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.

Comparison of ASAS improvement criteria for ankylosing spondylitis with clinically relevant improvement according to an expert panel

Objective: To investigate whether the recently developed (statistically derived) "ASsessment in Ankylosing Spondylitis Working Group" improvement criteria (ASAS-IC) for ankylosing spondylitis (AS) reflect clinically relevant improvement according to the opinion of an expert panel. Methods: The ASAS-IC consist of four domains: physical function, spinal pain, patient global assessment, and inflammation. Scores on these four domains of 55 patients with AS, who had participated in a non-steroidal anti-inflammatory drug efficacy trial, were presented to an international expert panel (consisting of patients with AS and members of the ASAS Working Group) in a three round Delphi exercise. The number of (non-) responders according to the ASAS-IC was compared with the final-consensus of the experts. The most important domains in the opinion of the experts were identified, and also selected with discriminant analysis. A number of provisional criteria sets that best represented the consensus of the experts were defined. Using other datasets, these clinically derived criteria sets as well as the statistically derived ASAS-IC were then tested for discriminative properties and for agreement with the end of trial efficacy by patient and doctor. Results: Forty experts completed the three Delphi rounds. The experts considered twice as many patients to be responders than the ASAS-IC (42 v 21). Overall agreement between experts and ASAS-IC was 62%. Spinal pain was considered the most important domain by most experts and was also selected as such by discriminant analysis. Provisional criteria sets with an agreement of greater than or equal to 80% compared with the consensus of the experts showed high placebo response rates (27-42%), in contrast with the ASAS-IC with a predefined placebo response rate of 25%. All criteria sets and the ASAS-IC discriminated well between active and placebo treatment (chi(2) = 36-45; p < 0.001). Compared with the end of trial efficacy assessment, the provisional criteria sets showed an agreement of 71-82%, sensitivity of 67-83%, and specificity of 81-88%. The ASAS-IC showed an agreement of 70%, sensitivity of 62%, and specificity of 89%. Conclusion: The ASAS-IC are strict in defining response, are highly specific, and consequently show lower sensitivity than the clinically derived criteria sets. However, those patients who are considered as responders by applying the ASAS-IC are acknowledged as such by the expert panel as well as by. patients' and doctors' judgments, and are therefore likely to be true responders.

Understanding consumer evaluation criteria for repurchase in a performing arts context

The purpose of this paper is to examine consumers' experience of a performing arts service to identify the predictors of audience behaviour especially as related to positive repurchase intention. Experiential service settings such as the performing arts have been cited in recent research as service contexts that may challenge current theory that repurchase intention is driven by service quality and customer satisfaction. It is posited that consumer emotions and the hedonic nature of the consumption experience may complicate the evaluation process to repurchase intention in a setting such as the performing arts. Qualitative semi-structured indepth interviews were undertaken of twenty-six performing arts consumers using a pool of questions and prompts developed from a review of the extant literature. Transcribed field notes were examined for key words and phrases and data was divided into the main emergent themes related to each of the questions and also coded for confirmation and is-confirmation of the extant literature constructs and relationships. The dimensions of service experience,price, service quality, target goal-directed emotions and non-target appraisal emotions were identified as driving repurchase intention in a performing arts setting. Customer satisfaction in this setting appears to result from emotional factors rather than expectancy dis-confirmation. This research supports the notion that an experiential consumption experience such as the performing arts will challenge the current theory of the drivers of repurchase intention and suggests that a more thorough large scale examination of these dimensions in this service setting is warranted.

The behavioural homogeneity evaluation framework:Multi-level evaluations of consumer involvement in international segmentation

This paper presents a generic strategic framework of alternative international marketing strategies and market segmentation based on intra- and inter-cultural behavioural homogeneity. Consumer involvement (CI) is proposed as a pivotal construct to capture behavioural homogeneity, for the identification of market segments. Results from a five-country study demonstrate how the strategic framework can be valuable in managerial decision-making. First, there is evidence for the cultural invariance of the measurement of CI, allowing a true comparison of inter- and intra-cultural behavioural homogeneity. Second, CI influences purchase behaviour, and its evaluation provides a rich source of information for responsive market segmentation. Finally, a decomposition of behavioural variance suggests that national-cultural environment and nationally transcendent variables explain differences in behaviour. The Behavioural Homogeneity Evaluation Framework therefore suggests appropriate international marketing strategies, providing practical guidance for implementing involvement-contingent strategies. © 2007 Academy of International Business. All rights reserved.

Mathematical methods in power system stability studies

In this thesis various mathematical methods of studying the transient and dynamic stabiIity of practical power systems are presented. Certain long established methods are reviewed and refinements of some proposed. New methods are presented which remove some of the difficulties encountered in applying the powerful stability theories based on the concepts of Liapunov. Chapter 1 is concerned with numerical solution of the transient stability problem. Following a review and comparison of synchronous machine models the superiority of a particular model from the point of view of combined computing time and accuracy is demonstrated. A digital computer program incorporating all the synchronous machine models discussed, and an induction machine model, is described and results of a practical multi-machine transient stability study are presented. Chapter 2 reviews certain concepts and theorems due to Liapunov. In Chapter 3 transient stability regions of single, two and multi~machine systems are investigated through the use of energy type Liapunov functions. The treatment removes several mathematical difficulties encountered in earlier applications of the method. In Chapter 4 a simple criterion for the steady state stability of a multi-machine system is developed and compared with established criteria and a state space approach. In Chapters 5, 6 and 7 dynamic stability and small signal dynamic response are studied through a state space representation of the system. In Chapter 5 the state space equations are derived for single machine systems. An example is provided in which the dynamic stability limit curves are plotted for various synchronous machine representations. In Chapter 6 the state space approach is extended to multi~machine systems. To draw conclusions concerning dynamic stability or dynamic response the system eigenvalues must be properly interpreted, and a discussion concerning correct interpretation is included. Chapter 7 presents a discussion of the optimisation of power system small sjgnal performance through the use of Liapunov functions.

Evaluation of PCR in the molecular diagnosis of endocarditis

Objective. Infective endocarditis (IE) is diagnosed by the Duke criteria, which can be inconclusive particularly when blood cultures are negative. This study investigated the application of polymerase chain reaction (PCR) to identify bacterial DNA in excised valvular tissue, and its role in establishing the diagnosis of IE. Methods. Ninety-eight patients undergoing valve replacement surgery were studied. Twenty-eight patients were confirmed as definite for endocarditis by the Duke criteria; nine were considered as possible and 61 had no known or previous microbial infection of the endocardium. A broad-range PCR technique was used to amplify prokaryotic 16S rRNA genes present within homogenised heart valve tissue. Subsequent DNA sequencing of the PCR amplicon allowed identification of the infecting microorganism. Results. PCR results demonstrated the presence of bacterial DNA in the heart valves obtained from 14 out of 20 (70%) definite IE patients with positive blood cultures preoperatively. The causative microorganism for one patient with definite culture negative endocarditis was identified by PCR. Two out of nine (22%) of the valves from possible endocarditis patients also had bacterial DNA present converting them into the definite criteria whereas in the valves of seven out of nine (78%) of these patients no bacterial DNA was detected. Conclusion. The application of PCR to the explanted valves in patients with possible or confirmed diagnosis can augment the Duke criteria thereby improving post-surgical antimicrobial therapeutic options. © 2003 The British Infection Society. Published by Elsevier Ltd. All rights reserved.

The development and evaluation of distance learning materials for administrative personnel in a multi-national company

There has been substantial research into the role of distance learning in education. Despite the rise in the popularity and practice of this form of learning in business, there has not been a parallel increase in the amount of research carried out in this field. An extensive investigation was conducted into the entire distance learning system of a multi-national company with particular emphasis on the design, implementation and evaluation of the materials. In addition, the performance and attitudes of trainees were examined. The results of a comparative study indicated that trainees using distance learning had significantly higher test scores than trainees using conventional face-to-face training. The influence of the previous distance learning experience, educational background and selected study environment of trainees was investigated. Trainees with previous experience of distance learning were more likely to complete the course and with significantly higher test scores than trainees with no previous experience. The more advanced the educational background of trainees, the greater the likelihood of their completing the course, although there was no significant difference in the test scores achieved. Trainees preferred to use the materials at home and those opting to study in this environment scored significantly higher than those studying in the office, the study room at work or in a combination of environments. The influence of learning styles (Kolb, 1976) was tested. The results indicated that the convergers had the greatest completion rates and scored significantly higher than trainees with the assimilator, accommodator and diverger learning styles. The attitudes of the trainees, supervisors and trainers were examined using questionnaire, interview and discussion techniques. The findings highlighted the potential problems of lack of awareness and low motivation which could prove to be major obstacles to the success of distance learning in business.