Insights into opium poppy (Papaver spp.) genetic diversity from genotyping-by-sequencing analysis

Opium poppy (Papaver somniferum) is one of the world’s oldest medicinal plants and a versatile model system to study secondary metabolism. However, our knowledge of its genetic diversity is limited, restricting utilization of the available germplasm for research and crop improvement. We used genotyping-by-sequencing to investigate the extent of genetic diversity and population structure in a collection of poppy germplasm consisting of 91 accessions originating in 30 countries of Europe, North Africa, America, and Asia. We identified five genetically distinct subpopulations using discriminate analysis of principal components and STRUCTURE analysis. Most accessions obtained from the same country were grouped together within subpopulations, likely a consequence of the restriction on movement of poppy germplasm. Alkaloid profiles of accessions were highly diverse, with morphine being dominant. Phylogenetic analysis identified genetic groups that were largely consistent with the subpopulations detected and that could be differentiated broadly based on traits such as number of branches and seed weight. These accessions and the associated genotypic data are valuable resources for further genetic diversity analysis, which could include definition of poppy core sets to facilitate genebank management and use of the diversity for genetic improvement of this valuable crop.

The development of the International Classification of Functioning, Disability and Health Core Sets for deafblindness: A study protocol

Background Individuals with deafblindness experience a combination of hearing and vision impairments. The World Health Organization has developed a global framework referred to as the International Classification of Functioning, Disability and Health (ICF) to describe health and functioning. From the full ICF classification, a selection of categories, referred to as ICF Core Sets, provide users with a tool to describe functioning and disability in specific health conditions. There has been no ICF Core Set created for deafblindness. Given that core sets are instrumental in improving clinical practice, research, and service delivery, the aim of this study is to develop an ICF Core Set for deafblindness. Methods As part of the preparatory phase in the ICF Core Set development, there are four studies that will be conducted. This includes the [1] systematic literature review that examines the researcher’s perspective, [2] qualitative study focusing on the individuals with deafblindness experience, [3] experts survey that looks at health professional’s perspective, and [4] empirical study that examines the clinical perspective. The studies will be conducted using the principles outlined by the ICF Research Branch for the development of ICF Core Sets. The systematic literature review protocol was submitted for registration on PROSPERO CRD42021247952. Discussion An ICF Core Set created for deafblindness will benefit individuals living with deafblindness who are often excluded from social participation, policies, and services. An ICF Core Set for deafblindness will have a significant impact on healthcare professionals, policymakers, researchers, service providers and individuals with deafblindness by facilitating communication among all stakeholder to support the functioning of those with deafblindness.

ICF Linking and Cognitive Interviewing Are Complementary Methods for Optimizing Content Validity of Outcome Measures: An Integrated Methods Review

Content validity is a fundamental requirement of outcome measures. After reviewing operational needs and existing definitions, content validity we as defined as: the extent to which a measure provides a comprehensive and true assessment of the key relevant elements of a specified construct or attribute across a defined range, clearly and equitably for a stated target audience and context. ICF linkage rules from 2002, 2005, and 2019 have provide increasingly clear processes for describing and evaluating content of outcome measures. ICF Core Sets provide international reference standards of the core constructs of importance for different health conditions. Both are important as reference standards during content validation. To summarize their use as reference standards, the following summary indicators were proposed: (1) Measure to ICF linkage, (2) Measure to (Brief or Comprehensive) Core Set Absolute Linkage, (3) Measure to (Brief or Comprehensive) Core Set Unique Linkage, (4) Core Set Representation, and (5) Core Set Unique Disability Representation. Methods to assess how respondents engage with content are needed to complement ICF-linking. Cognitive interviewing is an ideal method since it used to explore how respondents interpret and calibrate response to individual items on an outcome measure. We proposed a framework for classifying these responses: Clarity/Comprehension, Relevance, Inadequate response definition, Reference Point, Perspective modification, and Calibration Across Items. Our analysis of 24 manuscripts that used ICF linking for content validation since updated linking rules were published found that authors typically used linking to validate existing measures, involved multiple raters, used 2005 linking rules, summarized content at a concept level (e.g., impairment, activity, participation) and/or use core sets as a reference standard. Infrequently, ICF linking was used to create item pools/conceptual frameworks for new measures, applied the full scope of the 2019 linking rules, used summary indicators, or integrated ICF-linking with qualitative methods like cognitive interviews. We conclude that ICF linkage is a powerful tool for content validity during development or validation of PROM. Best practices include use of updated ICF linking rules, triangulation of ICF linking with participant assessments of clarity and relevance preferably obtained using cognitive interview methods, and application of defined summary indicators.

An Integrated Account of Expert Perspectives on Functioning in Schizophrenia

An integrated and interdisciplinary care system for individuals with schizophrenia is essential, which implies the need for a tool that assesses the difficulties and contextual factors of relevance to their functioning, and facilitates coordinated working across the different professions involved in their care. The International Classification of Functioning, Disability and Health Core Sets (ICF-CS) cover these requirements. This study aimed to evaluate the content validity of the ICF-CSs for schizophrenia from the perspective of experts. Six three-round Delphi studies were conducted with expert panels from different professional backgrounds which have played a significant role in the treatment of individuals with schizophrenia (psychiatry, psychology, nursing, occupational therapy, social work and physiotherapy). In total, 790 experts from 85 different countries participated in the first round. In total, 90 ICF categories and 28 Personal factors reached expert consensus (reached consensus from four or more professional perspectives). All the categories in the brief version of the ICF-CS for schizophrenia reached consensus from all the professional perspectives considered. As for the comprehensive version, 89.7% of its categories reached expert consensus. The results support the worldwide content validity of the ICF-CSs for schizophrenia from an expert perspective and underline the importance of assessing functioning by considering all the components implied.

Measuring Early Childhood Development Among 4–6 Year Olds: The Identification of Psychometrically Robust Items Across Diverse Contexts

The last 15 years have seen an explosion of measurement tools for assessing the development of young children in low- and middle- income countries. This paper builds on and contributes to that literature by identifying a core set of caregiver-report items and a core set of direct assessment items that measure key developmental domains for children aged 4–6 (48–83 months) and that demonstrate adequate psychometric properties across diverse contexts, the first in this age group to the authors' knowledge. Data were harmonized from previous early childhood measurement efforts in 12 countries that all used the same base measurement tool. Data analyses yielded 20 caregiver report items and 84 child direct assessment items (grouped into 16 tasks) that show strong item-level statistics across countries and that cover the domains of early literacy, early numeracy, executive functioning, and social-emotional competencies. Next steps include adding data and items from other measurement tools to the same analytical framework and field testing across a number of contexts and early childhood measurement efforts. The vision is for the resulting core sets of items, along with guidance on data collection, management, and analysis, to serve as global public goods so that they can (i) present a starting point for linking across different early childhood measurement tools for children aged 4–6; (ii) increase quality across measurement efforts; and (iii) facilitate the scale up of early childhood measurement. When supplemented with items that capture local contexts and their measurement needs, these core sets of items should help to advance understanding of universal and context-specific factors that underlie child development and thus help policymakers make decisions that ensure children receive the quality early childhood care and education they need in order to reach their full potential.

Learning from Docked Ligands: Ligand-Based Features Rescue Structure-Based Scoring Functions When Trained On Docked Poses

Machine learning scoring functions for protein-ligand binding affinity have been found to consistently outperform classical scoring functions when trained and tested on crystal structures of bound protein-ligand complexes. However, it is less clear how these methods perform when applied to docked poses of complexes.<br><br>We explore how the use of docked, rather than crystallographic, poses for both training and testing affects the performance of machine learning scoring functions. Using the PDBbind Core Sets as benchmarks, we show that the performance of a structure-based machine learning scoring function trained and tested on docked poses is lower than that of the same scoring function trained and tested on crystallographic poses. We construct a hybrid scoring function by combining both structure-based and ligand-based features, and show that its ability to predict binding affinity using docked poses is comparable to that of purely structure-based scoring functions trained and tested on crystal poses. Despite strong performance on docked poses of the PDBbind Core Sets, we find that our hybrid scoring function fails to generalise to anew data set, demonstrating the need for improved scoring functions and additional validation benchmarks. <br><br>Code and data to reproduce our results are available from https://github.com/oxpig/learning-from-docked-poses.