquatic and free-floating, their most striking qualities are a capacity for explosive reproduction and an almost complete lack of fibrous material. They are widely used for reducing chemical loading in facultative sewage lagoons, but their greatest potential lies in their ability to produce large quantities of protein rich biomass, suitable for feeding to a wide range of animals, including fish, poultry and cattle. Despite these qualities there are numerous impediments to these plants being incorporated into western farming systems. Large genetically determined variations in growth in response to nutrients and climate, apparent anti-nutritional factors, concerns about sequestration of heavy metals and possible transference of pathogens raise questions about the safety and usefulness of these plants. A clear understanding of how to address and overcome these impediments needs to be developed before duckweed is widely accepted for nutrient reclamation and as a source of animal feed.

Practical considerations for the measurement of free light chains in serum

Background: A new immunoassay for free light chain measurements has been reported to be useful for the diagnosis and monitoring of monoclonal light chain diseases and nonsecretory myeloma. We describe experience with and some potential pitfalls of the assay. Methods: The assay was assessed for precision, sample type and stability, recovery, and harmonization of results between two analyzers on which the reagents are used. Free-light-chain concentrations were measured in healthy individuals (to determine biological variation), patients with monoclonal gammopathy of undetermined significance, myeloma patients after autologous stem cell transplants, and patients with renal disease. Results: Analytical imprecision (CV) was 6-11% for kappa and A free-light-chain measurement and 16% for the calculated kappa/lambda ratio. Biological variation was generally insignificant compared with analytical variation. Despite the same reagent source, values were not completely harmonized between assay systems and may produce discordant free-light-chain ratios. In some patients with clinically stable myeloma, or post transplantation, or with monoclonal gammopathy of undetermined significance, free-light-chain concentration and ratio were within the population reference interval despite the presence of monoclonal intact immunoglobulin in serum. In other patients with monoclonal gammopathy of undetermined significance, values were abnormal although there was no clinical evidence of progression to multiple myeloma. Conclusions: The use of free-light-chain measurements alone cannot differentiate some groups of patients with monoclonal gammopathy from healthy individuals. As with the introduction of any new test, it is essential that more scientific data about use of this assay in different subject groups are available so that results can be interpreted with clinical certainty. (C) 2003 American Association for Clinical Chemistry.

SubCM: A tool for improved visibility of software change in an industrial setting

Software Configuration Management is the discipline of managing large collections of software development artefacts from which software products are built. Software configuration management tools typically deal with artefacts at fine levels of granularity - such as individual source code files - and assist with coordination of changes to such artefacts. This paper describes a lightweight tool, designed to be used on top of a traditional file-based configuration management system. The add-on tool support enables users to flexibly define new hierarchical views of product structure, independent of the underlying artefact-repository structure. The tool extracts configuration and change data with respect to the user-defined hierarchy, leading to improved visibility of how individual subsystems have changed. The approach yields a range of new capabilities for build managers, and verification and validation teams. The paper includes a description of our experience using the tool in an organization that builds large embedded software systems.

Dietary carbohydrate source affects glucose concentrations, insulin secretion, and food intake in overweight cats

This study was undertaken to assess the impact of dietary carbohydrate source on food intake, body composition, glucose tolerance, insulin sensitivity, and glucose and insulin concentrations in overweight and obese cats with reduced insulin sensitivity. Sixteen overweight and obese cats were divided into two groups and randomly allocated one of two extruded diets formulated to contain similar starch content (33%) from different cereal sources (sorghum and corn versus rice). Meal response, glucose tolerance and insulin sensitivity tests were performed before and after a 6-week weight-maintenance phase and after an additional 8-week free-access feeding phase. Dual energy x-ray absorptiometry (DEXA)-derived body composition was determined in each cat before the study and after each test phase. Food intake was measured daily and body weight measured twice weekly for the duration of the study. When compared with the sorghum/corn-based diet, cats fed the rice-based diet consumed more energy and gained more weight in response to free-access feeding. Cats fed the rice-based diet also tended to have higher glucose concentrations and insulin secretion in response to a glucose load or a test meal. We conclude that a sorghum and corn blend is a superior carbohydrate source than rice for overweight cats with glucose intolerance and reduced insulin sensitivity. Such a diet may help to minimize overeating and additional weight gain, and may also reduce the risk of developing type 2 diabetes mellitus. (C) 2004 Elsevier Inc. All rights reserved.

The influence of dietary sodium chloride, Arginine : Lysine ratio, and methionine source on apparent ileal digestibility of arginine and lysine in acutely heat-stressed broilers

The present study was carried out to determine the ileal digestibility of Arg and Lys in acutely heatstressed broilers using diets varying in Arg:Lys ratio, NaCl concentration, and Met Source. Male broilers were maintained at 22degreesC from 21 to 33 d of age and then at 32degreesC from 33 to 38 d of age. From 28 to 38 d of age, birds were fed a diet with an Arg:Lys ratio of 1.05 and 3 g of supplemental NaCl/kg of diet with or without L-arg free base to increase the Arg:Lys to 1.35, and with or without 3 g/kg of additional NaCl. Methionine was supplied as equimolar amounts of DL-Met or 2-hydroxy-4-(methylthio)-butanoic acid in a 2 x 2 x 2 design. At 38 d of age, digesta were collected from the terminal ileum, and amino acid analyses were conducted on feed and digesta samples and compared with acid-insoluble ash (dietary celite) to calculate the apparent ileal digestibilities of Lys and Arg. Increasing the NaCl concentration and the presence of HMB significantly decreased the digestibility of both Arg and Lys, whereas increasing the Arg:Lys ratio increased the digestibility of only Arg but did increase BW gain (P = 0.08). An interaction between dietary NaCl and Arg:Lys ratio as well as the 3-way interaction suggested that dietary NaCl could affect the apparent ileal digestibility of Arg and Lys at certain Arg:Lys ratios and the response may be influenced by the Met source.

Assumption-free estimation of heritability from genome-wide identity-by-descent sharing between full siblings

The study of continuously varying, quantitative traits is important in evolutionary biology, agriculture, and medicine. Variation in such traits is attributable to many, possibly interacting, genes whose expression may be sensitive to the environment, which makes their dissection into underlying causative factors difficult. An important population parameter for quantitative traits is heritability, the proportion of total variance that is due to genetic factors. Response to artificial and natural selection and the degree of resemblance between relatives are all a function of this parameter. Following the classic paper by R. A. Fisher in 1918, the estimation of additive and dominance genetic variance and heritability in populations is based upon the expected proportion of genes shared between different types of relatives, and explicit, often controversial and untestable models of genetic and non-genetic causes of family resemblance. With genome-wide coverage of genetic markers it is now possible to estimate such parameters solely within families using the actual degree of identity-by-descent sharing between relatives. Using genome scans on 4,401 quasi-independent sib pairs of which 3,375 pairs had phenotypes, we estimated the heritability of height from empirical genome-wide identity-by-descent sharing, which varied from 0.374 to 0.617 (mean 0.498, standard deviation 0.036). The variance in identity-by-descent sharing per chromosome and per genome was consistent with theory. The maximum likelihood estimate of the heritability for height was 0.80 with no evidence for non-genetic causes of sib resemblance, consistent with results from independent twin and family studies but using an entirely separate source of information. Our application shows that it is feasible to estimate genetic variance solely from within- family segregation and provides an independent validation of previously untestable assumptions. Given sufficient data, our new paradigm will allow the estimation of genetic variation for disease susceptibility and quantitative traits that is free from confounding with non-genetic factors and will allow partitioning of genetic variation into additive and non-additive components.

Flexible proof reuse for software verification

Proof reuse, or analogical reasoning, involves reusing the proof of a source theorem in the proof of a target conjecture. We have developed a method for proof reuse that is based on the generalisation replay paradigm described in the literature, in which a generalisation of the source proof is replayed to construct the target proof. In this paper, we describe the novel aspects of our method, which include a technique for producing more accurate source proof generalisations (using knowledge of the target goal), as well as a flexible replay strategy that allows the user to set various parameters to control the size and the shape of the search space. Finally, we report on the results of applying this method to a case study from the realm of software verification.

Investigation of the Effect of Array Geometry on the Performance of Free-Space Optical Interconnects

The effect of transmitter and receiver array configurations on the stray-light and diffraction-caused crosstalk in free-space optical interconnects was investigated. The optical system simulation software (Code V) is used to simulate both the stray-light and diffraction-caused crosstalk. Experimentally measured, spectrally-resolved, near-field images of VCSEL higher order modes were used as extended sources in our simulation model. In addition, we have included the electrical and optical noise in our analysis to give more accurate overall performance of the FSOI system. Our results show that by changing the square lattice geometry to a hexagonal configuration, we obtain an overall signal-to-noise ratio improvement of 3 dB. Furthermore, system density is increased by up to 4 channels/mm2.

Novel array geometries for free-space optical interconnects with improved signal-to-noise ratio

We investigate the effect of transmitter and receiver array configurations on the stray-light and diffraction-caused crosstalk in free-space optical interconnects. The optical system simulation software (Code V) is used to simulate both the stray-light and diffraction-caused crosstalk. Experimentally measured, spectrally-resolved, near-field images of VCSEL higher order modes were used as extended sources in our simulation model. Our results show that by changing the square lattice geometry to a hexagonal configuration, we obtain the reduction in the stray-light crosstalk of up to 9 dB and an overall signal-to-noise ratio improvement of 3 dB.