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International Journal of Health Policy... Dec 2021The potential role of the food and beverage industry in addressing diet-related disease is much debated, particularly amidst evidence of the targeted strategies,...
BACKGROUND
The potential role of the food and beverage industry in addressing diet-related disease is much debated, particularly amidst evidence of the targeted strategies, including voluntary self-regulation, used by the industry to influence policy in their favour. At the same time, the need for more comprehensive action to address unhealthy diets has led to a focus on increasing the accountability of different stakeholders. However, there has been limited evaluation of the impact of accountability initiatives on food and beverage company policies and practices. This study evaluated the impact of the BIA-Obesity (Business Impact Assessment - Obesity and population nutrition) Australia Initiative that benchmarked major Australian food and beverage companies on their nutrition-related policies.
METHODS
Evaluation was conducted against the pre-specified logic model for BIA-Obesity and established frameworks for analysing organisational change and corporate political activity. Outcomes evaluated included company engagement with the Initiative, level of media coverage, and impact of the Initiative on company policies and practices based on the perspectives of company representatives. A mixed methods design was employed, including surveys and in-depth interviews with company representatives, and media reports.
RESULTS
Approximately half of invited companies participated in the evaluation of the BIA-Obesity Australia Initiative. A number of company representatives indicated that the Initiative had influenced their company's nutrition policies, strategies, and disclosure practices, and had raised their company's awareness of the importance of addressing nutrition issues.
CONCLUSION
Company representatives perceive benchmarking and accountability initiatives as helpful for provoking improvements in nutrition-related policies and practices in their companies. However, the benefits of these initiatives need to be assessed in the context of the broader political and economic environment. Whilst the focus of accountability initiatives, such as BIA-Obesity, are on industry self-regulation efforts, they can also play an important role in drawing attention to the need for increased government regulation.
Topics: Australia; Benchmarking; Beverages; Food Industry; Humans; Nutrition Policy; Obesity
PubMed: 32861228
DOI: 10.34172/ijhpm.2020.147 -
Nucleic Acids Research Nov 2020Systematic evaluation of genome-wide Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) off-target profiles is a fundamental step for the successful...
Systematic evaluation of genome-wide Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) off-target profiles is a fundamental step for the successful application of the CRISPR system to clinical therapies. Many experimental techniques and in silico tools have been proposed for detecting and predicting genome-wide CRISPR off-target profiles. These techniques and tools, however, have not been systematically benchmarked. A comprehensive benchmark study and an integrated strategy that takes advantage of the currently available tools to improve predictions of genome-wide CRISPR off-target profiles are needed. We focused on the specificity of the traditional CRISPR SpCas9 system for gene knockout. First, we benchmarked 10 available genome-wide off-target cleavage site (OTS) detection techniques with the published OTS detection datasets. Second, taking the datasets generated from OTS detection techniques as the benchmark datasets, we benchmarked 17 available in silico genome-wide OTS prediction tools to evaluate their genome-wide CRISPR off-target prediction performances. Finally, we present the first one-stop integrated Genome-Wide Off-target cleavage Search platform (iGWOS) that was specifically designed for the optimal genome-wide OTS prediction by integrating the available OTS prediction algorithms with an AdaBoost ensemble framework.
Topics: Algorithms; Benchmarking; CRISPR-Cas Systems; Cell Line, Tumor; Computer Simulation; Databases, Genetic; Gene Editing; Gene Knockout Techniques; Genome; Genomics; Humans; Models, Molecular; RNA, Guide, CRISPR-Cas Systems; Whole Genome Sequencing
PubMed: 33137817
DOI: 10.1093/nar/gkaa930 -
Bioinformatics (Oxford, England) Nov 2023Biomedical entity linking (BEL) is the task of grounding entity mentions to a knowledge base (KB). It plays a vital role in information extraction pipelines for the life... (Review)
Review
MOTIVATION
Biomedical entity linking (BEL) is the task of grounding entity mentions to a knowledge base (KB). It plays a vital role in information extraction pipelines for the life sciences literature. We review recent work in the field and find that, as the task is absent from existing benchmarks for biomedical text mining, different studies adopt different experimental setups making comparisons based on published numbers problematic. Furthermore, neural systems are tested primarily on instances linked to the broad coverage KB UMLS, leaving their performance to more specialized ones, e.g. genes or variants, understudied.
RESULTS
We therefore developed BELB, a biomedical entity linking benchmark, providing access in a unified format to 11 corpora linked to 7 KBs and spanning six entity types: gene, disease, chemical, species, cell line, and variant. BELB greatly reduces preprocessing overhead in testing BEL systems on multiple corpora offering a standardized testbed for reproducible experiments. Using BELB, we perform an extensive evaluation of six rule-based entity-specific systems and three recent neural approaches leveraging pre-trained language models. Our results reveal a mixed picture showing that neural approaches fail to perform consistently across entity types, highlighting the need of further studies towards entity-agnostic models.
AVAILABILITY AND IMPLEMENTATION
The source code of BELB is available at: https://github.com/sg-wbi/belb. The code to reproduce our experiments can be found at: https://github.com/sg-wbi/belb-exp.
Topics: Benchmarking; Data Mining; Software; Language; Natural Language Processing
PubMed: 37975879
DOI: 10.1093/bioinformatics/btad698 -
Clinical Psychology Review Aug 2022To estimate treatment refusal and treatment dropout rates for cognitive analytic therapy (CAT) and then benchmark these rates against other psychotherapies. (Meta-Analysis)
Meta-Analysis Review
AIM
To estimate treatment refusal and treatment dropout rates for cognitive analytic therapy (CAT) and then benchmark these rates against other psychotherapies.
METHOD
PROSPERO registration CRD4202017081. Systematic searches found CAT treatment studies reporting treatment refusal and dropout rates. Studies were narratively and quantitatively synthesised in a proportional random-effects meta-analysis and moderator analyses were performed. Secondary analyses compared refusal and dropout rates for CAT versus other psychotherapies via direct comparisons in the original studies and via benchmarking these rates against other acceptability meta-analyses for other psychotherapies.
RESULTS
Thirty-four CAT studies were included in the review. The treatment refusal rate was 15.35% (k = 9, 95% CIs 8.78-23.21). The treatment dropout rate was 18.69% (k = 34, 95% CI's 15.02-22.62). CAT generated significantly lower dropout rates relative to treatment comparators in the original studies (OR = 0.67; 95% CI 0.48-0.93). Country and younger age were significant moderators of dropout rates. CAT had a comparable treatment refusal rate and was towards the lower end of the dropout range when benchmarked against other psychotherapies.
CONCLUSIONS
CAT as a brief and integrative psychotherapy for individuals presenting with typically complex psychological disorders appears a relatively acceptable intervention to patients.
Topics: Benchmarking; Cognition; Humans; Patient Dropouts; Psychotherapy; Treatment Refusal
PubMed: 35914380
DOI: 10.1016/j.cpr.2022.102187 -
Methods of Information in Medicine 2007Benchmarking statements provide a mechanism for making academic standards explicit within a subject area. They allow comparisons between courses to be based on learning... (Review)
Review
OBJECTIVES
Benchmarking statements provide a mechanism for making academic standards explicit within a subject area. They allow comparisons between courses to be based on learning outcomes rather than by defining a curriculum. No such statement has been produced for informatics. In the absence of any established benchmarking statements for informatics a new biomedical informatics course at St. George's has developed a first benchmarking statement - which defines the skills knowledge and understanding a biomedical informatics student should acquire by the time they complete the course.
METHODS
Review of national biomedical science and computing subject benchmarking statements and academic educational objectives and national occupational competencies in informatics.
RESULTS
We have developed a twenty-item benchmarking statement and this is available on-line at: http://www.gpinformatics.org/benchmark2006/. This benchmarking statement includes a definition and justification for all twenty statements. We found international educational objectives and national informatics competencies useful and these are mapped to each one. National subject benchmarks for computing and biomedical science were less useful and have not been systematically mapped.
CONCLUSIONS
Benchmarking the skills, knowledge and understanding that a student should acquire during their course of study may be more useful than setting a standard curriculum. This benchmarking statement is a first step towards defining the learning outcomes and competencies a student of this discipline should acquire. The international informatics community should consider moving from a standard curriculum to an agreed subject benchmarking statement for medical, health and biomedical informatics.
Topics: Benchmarking; Medical Informatics; United States
PubMed: 17694230
DOI: 10.1160/me0442 -
Journal of Hepatology Feb 2022The concept of benchmarking is established in the field of transplant surgery; however, benchmark values for donation after circulatory death (DCD) liver transplantation...
BACKGROUND & AIMS
The concept of benchmarking is established in the field of transplant surgery; however, benchmark values for donation after circulatory death (DCD) liver transplantation are not available. Thus, we aimed to identify the best possible outcomes in DCD liver transplantation and to propose outcome reference values.
METHODS
Based on 2,219 controlled DCD liver transplantations, collected from 17 centres in North America and Europe, we identified 1,012 low-risk, primary, adult liver transplantations with a laboratory MELD score of ≤20 points, receiving a DCD liver with a total donor warm ischemia time of ≤30 minutes and asystolic donor warm ischemia time of ≤15 minutes. Clinically relevant outcomes were selected and complications were reported according to the Clavien-Dindo-Grading and the comprehensive complication index (CCI). Corresponding benchmark cut-offs were based on median values of each centre, where the 75-percentile was considered.
RESULTS
Benchmark cases represented between 19.7% and 75% of DCD transplantations in participating centres. The 1-year retransplant and mortality rates were 4.5% and 8.4% in the benchmark group, respectively. Within the first year of follow-up, 51.1% of recipients developed at least 1 major complication (≥Clavien-Dindo-Grade III). Benchmark cut-offs were ≤3 days and ≤16 days for ICU and hospital stay, ≤66% for severe recipient complications (≥Grade III), ≤16.8% for ischemic cholangiopathy, and ≤38.9 CCI points 1 year after transplant. Comparisons with higher risk groups showed more complications and impaired graft survival outside the benchmark cut-offs. Organ perfusion techniques reduced the complications to values below benchmark cut-offs, despite higher graft risk.
CONCLUSIONS
Despite excellent 1-year survival, morbidity in benchmark cases remains high. Benchmark cut-offs targeting morbidity parameters offer a valid tool to assess the protective value of new preservation technologies in higher risk groups and to provide a valid comparator cohort for future clinical trials.
LAY SUMMARY
The best possible outcomes after liver transplantation of grafts donated after circulatory death (DCD) were defined using the concept of benchmarking. These were based on 2,219 liver transplantations following controlled DCD donation in 17 centres worldwide. Donor and recipient combinations with higher risk had significantly worse outcomes. However, the use of novel organ perfusion technology helped high-risk patients achieve similar outcomes as the benchmark cohort.
Topics: Aged; Area Under Curve; Benchmarking; Cohort Studies; Female; Humans; Kaplan-Meier Estimate; Liver Transplantation; Male; Middle Aged; Organ Dysfunction Scores; Outcome Assessment, Health Care; Postoperative Complications; Proportional Hazards Models; ROC Curve; Shock; Tissue and Organ Procurement
PubMed: 34655663
DOI: 10.1016/j.jhep.2021.10.004 -
Journal of Rehabilitation Medicine Oct 2022The European Academy of Rehabilitation Medicine (EARM) held a debate in Hannover, Germany, on 1st of September 2016 on the pros and cons of randomized controlled...
Pros and Cons of Randomized Controlled Trials and Benchmarking Controlled Trials in Rehabilitation: An Academic Debate within the European Academy of Rehabilitation Medicine.
The European Academy of Rehabilitation Medicine (EARM) held a debate in Hannover, Germany, on 1st of September 2016 on the pros and cons of randomized controlled trials (RCTs) and observational effectiveness studies (benchmarking controlled trials; BCTs). The debate involved a chairperson, a person presenting the substance of the debate, an opponent, and a rapporteur. The academicians participated in the discussion. Eight propositions and proposed statements formed the substance of the debate. There was agreement that a study question should be the starting point of an effectiveness study, and not the study method, i.e. RCT or BCT. The term "benchmarking" was questioned: does it mean market-oriented medicine? It was clarified that benchmarking refers to the methodological features of this study design: there must always be a comparison between peers. It was agreed that BCTs might be better than RCTs for use in rehabilitation studies, in which one often needs multi-centred studies, such as in the assessment of the effectiveness of pathways when there is complexity of processes, health systems, organizational issues, structures and facilities; or where interactions between therapists, doctors and patients differ between centres; and when assessing the implementation of rehabilitation. In addition, BCTs may deal with ethical issues, e.g. the acceptability of interventions, more easily than RCTs. Recommendations regarding the different approaches (RCTs or BCTs) should be provided by the scientific rehabilitation societies. Concern over the validity of BCTs was considered justified, as the validity criteria of BCTs cover all those related to RCTs and include the risk of selection bias between treatment arms. Appropriate description of the essentials of the study object, including adequate description of how the interventions were actualized in comparison to the study plan, are essential features for a valid and generalizable study for both RCTs and BCTs. BCTs are necessary to widen the evidence-base of effectiveness in rehabilitation. It was suggested that the rehabilitation field should support the concept of BCTs. It was proposed that education regarding BCTs is indicated, and stakeholders need to be convinced that BCTs are a valid alternative to RCTs. EARM and other physical and rehabilitation medicine (PRM) bodies could advance the use of BCTs for clinical and health policy decision-making.
Topics: Benchmarking; Germany; Humans; Physical and Rehabilitation Medicine; Randomized Controlled Trials as Topic
PubMed: 35797064
DOI: 10.2340/jrm.v54.2511 -
Genome Biology Dec 2019Insufficient performance of optimization-based approaches for the fitting of mathematical models is still a major bottleneck in systems biology. In this article, the... (Review)
Review
Insufficient performance of optimization-based approaches for the fitting of mathematical models is still a major bottleneck in systems biology. In this article, the reasons and methodological challenges are summarized as well as their impact in benchmark studies. Important aspects for achieving an increased level of evidence for benchmark results are discussed. Based on general guidelines for benchmarking in computational biology, a collection of tailored guidelines is presented for performing informative and unbiased benchmarking of optimization-based fitting approaches. Comprehensive benchmark studies based on these recommendations are urgently required for the establishment of a robust and reliable methodology for the systems biology community.
Topics: Benchmarking; Models, Biological; Systems Biology
PubMed: 31842943
DOI: 10.1186/s13059-019-1887-9 -
Journal of Infection and Public Health Oct 2013Growing numbers of healthcare facilities are routinely collecting standardized data on healthcare-associated infection (HAI), which can be used not only to track... (Review)
Review
Growing numbers of healthcare facilities are routinely collecting standardized data on healthcare-associated infection (HAI), which can be used not only to track internal performance but also to compare local data to national and international benchmarks. Benchmarking overall (crude) HAI surveillance metrics without accounting or adjusting for potential confounders can result in misleading conclusions. Methods commonly used to provide risk-adjusted metrics include multivariate logistic regression analysis, stratification, indirect standardization, and restrictions. The characteristics of recognized benchmarks worldwide, including the advantages and limitations are described. The choice of the right benchmark for the data from the Gulf Cooperation Council (GCC) states is challenging. The chosen benchmark should have similar data collection and presentation methods. Additionally, differences in surveillance environments including regulations should be taken into consideration when considering such a benchmark. The GCC center for infection control took some steps to unify HAI surveillance systems in the region. GCC hospitals still need to overcome legislative and logistic difficulties in sharing data to create their own benchmark. The availability of a regional GCC benchmark may better enable health care workers and researchers to obtain more accurate and realistic comparisons.
Topics: Benchmarking; Communicable Disease Control; Cross Infection; Epidemiologic Methods; Humans; Topography, Medical
PubMed: 23999329
DOI: 10.1016/j.jiph.2013.05.001 -
International Journal of Medical... Feb 2015This review aimed to provide a comprehensive overview of the current state of evidence for the use of clinical and quality dashboards in health care environments. (Review)
Review
AIM
This review aimed to provide a comprehensive overview of the current state of evidence for the use of clinical and quality dashboards in health care environments.
METHODS
A literature search was performed for the dates 1996-2012 on CINAHL, Medline, Embase, Cochrane Library, PsychInfo, Science Direct and ACM Digital Library. A citation search and a hand search of relevant papers were also conducted.
RESULTS
One hundred and twenty two full text papers were retrieved of which 11 were included in the review. There was considerable heterogeneity in implementation setting, dashboard users and indicators used. There was evidence that in contexts where dashboards were easily accessible to clinicians (such as in the form of a screen saver) their use was associated with improved care processes and patient outcomes.
CONCLUSION
There is some evidence that implementing clinical and/or quality dashboards that provide immediate access to information for clinicians can improve adherence to quality guidelines and may help improve patient outcomes. However, further high quality detailed research studies need to be conducted to obtain evidence of their efficacy and establish guidelines for their design.
Topics: Benchmarking; Humans; Management Information Systems; Patient Care; Process Assessment, Health Care; Quality Assurance, Health Care
PubMed: 25453274
DOI: 10.1016/j.ijmedinf.2014.10.001