Evaluation and comparison of mammalian subcellular localization prediction methods

Background: Determination of the subcellular location of a protein is essential to understanding its biochemical function. This information can provide insight into the function of hypothetical or novel proteins. These data are difficult to obtain experimentally but have become especially important since many whole genome sequencing projects have been finished and many resulting protein sequences are still lacking detailed functional information. In order to address this paucity of data, many computational prediction methods have been developed. However, these methods have varying levels of accuracy and perform differently based on the sequences that are presented to the underlying algorithm. It is therefore useful to compare these methods and monitor their performance. Results: In order to perform a comprehensive survey of prediction methods, we selected only methods that accepted large batches of protein sequences, were publicly available, and were able to predict localization to at least nine of the major subcellular locations (nucleus, cytosol, mitochondrion, extracellular region, plasma membrane, Golgi apparatus, endoplasmic reticulum (ER), peroxisome, and lysosome). The selected methods were CELLO, MultiLoc, Proteome Analyst, pTarget and WoLF PSORT. These methods were evaluated using 3763 mouse proteins from SwissProt that represent the source of the training sets used in development of the individual methods. In addition, an independent evaluation set of 2145 mouse proteins from LOCATE with a bias towards the subcellular localization underrepresented in SwissProt was used. The sensitivity and specificity were calculated for each method and compared to a theoretical value based on what might be observed by random chance. Conclusion: No individual method had a sufficient level of sensitivity across both evaluation sets that would enable reliable application to hypothetical proteins. All methods showed lower performance on the LOCATE dataset and variable performance on individual subcellular localizations was observed. Proteins localized to the secretory pathway were the most difficult to predict, while nuclear and extracellular proteins were predicted with the highest sensitivity.

Apparent motion photometry:evaluation and reliability of a novel method for the measurement of macular pigment

Background/aims Macular pigment is thought to protect the macula against exposure to light and oxidative stress, both of which may play a role in the development of age-related macular degeneration. The aim was to clinically evaluate a novel cathode-ray-tube-based method for measurement of macular pigment optical density (MPOD) known as apparent motion photometry (AMP). Methods The authors took repeat readings of MPOD centrally (0°) and at 3° eccentricity for 76 healthy subjects (mean (±SD) 26.5±13.2 years, range 18–74 years). Results The overall mean MPOD for the cohort was 0.50±0.24 at 0°, and 0.28±0.20 at 3° eccentricity; these values were significantly different (t=-8.905, p<0.001). The coefficients of repeatability were 0.60 and 0.48 for the 0 and 3° measurements respectively. Conclusions The data suggest that when the same operator is taking repeated 0° AMP MPOD readings over time, only changes of more than 0.60 units can be classed as clinically significant. In other words, AMP is not suitable for monitoring changes in MPOD over time, as increases of this magnitude would not be expected, even in response to dietary modification or nutritional supplementation.

International technology transfer and collaborative new product development:evidence and a case from the machine tool industry

In recent years, it has become increasingly common for companies to improve their competitiveness and find new markets by extending their operations through international new product development collaborations involving technology transfer. Technology development, cost reduction and market penetration are seen as the foci in such collaborative operations with the aim being to improve the competitive position of both partners. In this paper, the case of technology transfer through collaborative new product development in the machine tool sector is used to provide a typical example of such partnerships. The paper outlines the links between the operational aspects of collaborations and their strategic objectives. It is based on empirical data collected from the machine tool industries in the UK and China. The evidence includes longitudinal case studies and questionnaire surveys of machine tool manufacturers in both countries. The specific case of BSA Tools Ltd and its Chinese partner the Changcheng Machine Tool Works is used to provide an in-depth example of the operational development of a successful collaboration. The paper concludes that a phased coordination of commercial, technical and strategic interactions between the two partners is essential for such collaborations to work.

Integrated project evaluation and selection using multiple-attribute decision-making technique

The evaluation and selection of industrial projects before investment decision is customarily done using marketing, technical and financial information. Subsequently, environmental impact assessment and social impact assessment are carried out mainly to satisfy the statutory agencies. Because of stricter environment regulations in developed and developing countries, quite often impact assessment suggests alternate sites, technologies, designs, and implementation methods as mitigating measures. This causes considerable delay to complete project feasibility analysis and selection as complete analysis requires to be taken up again and again till the statutory regulatory authority approves the project. Moreover, project analysis through above process often results sub-optimal project as financial analysis may eliminate better options, as more environment friendly alternative will always be cost intensive. In this circumstance, this study proposes a decision support system, which analyses projects with respect to market, technicalities, and social and environmental impact in an integrated framework using analytic hierarchy process, a multiple-attribute decision-making technique. This not only reduces duration of project evaluation and selection, but also helps select optimal project for the organization for sustainable development. The entire methodology has been applied to a cross-country oil pipeline project in India and its effectiveness has been demonstrated. © 2005 Elsevier B.V. All rights reserved.

Business information systems:technology, development and management for the e-business with Webct pin card

This is an online course pack consisting of Chaffey: Business Information Systems ISBN: 027365540X and access to a Pearson Education online course ISBN: 0273673491