Quality practices and problems in free software projects

Free software and open source projects are often perceived to be of high quality. It has been suggested that the high level of quality found in some free software projects is related to the open development model which promotes peer review. While the quality of some free software projects is comparable to, if not better than, that of closed source software, not all free software projects are successful and of high quality. Even mature and successful projects face quality problems; some of these are related to the unique characteristics of free software and open source as a distributed development model led primarily by volunteers. In exploratory interviews performed with free software and open source developers, several common quality practices as well as actual quality problems have been identified. The results of these interviews are presented in this paper in order to take stock of the current status of quality in free software projects and to act as a starting point for the implementation of quality process improvement strategies.

Free energy surface reconstruction from umbrella samples using Gaussian process regression

We demonstrate how the Gaussian process regression approach can be used to efficiently reconstruct free energy surfaces from umbrella sampling simulations. By making a prior assumption of smoothness and taking account of the sampling noise in a consistent fashion, we achieve a significant improvement in accuracy over the state of the art in two or more dimensions or, equivalently, a significant cost reduction to obtain the free energy surface within a prescribed tolerance in both regimes of spatially sparse data and short sampling trajectories. Stemming from its Bayesian interpretation the method provides meaningful error bars without significant additional computation. A software implementation is made available on www.libatoms.org.

Free energy surface reconstruction from umbrella samples using Gaussian process regression II: Multiple collective variables

We demonstrate how a prior assumption of smoothness can be used to enhance the reconstruction of free energy profiles from multiple umbrella sampling simulations using the Bayesian Gaussian process regression approach. The method we derive allows the concurrent use of histograms and free energy gradients and can easily be extended to include further data. In Part I we review the necessary theory and test the method for one collective variable. We demonstrate improved performance with respect to the weighted histogram analysis method and obtain meaningful error bars without any significant additional computation. In Part II we consider the case of multiple collective variables and compare to a reconstruction using least squares fitting of radial basis functions. We find substantial improvements in the regimes of spatially sparse data or short sampling trajectories. A software implementation is made available on www.libatoms.org.

Detection of microcystins in environmental samples using surface plasmon resonance biosensor

An indirect inhibitive surface plasmon resonance (SPR) immunoassay was developed for the microcystins (MCs) detection. The bioconjugate of MC-LR and bovine serum albumin (BSA) was immobilized on a CM5 sensor chip. A serial premixture of MC-LR standards (or samples) and monoclonal antibody (mAb) were injected over the functional sensor surface, and the subsequent specific immunoreaction was monitored on the BIAcore 3000 biosensor and generated a signal with an increasing intensity in response to the decreasing MCs concentration. The developed SPR immunoassay has a wide quantitative range in 1-100 mu g L-1. Although not as sensitive as conventional enzyme-linked immunosorbent assay (ELISA), the SPR biosensor offered unique advantages: (I) the sensor chip could be reusable without any significant loss in its binding activity after 50 assay-regeneration cycles, (2) one single assay could be accomplished in 50 min (including 30-min preincubation and 20-min BIAcore analysis), and (3) this method did not require multiple steps. The SPR biosensor was also used to detect MCs in environmental samples, and the results compared well with those obtained by ELISA. We conclude that the SPR biosensor offers outstanding advantages for the MCs detection and may be further developed as a field-portable sensor for real-time monitoring of MCs on site in the near future. (C) 2009 Published by Elsevier B.V.

Rapid quantification of total microcystins in cyanobacterial samples by periodate-permanganate oxidation and reversed-phase liquid chromatography

Microcystins (MCs) comprise a family of more than 80 related cyclic hepatotoxic heptapeptides. Oxidation of MCs causes cleavage of the chemically unique C-20 beta-amino acid (2S, 3S, 8S, 9S)-3-amino-9-methoxy-2,6,8-trimethyl-10-phenyldeca-4,6-dienoic acid (Adda) amino to form 2-methyl-3-methoxy-4-phenylbutanoic acid (MMPB), which has been exploited to enable analysis of the entire family. In the present study, the reaction conditions (e.g. concentration of the reactants. temperature and pH) used in the production of MMPB by oxidation of cyanobacterial samples with permanganate-periodate were optimized through a series of well-controlled batch experiments. The oxidation product (MMPB) was then directly analyzed by high-performance liquid chromatography with diode array detection. The results of this study provided insight into the influence of reaction conditions on the yield of MMPB. Specifically, the optimal conditions, including a high dose of permanganate (>= 50 mM) in saturated periodate solution at ambient temperature under alkaline conditions (pH similar to 9) over 1-4 h were proposed, as indicated by a MMPB yield of greater than 85%. The technique developed here was applied to determine the total concentration of MCs in cyanobacterial bloom samples, and indicated that the MMPB technique was a highly sensitive and accurate method of quantifying total MCs. Additionally, these results will aid in development of a highly effective analytical method for detection of MMPB as an oxidation product for evaluation of total MCs in a wide range of environmental sample matrices, including natural waters, soils (sediments) and animal tissues. (C) 2009 Elsevier B.V. All rights reserved.

Articulating current service development practices: a qualitative analysis of eleven mental health projects.

BACKGROUND: The utilisation of good design practices in the development of complex health services is essential to improving quality. Healthcare organisations, however, are often seriously out of step with modern design thinking and practice. As a starting point to encourage the uptake of good design practices, it is important to understand the context of their intended use. This study aims to do that by articulating current health service development practices. METHODS: Eleven service development projects carried out in a large mental health service were investigated through in-depth interviews with six operation managers. The critical decision method in conjunction with diagrammatic elicitation was used to capture descriptions of these projects. Stage-gate design models were then formed to visually articulate, classify and characterise different service development practices. RESULTS: Projects were grouped into three categories according to design process patterns: new service introduction and service integration; service improvement; service closure. Three common design stages: problem exploration, idea generation and solution evaluation - were then compared across the design process patterns. Consistent across projects were a top-down, policy-driven approach to exploration, underexploited idea generation and implementation-based evaluation. CONCLUSIONS: This study provides insight into where and how good design practices can contribute to the improvement of current service development practices. Specifically, the following suggestions for future service development practices are made: genuine user needs analysis for exploration; divergent thinking and innovative culture for idea generation; and fail-safe evaluation prior to implementation. Better training for managers through partnership working with design experts and researchers could be beneficial.

A novel chemiluminescent immunoassay for microcystin (MC) detection based on gold nanoparticles label and its application to MC analysis in aquatic environmental samples

A novel chemiluminescent immunoassay method based on gold nanoparticles was developed for the detection of microcystins (MCs). The immunoassay included three main steps: indirect competitive immunoreaction, oxidative dissolution of gold nanoparticles, and indirect determination for MCs with Au3+-catalysed luminol chemiluminesent system. The method has a wide working range (0.05-10 mu g L-1, r(2) = 0.9914), the limit of detection was determined to be 0.024 mu g L-1, which is much lower than the World Health Organization's proposed guidelines (1 mu g L-1) for drinking-water. The proposed method was applied to MC analysis in natural water and fish tissue samples, and most results in the proposed method were in agreement with the conventional indirect competitive enzyme-linked immunosorbent assay method, which indicated that the new chemiluminescent immunoassay was sensitive, reliable, and suitable for MC analysis in natural water and fish tissue samples.

Taxonomic notes on water bloom forming Microcystis species (Cyanophyta) from China - An example from samples of the Dianchi Lake

Ten common species of Microcystis, based on the examination of water samples from the Dianchi Lake, Yunnan, China, were morphologically described, and their taxonomy was also discussed. They are Microcystis aeruginosa, M botrys, M firma, M flos-aquae, M ichthyoblabe, M novacekii, M pseudofilamentosa, M smithii, M viridis and M wesenbergii. Taxonomic status of other Microcystis species reported in China was also evaluated.

Negative Effects of Relative Proximity and Absolute Geography on Open Innovation Practices in High-tech SMEs in the UK

© 2014 IEEE. This exploratory study addresses a gap in management literature by addressing the role of location in the continuously expanding field of open innovation research. In this context, we analyze potential negative effects of absolute geography and relative proximity on open innovation practices in high-tech small and medium-sized enterprises (SMEs) in the United Kingdom. Drawing upon cluster theory and business ecosystem literature, the analysis from three SME case studies in the East of England suggests that presumed 'favorable' location variables, such as close relative proximity between partners and the presence of economic clusters, can have certain negative effects on open innovation practices.