Meta-analysis of cotton fiber quality QTLs across diverse environments in a Gossypium hirsutum x G. barbadense RIL population

<p>Abstract</p> <p>Background</p> <p>Cotton fibers (produced by <it>Gossypium </it>species) are the premier natural fibers for textile production. The two tetraploid species, <it>G. barbadense </it>(Gb) and <it>G. hirsutum </it>(Gh), differ significantly in their fiber properties, the former having much longer, finer and stronger fibers that are highly prized. A better understanding of the genetics and underlying biological causes of these differences will aid further improvement of cotton quality through breeding and biotechnology. We evaluated an inter-specific <it>Gh </it>× <it>Gb </it>recombinant inbred line (RIL) population for fiber characteristics in 11 independent experiments under field and glasshouse conditions. Sites were located on 4 continents and 5 countries and some locations were analyzed over multiple years.</p> <p>Results</p> <p>The RIL population displayed a large variability for all major fiber traits. QTL analyses were performed on a per-site basis by composite interval mapping. Among the 651 putative QTLs (LOD > 2), 167 had a LOD exceeding permutation based thresholds. Coincidence in QTL location across data sets was assessed for the fiber trait categories strength, elongation, length, length uniformity, fineness/maturity, and color. A meta-analysis of more than a thousand putative QTLs was conducted with MetaQTL software to integrate QTL data from the RIL and 3 backcross populations (from the same parents) and to compare them with the literature. Although the global level of congruence across experiments and populations was generally moderate, the QTL clustering was possible for 30 trait x chromosome combinations (5 traits in 19 different chromosomes) where an effective co-localization of unidirectional (similar sign of additivity) QTLs from at least 5 different data sets was observed. Most consistent meta-clusters were identified for fiber color on chromosomes c6, c8 and c25, fineness on c15, and fiber length on c3.</p> <p>Conclusions</p> <p>Meta-analysis provided a reliable means of integrating phenotypic and genetic mapping data across multiple populations and environments for complex fiber traits. The consistent chromosomal regions contributing to fiber quality traits constitute good candidates for the further dissection of the genetic and genomic factors underlying important fiber characteristics, and for marker-assisted selection.</p

Meta-analysis of cotton fiber quality QTLs across diverse environments in a Gossypium hirsutum x G. barbadense RIL population

Background: Cotton fibers (produced by #Gossypium# species) are the premier natural fibers for textile production. The two tetraploid species, #G. barbadense# (Gb) and #G. hirsutum# (Gh), differ significantly in their fiber properties, the former having much longer, finer and stronger fibers that are highly prized. A better understanding of the genetics and underlying biological causes of these differences will aid further improvement of cotton quality through breeding and biotechnology. We evaluated an inter-specific Gh × Gb recombinant inbred line (RIL) population for fiber characteristics in 11 independent experiments under field and glasshouse conditions. Sites were located on 4 continents and 5 countries and some locations were analyzed over multiple years. Results: The RIL population displayed a large variability for all major fiber traits. QTL analyses were performed on a persite basis by composite interval mapping. Among the 651 putative QTLs (LOD &gt; 2), 167 had a LOD exceeding permutation based thresholds. Coincidence in QTL location across data sets was assessed for the fiber trait categories strength, elongation, length, length uniformity, fineness/maturity, and color. A meta-analysis of more than a thousand putative QTLs was conducted with MetaQTL software to integrate QTL data from the RIL and 3 backcross populations (from the same parents) and to compare them with the literature. Although the global level of congruence across experiments and populations was generally moderate, the QTL clustering was possible for 30 trait x chromosome combinations (5 traits in 19 different chromosomes) where an effective co-localization of unidirectional (similar sign of additivity) QTLs from at least 5 different data sets was observed. Most consistent meta-clusters were identified for fiber color on chromosomes c6, c8 and c25, fineness on c15, and fiber length on c3. Conclusions: Meta-analysis provided a reliable means of integrating phenotypic and genetic mapping data across multiple populations and environments for complex fiber traits. The consistent chromosomal regions contributing to fiber quality traits constitute good candidates for the further dissection of the genetic and genomic factors underlying important fiber characteristics, and for marker-assisted selection. (Résumé d'auteur

Bridging health technology assessment (HTA) with multicriteria decision analyses (MCDA): field testing of the EVIDEM framework for coverage decisions by a public payer in Canada

<p>Abstract</p> <p>Background</p> <p>Consistent healthcare decisionmaking requires systematic consideration of decision criteria and evidence available to inform them. This can be tackled by combining multicriteria decision analysis (MCDA) and Health Technology Assessment (HTA). The objective of this study was to field-test a decision support framework (EVIDEM), explore its utility to a drug advisory committee and test its reliability over time.</p> <p>Methods</p> <p>Tramadol for chronic non-cancer pain was selected by the health plan as a case study relevant to their context. Based on extensive literature review, a by-criterion HTA report was developed to provide synthesized evidence for each criterion of the framework (14 criteria for the MCDA Core Model and 6 qualitative criteria for the Contextual Tool). During workshop sessions, committee members tested the framework in three steps by assigning: 1) weights to each criterion of the MCDA Core Model representing individual perspective; 2) scores for tramadol for each criterion of the MCDA Core Model using synthesized data; and 3) qualitative impacts of criteria of the Contextual Tool on the appraisal. Utility and reliability of the approach were explored through discussion, survey and test-retest. Agreement between test and retest data was analyzed by calculating intra-rater correlation coefficients (ICCs) for weights, scores and MCDA value estimates.</p> <p>Results</p> <p>The framework was found useful by the drug advisory committee in supporting systematic consideration of a broad range of criteria to promote a consistent approach to appraising healthcare interventions. Directly integrated in the framework as a "by-criterion" HTA report, synthesized evidence for each criterion facilitated its consideration, although this was sometimes limited by lack of relevant data. Test-retest analysis showed fair to good consistency of weights, scores and MCDA value estimates at the individual level (ICC ranging from 0.676 to 0.698), thus lending some support for the reliability of the approach. Overall, committee members endorsed the inclusion of most framework criteria and revealed important areas of discussion, clarification and adaptation of the framework to the needs of the committee.</p> <p>Conclusions</p> <p>By promoting systematic consideration of all decision criteria and the underlying evidence, the framework allows a consistent approach to appraising healthcare interventions. Further testing and validation are needed to advance MCDA approaches in healthcare decisionmaking.</p

Evidence for multi-fragmentation and mass shedding of boulders on rubble-pile binary asteroid system (65803) Didymos

Asteroids smaller than 10 km are thought to be rubble piles formed from the reaccumulation of fragments produced in the catastrophic disruption of parent bodies. Ground-based observations reveal that some of these asteroids are today binary systems, in which a smaller secondary orbits a larger primary asteroid. However, how these asteroids became binary systems remains unclear. Here, we report the analysis of boulders on the surface of the stony asteroid (65803) Didymos and its moonlet, Dimorphos, from data collected by the NASA DART mission. The size-frequency distribution of boulders larger than 5 m on Dimorphos and larger than 22.8 m on Didymos confirms that both asteroids are piles of fragments produced in the catastrophic disruption of their progenitors. Dimorphos boulders smaller than 5 m have size best-fit by a Weibull distribution, which we attribute to a multi-phase fragmentation process either occurring during coalescence or during surface evolution. The density per km2 of Dimorphos boulders ≥1 m is 2.3x with respect to the one obtained for (101955) Bennu, while it is 3.0x with respect to (162173) Ryugu. Such values increase once Dimorphos boulders ≥5 m are compared with Bennu (3.5x), Ryugu (3.9x) and (25143) Itokawa (5.1x). This is of interest in the context of asteroid studies because it means that contrarily to the single bodies visited so far, binary systems might be affected by subsequential fragmentation processes that largely increase their block density per km2. Direct comparison between the surface distribution and shapes of the boulders on Didymos and Dimorphos suggest that the latter inherited its material from the former. This finding supports the hypothesis that some asteroid binary systems form through the spin up and mass shedding of a fraction of the primary asteroid.This work was supported by the Italian Space Agency (ASI) within the LICIACube project (ASI-INAF agreement n. 2019-31-HH.0) and HERA project (ASI-INAF agreement n. 2022-8-HH.0). This work was also supported by the DART mission, NASA Contract 80MSFC20D0004. S.C. acknowledges funding from the Crosby Distinguished Postdoctoral Fellowship Program of the Department of Earth, Atmospheric and Planetary Science, Massachusetts Institute of Technology. R.N. acknowledges support from NASA/FINESST (NNH20ZDA001N). N.M. and C.R. acknowledge funding support from the European Commission’s Horizon 2020 research and innovation program under grant agreement No 870377 (NEO-MAPP project) and support from the Centre National d’Etudes Spatiales (CNES), focussed on the Hera space mission. S.D.R. acknowledges support from the Swiss National Science Foundation (project number 200021\207359). L.P. contribution was supported by the Margarita Salas postdoctoral grant funded by the Spanish Ministry of Universities—NextGenerationEU and CIAPOS/2022/066 postdoctoral grant (European Social Fund). Ö.K. acknowledges funding support from the PRODEX program managed by the European Space Agency (ESA) with help of the Belgian Science Policy Office (BELSPO). P.M. acknowledges funding support from the French space agency CNES, ESA, and The University of Tokyo

'Excellence' and exclusion:the individual costs of institutional competitiveness

A performance-based funding system like the United Kingdom’s ‘Research Excellence Framework’ (REF) symbolizes the re-rationalization of higher education according to neoliberal ideology and New Public Management technologies. The REF is also significant for disclosing the kinds of behaviour that characterize universities’ response to government demands for research auditability. In this paper, we consider the casualties of what Henry Giroux (2014) calls “neoliberalism’s war on higher education” or more precisely the deleterious consequences of non-participation in the REF. We also discuss the ways with which higher education’s competition fetish, embodied within the REF, affects the instrumentalization of academic research and the diminution of academic freedom, autonomy and criticality

Effects of eight neuropsychiatric copy number variants on human brain structure

Many copy number variants (CNVs) confer risk for the same range of neurodevelopmental symptoms and psychiatric conditions including autism and schizophrenia. Yet, to date neuroimaging studies have typically been carried out one mutation at a time, showing that CNVs have large effects on brain anatomy. Here, we aimed to characterize and quantify the distinct brain morphometry effects and latent dimensions across 8 neuropsychiatric CNVs. We analyzed T1-weighted MRI data from clinically and non-clinically ascertained CNV carriers (deletion/duplication) at the 1q21.1 (n = 39/28), 16p11.2 (n = 87/78), 22q11.2 (n = 75/30), and 15q11.2 (n = 72/76) loci as well as 1296 non-carriers (controls). Case-control contrasts of all examined genomic loci demonstrated effects on brain anatomy, with deletions and duplications showing mirror effects at the global and regional levels. Although CNVs mainly showed distinct brain patterns, principal component analysis (PCA) loaded subsets of CNVs on two latent brain dimensions, which explained 32 and 29% of the variance of the 8 Cohen’s d maps. The cingulate gyrus, insula, supplementary motor cortex, and cerebellum were identified by PCA and multi-view pattern learning as top regions contributing to latent dimension shared across subsets of CNVs. The large proportion of distinct CNV effects on brain morphology may explain the small neuroimaging effect sizes reported in polygenic psychiatric conditions. Nevertheless, latent gene brain morphology dimensions will help subgroup the rapidly expanding landscape of neuropsychiatric variants and dissect the heterogeneity of idiopathic conditions

Dynamiques humaines et organisationnelles entourant les activités d’évaluation des technologies et des modes d’intervention en milieu hospitalier universitaire au Québec

En 1992, le ministère de la Santé et des Services sociaux (MSSS) du Québec faisait de l'évaluation des technologies et modes d'intervention (ETMI), par la Loi sur les services de santé et les services sociaux (LSSSS), l'une des quatre conditions à remplir pour être reconnu comme centre hospitalier universitaire (CHU) ou institut universitaire (IU). Il a fallu attendre les années 2000 pour observer la concrétisation de cette nouvelle mission. En effet, l’importance d’assurer une cohérence et une convergence entre les soins, l’enseignement, la recherche et l’ETMI, ainsi que l’évidence des besoins particuliers des hôpitaux universitaires, ont été reconnus. Ceci a donné lieu à l’élaboration de diverses stratégies d’implantation de l’ETMI, variant d’un établissement à l’autre, et menant à la création des premières unités d'évaluation des technologies et modes d'intervention en santé (UETMI) en milieu hospitalier universitaire québécois. L’ETMI est un processus multidisciplinaire qui utilise des méthodes explicites pour déterminer la valeur de technologies nouvelles ou déjà implantées. L’hôpital universitaire représente un emplacement de choix pour la réalisation des activités d’ETMI puisqu’il s’agit du principal lieu d’accueil des technologies. La réalisation des activités d’ETMI s’y effectue toutefois dans un contexte où producteurs et utilisateurs des connaissances accomplissent leur mandat au sein de la même organisation. Pour bénéficier de manière optimale de l’ETMI, il est nécessaire de bien cerner l’influence de celle-ci. Une étude de cas multiple a été réalisée afin d’analyser et comprendre l’évolution de la concrétisation de la mission d’ETMI dans les CHU. L’analyse stratégique de Crozier et Friedberg (1977) a été retenue comme cadre théorique. Cette thèse présente le contexte organisationnel et les activités d’ETMI de deux CHU. La démarche de recherche qualitative effectuée a permis d’analyser les dynamiques humaines et organisationnelles entourant les activités d’ETMI de ces CHU. Cinq principaux constats ont émergé de l’analyse et supportent l’idée que l’environnement et la pratique évaluative sont d’importants facteurs à prendre en compte lors de la mesure de l’influence de l’ETMI. Les résultats suggèrent également l’intérêt d’opter pour une approche évaluative légitime et juste au bénéfice du bien commun et d’une plus grande influence de l’ETMI. Le secteur de la santé étant en continuelle évolution, d’autres travaux permettant de valider l’approche utilisée dans des contextes distincts ou encore pour des innovations technologiques particulières (p. ex., télésanté), pourront être réalisés dans le futur.In 1992, the Quebec Ministry of Health and Social Services determined, through the Act Respecting Health Services and Social Services, that Health Technology Assessment (HTA) was one of the four conditions to fulfilled to be recognized as a university hospital center (UHC) or a university institute (UI). However, it was necessary to wait until the 2000s to see this new mission adopted by the concerned parties. Indeed, the importance of ensuring consistency and convergence between care, teaching, research and HTA, as well as the obvious needs of UHC, have been recognized. This gave rise to the development of various HTA implementation strategies, varying from one establishment to another, and leading to the creation of the first HTA units in Quebec’s UHC. HTA is a multidisciplinary process that uses explicit methods to determine the value of new or existing technologies. The university hospital is a perfect location to conduct HTA activities considering that they are users of most technologies. However, HTA activities are carried out in a context where knowledge producers and knowledge users fulfill their mandate within the same organization. To benefit optimally from HTA, it is necessary to understand their influence. A multiple case study was conducted in order to analyze and understand the evolution of the HTA activities within UHC. The strategic analysis of Crozier and Friedberg (1977) was chosen as a theoretical framework. This thesis presents the organizational context and HTA activities of two UHC. The qualitative research process which was undertaken gave us the possibility to analyze the human and organizational dynamics surrounding the HTA activities of these UHC. Five main findings emerged from the analysis and support the idea that the environment and the assessment process are important factors to consider when measuring the influence of HTA. The results also suggest the advantage of opting for a legitimate and fair assessment process not only for the benefit of the common good but also to further the influence of HTA. As the health sector is constantly evolving, research to validate the approach used, either in other contexts or for technological innovations (e.g., e-Health), should be carried out in the future.En 1992, le ministère de la Santé et des Services sociaux (MSSS) du Québec faisait de l'évaluation des technologies et modes d'intervention (ETMI), par la Loi sur les services de santé et les services sociaux (LSSSS), l'une des quatre conditions à remplir pour être reconnu comme centre hospitalier universitaire (CHU) ou institut universitaire (IU). Il a fallu attendre les années 2000 pour observer la concrétisation de cette nouvelle mission. En effet, l’importance d’assurer une cohérence et une convergence entre les soins, l’enseignement, la recherche et l’ETMI, ainsi que l’évidence des besoins particuliers des hôpitaux universitaires, ont été reconnus. Ceci a donné lieu à l’élaboration de diverses stratégies d’implantation de l’ETMI, variant d’un établissement à l’autre, et menant à la création des premières unités d'évaluation des technologies et modes d'intervention en santé (UETMI) en milieu hospitalier universitaire québécois. L’ETMI est un processus multidisciplinaire qui utilise des méthodes explicites pour déterminer la valeur de technologies nouvelles ou déjà implantées. L’hôpital universitaire représente un emplacement de choix pour la réalisation des activités d’ETMI puisqu’il s’agit du principal lieu d’accueil des technologies. La réalisation des activités d’ETMI s’y effectue toutefois dans un contexte où producteurs et utilisateurs des connaissances accomplissent leur mandat au sein de la même organisation. Pour bénéficier de manière optimale de l’ETMI, il est nécessaire de bien cerner l’influence de celle-ci. Une étude de cas multiple a été réalisée afin d’analyser et comprendre l’évolution de la concrétisation de la mission d’ETMI dans les CHU. L’analyse stratégique de Crozier et Friedberg (1977) a été retenue comme cadre théorique. Cette thèse présente le contexte organisationnel et les activités d’ETMI de deux CHU. La démarche de recherche qualitative effectuée a permis d’analyser les dynamiques humaines et organisationnelles entourant les activités d’ETMI de ces CHU. Cinq principaux constats ont émergé de l’analyse et supportent l’idée que l’environnement et la pratique évaluative sont d’importants facteurs à prendre en compte lors de la mesure de l’influence de l’ETMI. Les résultats suggèrent également l’intérêt d’opter pour une approche évaluative légitime et juste au bénéfice du bien commun et d’une plus grande influence de l’ETMI. Le secteur de la santé étant en continuelle évolution, d’autres travaux permettant de valider l’approche utilisée dans des contextes distincts ou encore pour des innovations technologiques particulières (p. ex., télésanté), pourront être réalisés dans le futur.In 1992, the Quebec Ministry of Health and Social Services determined, through the Act Respecting Health Services and Social Services, that Health Technology Assessment (HTA) was one of the four conditions to fulfilled to be recognized as a university hospital center (UHC) or a university institute (UI). However, it was necessary to wait until the 2000s to see this new mission adopted by the concerned parties. Indeed, the importance of ensuring consistency and convergence between care, teaching, research and HTA, as well as the obvious needs of UHC, have been recognized. This gave rise to the development of various HTA implementation strategies, varying from one establishment to another, and leading to the creation of the first HTA units in Quebec’s UHC. HTA is a multidisciplinary process that uses explicit methods to determine the value of new or existing technologies. The university hospital is a perfect location to conduct HTA activities considering that they are users of most technologies. However, HTA activities are carried out in a context where knowledge producers and knowledge users fulfill their mandate within the same organization. To benefit optimally from HTA, it is necessary to understand their influence. A multiple case study was conducted in order to analyze and understand the evolution of the HTA activities within UHC. The strategic analysis of Crozier and Friedberg (1977) was chosen as a theoretical framework. This thesis presents the organizational context and HTA activities of two UHC. The qualitative research process which was undertaken gave us the possibility to analyze the human and organizational dynamics surrounding the HTA activities of these UHC. Five main findings emerged from the analysis and support the idea that the environment and the assessment process are important factors to consider when measuring the influence of HTA. The results also suggest the advantage of opting for a legitimate and fair assessment process not only for the benefit of the common good but also to further the influence of HTA. As the health sector is constantly evolving, research to validate the approach used, either in other contexts or for technological innovations (e.g., e-Health), should be carried out in the future

Variant selection during the c-to-ab phase transformation in hot-rolled bainitic TRIP-aided steels

The variant selection phenomenon during the austenite to bainite phase transformation in hot-rolled TRIP-aided steels was quantitatively characterized at the level of individual austenite grains. The reconstruction of the electron backscatter diffraction maps provided evidence that bainite grows by packets of laths sharing a common {1 1 1}y plane in the austenite. The affect of hot deformation is to reduce the number of packets that form. It is suggested that slip activity is important in understanding this effect.<br /