A web services choreography scenario for interoperating bioinformatics applications

BACKGROUND: Very often genome-wide data analysis requires the interoperation of multiple databases and analytic tools. A large number of genome databases and bioinformatics applications are available through the web, but it is difficult to automate interoperation because: 1) the platforms on which the applications run are heterogeneous, 2) their web interface is not machine-friendly, 3) they use a non-standard format for data input and output, 4) they do not exploit standards to define application interface and message exchange, and 5) existing protocols for remote messaging are often not firewall-friendly. To overcome these issues, web services have emerged as a standard XML-based model for message exchange between heterogeneous applications. Web services engines have been developed to manage the configuration and execution of a web services workflow. RESULTS: To demonstrate the benefit of using web services over traditional web interfaces, we compare the two implementations of HAPI, a gene expression analysis utility developed by the University of California San Diego (UCSD) that allows visual characterization of groups or clusters of genes based on the biomedical literature. This utility takes a set of microarray spot IDs as input and outputs a hierarchy of MeSH Keywords that correlates to the input and is grouped by Medical Subject Heading (MeSH) category. While the HTML output is easy for humans to visualize, it is difficult for computer applications to interpret semantically. To facilitate the capability of machine processing, we have created a workflow of three web services that replicates the HAPI functionality. These web services use document-style messages, which means that messages are encoded in an XML-based format. We compared three approaches to the implementation of an XML-based workflow: a hard coded Java application, Collaxa BPEL Server and Taverna Workbench. The Java program functions as a web services engine and interoperates with these web services using a web services choreography language (BPEL4WS). CONCLUSION: While it is relatively straightforward to implement and publish web services, the use of web services choreography engines is still in its infancy. However, industry-wide support and push for web services standards is quickly increasing the chance of success in using web services to unify heterogeneous bioinformatics applications. Due to the immaturity of currently available web services engines, it is still most practical to implement a simple, ad-hoc XML-based workflow by hard coding the workflow as a Java application. For advanced web service users the Collaxa BPEL engine facilitates a configuration and management environment that can fully handle XML-based workflow

A Discrete Choice Experiment to assess patients’ preferences for HIV treatment in the rural population in Colombia

"Aim: To elicit patients’ preferences for HIV treatment of the rural population in Colombia. Methods: A discrete choice experiment (DCE), conducted in a HIV clinic in Bogotá, was used to examine the trade-off between five HIV treatment attributes: effect on life expectancy, effect on physical activity, risk of moderate side-effects, accessibility to clinic, and economic costs to access controls. Attributes selection was based on literature review, expert consultation and a focus group with six patients. An efficient experimental design was used to define two versions of the questionnaire with each of 12 choice sets and a dominance task was added to check reliability. A mixed logit model was then used to analyse the data and sub-group analyses were conducted on the basis of age, gender, education, and sexual preference. Results: A total of 129 HIV patients were included for analysis. For all treatment attributes, significant differences between at least two levels were observed, meaning that all attributes were significant predictors of choice. Patients valued the effect on physical activity (conditional relative importance of 27.5%) and the effect on life expectancy (26.0%) the most. Sub-group analyses regard age and education showed significant differences: younger patients and high educated patients valued the effect on physical activity the most important, whereas older patients mostly valued the effect on life expectancy and low educated patients mostly valued the accessibility to clinic. Limitations: One potential limitation is selection bias, as only patients from one HIV clinic were reached. Additionally, questionnaires were partly administered in the waiting rooms, which potentially led to noise in the data. Conclusions: This study suggests that all HIV treatment characteristics included in this DCE were important and that HIV patients from rural Colombia valued short-term efficacy (i.e. effect on physical activity) and long-term efficacy (i.e. effect on life expectancy) the most. © 2020, © 2020 The Author(s). Published by Informa UK Limited, trading as Taylor and Francis Group.

A Discrete Choice Experiment to assess patients’ preferences for HIV treatment in the urban population in Colombia

Aim: This study aimed to assess patients' preferences for HIV treatment in an urban Colombian population. Methods: A Discrete Choice Experiment (DCE) was conducted. Urban Colombian HIV patients were asked to repetitively choose between two hypothetical treatments that differ in regard to five attributes 'effect on life expectancy', 'effect on physical activity', 'risk of moderate side effects, 'accessibility to clinic' and 'economic cost to access controls'. Twelve choice sets were made using an efficient design. A Mixed Logit Panel Model was used for the analysis and subgroup analyses were performed according to age, gender, education level and sexual preference. Results: A total of 224 HIV patients were included. All attributes were significant, indicating that there were differences between at least two levels of each attribute. Patients preferred to be able to perform all physical activity without difficulty, to have large positive effects on life expectancy, to travel less than 2 h, to have lower risk of side-effects and to have subsidized travel costs. The attributes 'effect on physical activity' and 'effects on life expectancy' were deemed the most important. Sub-analyses showed that higher educated patients placed more importance on the large positive effects of HIV treatment, and a more negative preference for subsidized travel cost (5% level). Limitations: A potential limitation is selection bias as it is difficult to make a systematic urban/rural division of respondents. Additional, questionnaires were partly administered in the waiting rooms, which potentially led to some noise in the data. Conclusions: Findings suggests that short-term efficacy (i.e. effect on physical activity) and long-term efficacy (i.e. effect on life expectancy) are the most important treatment characteristics for HIV urban patients in Colombia. Preference data could provide relevant information for clinical and policy decision-making to optimize HIV care

Sodium-glucose cotransporter 2 inhibitors (SGLT2i) and cardiac arrhythmias:a systematic review and meta-analysis

Following publication of the original article [1], the authors noticed an error in the second author’s name. The name of the second author, "Gregory Y. H. Lip", was incorrectly written as "Gregory-Y H Lip". This has been corrected with this erratum. The original article [1] has been corrected

Sodium-Glucose Cotransporter 2 Inhibitors and the Risk of Pneumonia and Septic Shock

CONTEXT: Individuals with type 2 diabetes mellitus (DM) have an increased risk of pneumonia and septic shock. Traditional glucose-lowering drugs have recently been found to be associated with a higher risk of infections. It remains unclear whether sodium-glucose cotransporter 2 inhibitors (SGLT2is), which have pleiotropic/anti-inflammatory effects, may reduce the risk of pneumonia and septic shock in DM. METHODS: MEDLINE, Embase, and ClinicalTrials.gov were searched from inception up to May 19, 2022, for randomized, placebo-controlled trials of SGLT2i that included patients with DM and reported outcomes of interest (pneumonia and/or septic shock). Study selection, data extraction, and quality assessment (using the Cochrane Risk of Bias Assessment Tool) were conducted by independent authors. A fixed-effects model was used to pool the relative risk (RRs) and 95% CI across trials. RESULTS: Out of 4568 citations, 26 trials with a total of 59 264 patients (1.9% developed pneumonia and 0.2% developed septic shock) were included. Compared with placebo, SGLT2is significantly reduced the risk of pneumonia (pooled RR 0.87, 95% CI 0.78-0.98) and septic shock (pooled RR 0.65, 95% CI 0.44-0.95). There was no significant heterogeneity of effect size among trials. Subgroup analyses according to the type of SGLT2i used, baseline comorbidities, glycemic control, duration of DM, and trial follow-up showed consistent results without evidence of significant treatment-by-subgroup heterogeneity (all P(heterogeneity) > .10). CONCLUSION: Among DM patients, SGLT2is reduced the risk of pneumonia and septic shock compared with placebo. Our findings should be viewed as hypothesis generating, with concepts requiring validation in future studies

Global article collection : essential reads from around the world

At the beginning of 2022, the Journal of Medical Economics (JME) published a Commentary highlighting the top five cited articles in 2021 [1]. This Commentary also included six articles from 2021—chosen by the Editor in Chief and Deputy Editor in Chief—that had a significant impact on the study of health economics. However, the JME editorial team noticed that the articles in the Commentary focused on research in the U.S. rather than reflecting the global diversity of the Journal’s content. This realization led to the publication of this Commentary that represents authors and articles from regions beyond North America. To create this Commentary, the Journal’s Editorial Board members and some of its highly-cited authors selected impactful and thought-provoking articles from the following global regions: Western and Eastern Europe, Africa, Asia, Australia, and South America. Continue reading for the full list of articles and accompanying commentaries

Comparison of statistical analysis methods for object case best–worst scaling

KLC received financial support for his research stay at the Department of Health Economics, Center for Public Health, Medical University of Vienna through the ‘Erasmus+ staff mobility grant’

A Review of the Theoretical Basis, Effects, and Cost Effectiveness of Online Smoking Cessation Interventions in the Netherlands: A Mixed-Methods Approach

Background: Tobacco smoking is a worldwide public health problem. In 2015, 26.3% of the Dutch population aged 18 years and older smoked, 74.4% of them daily. More and more people have access to the Internet worldwide; approximately 94% of the Dutch population have online access. Internet-based smoking cessation interventions (online cessation interventions) provide an opportunity to tackle the scourge of tobacco. Objective: The goal of this paper was to provide an overview of online cessation interventions in the Netherlands, while exploring their effectivity, cost effectiveness, and theoretical basis. Methods: A mixed-methods approach was used to identify Dutch online cessation interventions, using (1) a scientific literature search, (2) a grey literature search, and (3) expert input. For the scientific literature, the Cochrane review was used and updated by two independent researchers (n=651 identified studies), screening titles, abstracts, and then full-text studies between 2013 and 2016 (CENTRAL, MEDLINE, and EMBASE). For the grey literature, the researchers conducted a Google search (n=100 websites), screening for titles and first pages. Including expert input, this resulted in six interventions identified in the scientific literature and 39 interventions via the grey literature. Extracted data included effectiveness, cost effectiveness, theoretical factors, and behavior change techniques used. Results: Overall, many interventions (45 identified) were offered. Of the 45 that we identified, only six that were included in trials provided data on effectiveness. Four of these were shown to be effective and cost effective. In the scientific literature, 83% (5/6) of these interventions included changing attitudes, providing social support, increasing self-efficacy, motivating smokers to make concrete action plans to prepare their attempts to quit and to cope with challenges, supporting identity change and advising on changing routines, coping, and medication use. In all, 50% (3/6) of the interventions included a reward for abstinence. Interventions identified in the grey literature were less consistent, with inclusion of each theoretical factor ranging from 31% to 67% and of each behavior change technique ranging from 28% to 54%. Conclusions: Although the Internet may provide the opportunity to offer various smoking cessation programs, the user is left bewildered as far as efficacy is concerned, as most of these data are not available nor offered to the smokers. Clear regulations about the effectiveness of these interventions need to be devised to avoid disappointment and failed quitting attempts. Thus, there is a need for policy regulations to regulate the proliferation of these interventions and to foster their quality in the Netherlands.Mir