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Guidance on the assessment of the biological relevance of data in scientific assessments.

ABSTRACT: EFSA requested its Scientific Committee to prepare a guidance document providing generic issues and criteria to consider biological relevance, particularly when deciding on whether an observed effect is of biological relevance, i.e. is adverse (or shows a beneficial health effect) or not. The guidance document provides a general framework for establishing the biological relevance of observations at various stages of the assessment. Biological relevance is considered at three main stages related to the process of dealing with evidence: Development of the assessment strategy. In this context, specification of agents, effects, subjects and conditions in relation to the assessment question(s): Collection and extraction of data; Appraisal and integration of the relevance of the agents, subjects, effects and conditions, i.e. reviewing dimensions of biological relevance for each data set. A decision tree is developed to assist in the collection, identification and appraisal of relevant data for a given specific assessment question to be answered.

SUBMITTER: EFSA Scientific Committee

PROVIDER: S-EPMC7010076 | biostudies-literature | 2017 Aug

REPOSITORIES: biostudies-literature

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Guidance on the assessment of the biological relevance of data in scientific assessments.

Hardy Anthony A Benford Diane D Halldorsson Thorhallur T Jeger Michael John MJ Knutsen Helle Katrine HK More Simon S Naegeli Hanspeter H Noteborn Hubert H Ockleford Colin C Ricci Antonia A Rychen Guido G Schlatter Josef R JR Silano Vittorio V Solecki Roland R Turck Dominique D Younes Maged M Bresson Jean-Louis JL Griffin John J Hougaard Benekou Susanne S van Loveren Henk H Luttik Robert R Messean Antoine A Penninks André A Ru Giuseppe G Stegeman Jan Arend JA van der Werf Wopke W Westendorf Johannes J Woutersen Rudolf Antonius RA Barizzone Fulvio F Bottex Bernard B Lanzoni Anna A Georgiadis Nikolaos N Alexander Jan J

EFSA journal. European Food Safety Authority 20170803 8

EFSA requested its Scientific Committee to prepare a guidance document providing generic issues and criteria to consider biological relevance, particularly when deciding on whether an observed effect is of biological relevance, i.e. is adverse (or shows a beneficial health effect) or not. The guidance document provides a general framework for establishing the biological relevance of observations at various stages of the assessment. Biological relevance is considered at three main stages related ...[more]

PMID: 32625631

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Project description:EFSA Strategy 2027 outlines the need for fit-for-purpose protocols for EFSA generic scientific assessments to aid in delivering trustworthy scientific advice. This EFSA Scientific Committee guidance document helps address this need by providing a harmonised and flexible framework for developing protocols for EFSA generic assessments. The guidance replaces the 'Draft framework for protocol development for EFSA's scientific assessments' published in 2020. The two main steps in protocol development are described. The first is problem formulation, which illustrates the objectives of the assessment. Here a new approach to translating the mandated Terms of Reference into scientifically answerable assessment questions and sub-questions is proposed: the 'APRIO' paradigm (Agent, Pathway, Receptor, Intervention and Output). Owing to its cross-cutting nature, this paradigm is considered adaptable and broadly applicable within and across the various EFSA domains and, if applied using the definitions given in this guidance, is expected to help harmonise the problem formulation process and outputs and foster consistency in protocol development. APRIO may also overcome the difficulty of implementing some existing frameworks across the multiple EFSA disciplines, e.g. the PICO/PECO approach (Population, Intervention/Exposure, Comparator, Outcome). Therefore, although not mandatory, APRIO is recommended. The second step in protocol development is the specification of the evidence needs and the methods that will be applied for answering the assessment questions and sub-questions, including uncertainty analysis. Five possible approaches to answering individual (sub-)questions are outlined: using evidence from scientific literature and study reports; using data from databases other than bibliographic; using expert judgement informally collected or elicited via semi-formal or formal expert knowledge elicitation processes; using mathematical/statistical models; and - not covered in this guidance - generating empirical evidence ex novo. The guidance is complemented by a standalone 'template' for EFSA protocols that guides the users step by step through the process of planning an EFSA scientific assessment.

Project description:BackgroundSingle repetition, contraction-phase specific and total time-under-tension (TUT) are crucial mechano-biological descriptors associated with distinct morphological, molecular and metabolic muscular adaptations in response to exercise, rehabilitation and/or fighting sarcopenia. However, to date, no simple, reliable and valid method has been developed to measure these descriptors.ObjectiveIn this study we aimed to test whether accelerometer data obtained from a standard smartphone placed on the weight stack can be used to extract single repetition, contraction-phase specific and total TUT.MethodsTwenty-two participants performed two sets of ten repetitions of their 60% one repetition maximum with a self-paced velocity on nine commonly used resistance exercise machines. Two identical smartphones were attached on the resistance exercise weight stacks and recorded all user-exerted accelerations. An algorithm extracted the number of repetitions, single repetition, contraction-phase specific and total TUT. All exercises were video-recorded. The TUT determined from the algorithmically-derived mechano-biological descriptors was compared with the video recordings that served as the gold standard. The agreement between the methods was examined using Limits of Agreement (LoA). The association was calculated using the Pearson correlation coefficients and interrater reliability was determined using the intraclass correlation coefficient (ICC 2.1).ResultsThe error rate of the algorithmic detection of single repetitions derived from two smartphones accelerometers was 0.16%. Comparing algorithmically-derived, contraction-phase specific TUT against video, showed a high degree of correlation (r>0.93) for all exercise machines. Agreement between the two methods was high on all exercise machines as follows: LoA ranged from -0.3 to 0.3 seconds for single repetition TUT (0.1% of mean TUT), from -0.6 to 0.3 seconds for concentric contraction TUT (7.1% of mean TUT), from -0.3 to 0.5 seconds for eccentric contraction TUT (4.1% of mean TUT) and from -1.9 to 1.1 seconds for total TUT (0.5% of mean TUT). Interrater reliability for single repetition, contraction-phase specific TUT was high (ICC > 0.99).ConclusionData from smartphone accelerometer derived resistance exercise can be used to validly and reliably extract crucial mechano-biological descriptors. Moreover, the presented multi-analytical algorithmic approach enables researchers and clinicians to reliably and validly report missing mechano-biological descriptors.

Project description:BackgroundWith the rapid increase in genome sequencing projects for non-model organisms, numerous genome assemblies are currently in progress or available as drafts, but not made available as satisfactory, usable genomes. Data quality assessment of genome assemblies is gaining importance not only for people who perform the assembly/re-assembly processes, but also for those who attempt to use assemblies as maps in downstream analyses. Recent studies of the quality control, quality evaluation/ assessment of genome assemblies have focused on either quality control of reads before assemblies or evaluation of the assemblies with respect to their contiguity and correctness. However, correctness assessment depends on a reference and is not applicable for de novo assembly projects. Hence, development of methods providing both post-assembly and pre-assembly quality assessment reports for examining the quality/correctness of de novo assemblies and the input reads is worth studying.ResultsWe present SQUAT, an efficient tool for both pre-assembly and post-assembly quality assessment of de novo genome assemblies. The pre-assembly module of SQUAT computes quality statistics of reads and presents the analysis in a well-designed interface to visualize the distribution of high- and poor-quality reads in a portable HTML report. The post-assembly module of SQUAT provides read mapping analytics in an HTML format. We categorized reads into several groups including uniquely mapped reads, multiply mapped, unmapped reads; for uniquely mapped reads, we further categorized them into perfectly matched, with substitutions, containing clips, and the others. We carefully defined the poorly mapped (PM) reads into several groups to prevent the underestimation of unmapped reads; indeed, a high PM% would be a sign of a poor assembly that requires researchers' attention for further examination or improvements before using the assembly. Finally, we evaluate SQUAT with six datasets, including the genome assemblies for eel, worm, mushroom, and three bacteria. The results show that SQUAT reports provide useful information with details for assessing the quality of assemblies and reads.AvailabilityThe SQUAT software with links to both its docker image and the on-line manual is freely available at https://github.com/luke831215/SQUAT .

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Guidance on the assessment of the biological relevance of data in scientific assessments.

Publications

Guidance on the assessment of the biological relevance of data in scientific assessments.

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