Essential guidelines for computational method benchmarking

In computational biology and other sciences, researchers are frequently faced with a choice between several computational methods for performing data analyses. Benchmarking studies aim to rigorously compare the performance of different methods using well-characterized benchmark datasets, to determine the strengths of each method or to provide recommendations regarding suitable choices of methods for an analysis. However, benchmarking studies must be carefully designed and implemented to provide accurate, unbiased, and informative results. Here, we summarize key practical guidelines and recommendations for performing high-quality benchmarking analyses, based on our experiences in computational biology.Comment: Minor update

Essential guidelines for computational method benchmarking

In computational biology and other sciences, researchers are frequently faced with a choice between several computational methods for performing data analyses. Benchmarking studies aim to rigorously compare the performance of different methods using well-characterized benchmark datasets, to determine the strengths of each method or to provide recommendations regarding suitable choices of methods for an analysis. However, benchmarking studies must be carefully designed and implemented to provide accurate, unbiased, and informative results. Here, we summarize key practical guidelines and recommendations for performing high-quality benchmarking analyses, based on our experiences in computational biology

Diagnosis in vascular dementia, applying ‘Cochrane diagnosis rules’ to ‘dementia diagnostic tools’

In this issue of Clinical Science, Biesbroek and colleagues describe recent work on magnetic resonance imaging (MRI)-based cerebral lesion location and its association with cognitive decline. The authors conclude that diagnostic neuroimaging in dementia should shift from whole-brain evaluation to focused quantitative analysis of strategic brain areas. This commentary uses the review of lesion location mapping to discuss broader issues around studies of dementia test strategies. We draw upon work completed by the Cochrane Dementia and Cognitive Improvement Group designed to improve design, conduct and reporting of dementia biomarker studies

Effects of physical exercise on adiponectin, leptin, and inflammatory markers in childhood obesity: systematic review and meta-analysis

Background: New findings on adipose tissue physiology and obesity-Associated inflammation status suggest that modification of the adipokine level can be relevant for the long-Term prevention of obesity-Associated chronic disease. Objectives: The scope of the present study was to investigate the effectiveness of physical exercise in reducing the systemic inflammation related to obesity in children. Methods: We conducted a systematic review with meta-Analysis of controlled randomized trials, identified through electronic database search, which investigated the effect of physical exercise, without concomitant dietary intervention, on adiponectin, leptin, and/or other inflammatory markers in children up to age 18 years with a body mass index greater than the 95th percentile for age and sex. Results: Seven trials were included in the meta-Analysis, with a total of 250 participants. Compared with the control group without any lifestyle modification, the physical exercise resulted in a reduction in leptin [standardized mean difference (SMD)-1.13; 95% confidence interval (95%CI):-1.89 to-0.37; I2 = 79.9%] and interleukin-6 (SMD-0.84; 95%CI:-1.45 to-0.23, I2 = 0.9%) and an increase in adiponectin plasma concentration (SMD 0.69; 95%CI: 0.02-1.35; I2 = 74.3%). Conclusions: These results indicate that physical exercise improved the inflammatory state in children with obesity. It is unclear whether this effect can reduce the risk of cardiovascular and metabolic disease in adulthood. Clinical trials with a uniform intervention protocol and outcome measurements are required to put our knowledge on adipose tissue biology into a clinical perspective

Towards the Development of a Simulator for Investigating the Impact of People Management Practices on Retail Performance

Often models for understanding the impact of management practices on retail performance are developed under the assumption of stability, equilibrium and linearity, whereas retail operations are considered in reality to be dynamic, non-linear and complex. Alternatively, discrete event and agent-based modelling are approaches that allow the development of simulation models of heterogeneous non-equilibrium systems for testing out different scenarios. When developing simulation models one has to abstract and simplify from the real world, which means that one has to try and capture the 'essence' of the system required for developing a representation of the mechanisms that drive the progression in the real system. Simulation models can be developed at different levels of abstraction. To know the appropriate level of abstraction for a specific application is often more of an art than a science. We have developed a retail branch simulation model to investigate which level of model accuracy is required for such a model to obtain meaningful results for practitioners.Comment: 24 pages, 7 figures, 6 tables, Journal of Simulation 201

Use of nonintrusive sensor-based information and communication technology for real-world evidence for clinical trials in dementia

Cognitive function is an important end point of treatments in dementia clinical trials. Measuring cognitive function by standardized tests, however, is biased toward highly constrained environments (such as hospitals) in selected samples. Patient-powered real-world evidence using information and communication technology devices, including environmental and wearable sensors, may help to overcome these limitations. This position paper describes current and novel information and communication technology devices and algorithms to monitor behavior and function in people with prodromal and manifest stages of dementia continuously, and discusses clinical, technological, ethical, regulatory, and user-centered requirements for collecting real-world evidence in future randomized controlled trials. Challenges of data safety, quality, and privacy and regulatory requirements need to be addressed by future smart sensor technologies. When these requirements are satisfied, these technologies will provide access to truly user relevant outcomes and broader cohorts of participants than currently sampled in clinical trials

Development and selection of operational management strategies to achieve policy objectives

Since the reform of the EU Common Fisheries Policy in 2002, effort has been devoted to addressing the governance, scientific, social and economic issues required to introduce an ecosystem approach to fisheries management (EAFM) in Europe. Fisheries management needs to support the three pillars of sustainability (ecological, social and economic) and Fisheries Ecosystem Plans (FEPs) have been developed as a tool to assist managers considering the ecological, social and economic implications of their decision. Building upon previous studies (e.g. the FP5-funded European Fisheries Ecosystem Plan project), the core concept of the Making the European Fisheries Ecosystem Plan Operational (MEFEPO) project is to deliver operational frameworks (FEPs) for three regional seas. The project focus is on how best to make current institutional frameworks responsive to an EAFM at regional and pan-European levels in accordance with the principles of good governance. The regional seas selected for the project are the North Sea (NS), North Western Waters (NWW) and South Western Waters (SWW) RAC regions. The aim of this work package (WP5) was to develop operational objectives to achieve the ecological objectives identified for the 3 regional seas in WP2. This report describes the development and implementation of a transparent and formal process that should lead to identification of the “best” operational management strategies for an EAFM, based on sound scientific information and stakeholder involvement (e.g. regional industry groups, citizen groups, managers and other interest groups)