Faster Family-wise Error Control for Neuroimaging with a Parametric Bootstrap

In neuroimaging, hundreds to hundreds of thousands of tests are performed across a set of brain regions or all locations in an image. Recent studies have shown that the most common family-wise error (FWE) controlling procedures in imaging, which rely on classical mathematical inequalities or Gaussian random field theory, yield FWE rates that are far from the nominal level. Depending on the approach used, the FWER can be exceedingly small or grossly inflated. Given the widespread use of neuroimaging as a tool for understanding neurological and psychiatric disorders, it is imperative that reliable multiple testing procedures are available. To our knowledge, only permutation joint testing procedures have been shown to reliably control the FWER at the nominal level. However, these procedures are computationally intensive due to the increasingly available large sample sizes and dimensionality of the images, and analyses can take days to complete. Here, we develop a parametric bootstrap joint testing procedure. The parametric bootstrap procedure works directly with the test statistics, which leads to much faster estimation of adjusted \emph{p}-values than resampling-based procedures while reliably controlling the FWER in sample sizes available in many neuroimaging studies. We demonstrate that the procedure controls the FWER in finite samples using simulations, and present region- and voxel-wise analyses to test for sex differences in developmental trajectories of cerebral blood flow

Evaluation du pouvoir disjonctif des variables catégorielles impliquées dans la sélection du palmier à huile (Elaeis guineensis jacq.) en Côte d’Ivoire

En amélioration génétique du palmier à huile (Elaeis guineensis Jacq.), les variables catégorielles constituent une part majoritaire de l’information utilisée pour différencier, les populations de géniteurs issus du programme de sélection récurrente réciproque (SRR). Le pouvoir disjonctif de ces variables a été testé sur 134 géniteurs sélectionnés issus des populations du premier, deuxième et troisième cycle de SRR. Les variables catégorielles utilisées pour différencier ces populations sont celles qui ont permis d’avoir des informations sur les origines géographiques et les généalogies parentales des géniteurs. L’analyse factorielle de l’ensemble de ces variables catégorielles, a permis de déterminer le pouvoir disjonctif de chacun des deux principaux critères de divergences des populations de géniteurs sélectionnes. Le critère "origine géographique" a représenté 14 % d’expression de disjonction totale des populations de géniteurs sélectionnés. Le critère "généalogie parentale" a représenté 70 % d’expression de disjonction totale des populations de géniteurs sélectionnés. L’utilisation de ces deux critères de différenciation des populations de géniteurs sélectionnées peut constituer une bonne alternative à l’utilisation des données moléculaires dans les études de la diversité des populations de palmier à huile en sélection.Mots-clés : Palmier à huile, sélection, variable catégorielle, disjonction de populatio

Blame framing and prior knowledge influence moral judgments for people involved in the Tulsa Race Massacre among a combined Oklahoma and UK sample

IntroductionHow an event is framed impacts how people judge the morality of those involved, but prior knowledge can influence information processing about an event, which also can impact moral judgments. The current study explored how blame framing and self-reported prior knowledge of a historical act of racial violence, labeled as Riot, Massacre, or Event, impacted individual’s cumulative moral judgments regarding the groups involved in the Tulsa Race Massacre (Black Tulsans, the Tulsa Police, and White Tulsans).Methods and resultsThis study was collected in two cohorts including undergraduates attending the University of Oklahoma and individuals living in the United Kingdom. Participants were randomly assigned to a blame framing condition, read a factual summary of what happened in Tulsa in 1921, and then responded to various moral judgment items about each group. Individuals without prior knowledge had higher average Likert ratings (more blame) toward Black Tulsans and lower average Likert ratings (less blame) toward White Tulsans and the Tulsa Police compared to participants with prior knowledge. This finding was largest when what participants read was framed as a Massacre rather than a Riot or Event. We also found participants with prior knowledge significantly differed in how they made moral judgments across target groups; those with prior knowledge had lower average Likert ratings (less blame) for Black Tulsans and higher average Likert ratings (more blame) for White Tulsans on items pertaining to causal responsibility, intentionality, and punishment compared to participants without prior knowledge.DiscussionFindings suggest that the effect of blame framing on moral judgments is dependent on prior knowledge. Implications for how people interpret both historical and new events involving harmful consequences are discussed

Trends and seasonal variability in ammonia across major biomes in western and central Africa inferred from long-term series of ground-based and satellite measurements

Ammonia (NH3) is the most abundant alkaline component in the atmosphere. Changes in NH3 concentrations have important implications for atmospheric chemistry, air quality, and ecosystem integrity. We present a long-term ammonia (NH3) assessment in the western and central African regions within the framework of the International Network to study Deposition and Atmospheric chemistry in Africa (INDAAF) programme. We analyse seasonal variations and trends in NH3 concentrations and total column densities along an African ecosystem transect spanning dry savannas in Banizoumbou, Niger, and Katibougou, Mali; wet savannas in Djougou, Benin, and Lamto, Côte d'Ivoire; and forests in Bomassa, Republic of the Congo, and Zoétélé, Cameroon. We use a 21-year record of observations (1998–2018) from INDAAF passive samplers and an 11-year record of observations (2008–2018) of atmospheric vertical column densities from the Infrared Atmospheric Sounding Interferometer (IASI) to evaluate NH3 ground-based concentrations and total column densities, respectively. Climatic data (air temperature, rainfall amount, and leaf area index), as well as ammonia emission data of biomass combustion from the fourth version of the Global Fire Emissions Database (GFED4) and anthropogenic sources from the Community Emissions Data System (CEDS), were compared with total NH3 concentrations and total columns over the same periods. Annual mean ground-based NH3 concentrations are around 5.7–5.8 ppb in dry savannas, 3.5–4.7 ppb in wet savannas, and 3.4–5.6 ppb in forests. Annual IASI NH3 total column densities are 10.0–10.7 × 1015 molec. cm−2 in dry savanna, 16.0–20.9 × 1015 molec. cm−2 in wet savanna, and 12.4–13.8 × 1015 molec. cm−2 in forest stations. Non-parametric statistical Mann–Kendall trend tests applied to annual data show that ground-based NH3 concentrations increase at Bomassa (+2.56 % yr−1) but decrease at Zoétélé (−2.95 % yr−1) over the 21-year period. The 11-year period of IASI NH3 total column density measurements show yearly increasing trends at Katibougou (+3.46 % yr−1), Djougou (+2.24 % yr−1), and Zoétélé (+3.42 % yr−1). From the outcome of our investigation, we conclude that air temperature, leaf area index, and rainfall combined with biomass burning, agricultural, and residential activities are the key drivers of atmospheric NH3 in the INDAAF stations. The results also show that the drivers of trends are (1) agriculture in the dry savanna of Katibougou; (2) air temperature and agriculture in the wet savanna of Djougou and Lamto; and (3) leaf area index, air temperature, residential, and agriculture in the forest of Bomassa.</p

QTL detection by multi-parent linkage mapping in oil palm (Elaeis guineensis Jacq.)

A quantitative trait locus (QTL) analysis designed for a multi-parent population was carried out and tested in oil palm (Elaeis guineensis Jacq.), which is a diploid cross-fertilising perennial species. A new extension of the MCQTL package was especially designed for crosses between heterozygous parents. The algorithm, which is now available for any allogamous species, was used to perform and compare two types of QTL search for small size families, within-family analysis and across-family analysis, using data from a 2 × 2 complete factorial mating experiment involving four parents from three selected gene pools. A consensus genetic map of the factorial design was produced using 251 microsatellite loci, the locus of the Sh major gene controlling fruit shell presence, and an AFLP marker of that gene. A set of 76 QTLs involved in 24 quantitative phenotypic traits was identified. A comparison of the QTL detection results showed that the across-family analysis proved to be efficient due to the interconnected families, but the family size issue is just partially solved. The identification of QTL markers for small progeny numbers and for marker-assisted selection strategies is discussed

Molecular variability from two selection of BRT10 population in an inbreeding program of oil palm (Elaeis guineensis Jacq.) in Côte d’Ivoire

Genetic variability of two groups of palms composed with four progenies selected in BRT10 improved populations resulting from successive self-fertilizations of two parents LM2T and LM10T was studiedusing four polymorphic microsatellites DNA markers of Elaeis guineensis Jacq. The molecular variability of those progenies was analyzed and genetic diversity of each group of palms was deduced.The results of analysis of molecular variance revealed that 59.68% of variance can be explained by palms within each progeny, while 31.24% of total variance was partitioned between the two groups ofpalms. The program selection of self-fertilizations has created a distinct molecular structure within BRT10 improved populations resulting from LM2T and LM10T. Molecular analysis showed that thepartitioning of variance in this breeding program was higher among palms within each progeny than among the two groups of palms. Only the exploitation of molecular data revealed the truly diversifiedprogeny. The use of molecular data analysis in support with agro-morphological assessment should improve the cross performance while maintaining the genetic variation for further progress insubsequent selection cycles

Modelling land–atmosphere daily exchanges of NO, NH₃, and CO₂ in a semi-arid grazed ecosystem in Senegal

Three different models (STEP–GENDEC–NOflux, Zhang2010, and Surfatm) are used to simulate NO, CO2, and NH3 fluxes at the daily scale for 2 years (2012–2013) in a semi-arid grazed ecosystem at Dahra (15∘24′10′′&thinsp;N, 15∘25′56′′&thinsp;W, Senegal, Sahel). Model results are evaluated against experimental results acquired during three field campaigns. At the end of the dry season, when the first rains re-wet the dry soils, the model STEP–GENDEC–NOflux simulates the sudden mineralization of buried litter, leading to pulses in soil respiration and NO fluxes. The contribution of wet season fluxes of NO and CO2 to the annual mean is respectively 51&thinsp;% and 57&thinsp;%. NH3 fluxes are simulated by two models: Surfatm and Zhang2010. During the wet season, air humidity and soil moisture increase, leading to a transition between low soil NH3 emissions (which dominate during the dry months) and large NH3 deposition on vegetation during wet months. Results show a great impact of the soil emission potential, a difference in the deposition processes on the soil and the vegetation between the two models with however a close agreement of the total fluxes. The order of magnitude of NO, NH3, and CO2 fluxes is correctly represented by the models, as well as the sharp transitions between seasons, specific to the Sahel region. The role of soil moisture in flux magnitude is highlighted, whereas the role of soil temperature is less obvious. The simultaneous increase in NO and CO2 emissions and NH3 deposition at the beginning of the wet season is attributed to the availability of mineral nitrogen in the soil and also to microbial processes, which distribute the roles between respiration (CO2 emissions), nitrification (NO emissions), volatilization, and deposition (NH3 emission/deposition). The objectives of this study are to understand the origin of carbon and nitrogen compounds exchanges between the soil and the atmosphere and to quantify these exchanges on a longer timescale when only a few measurements have been performed.</p

Assessment of various strategies for the preservation of clonal genetic resources in oil-palm (Elaeis guineensis Jacq.)

Three different approaches for the preservation of oil palm (Elaeis guineensis Jacq.) clonal genetic resources and their impacts on the induction of the « mantled » somaclonal variation were assessed. In vitro long term preservation of somatic embryos stock-cultures was studied : after a 5 year cultivation period, 75 % of clonal lines were still normal. Between 8 and 13 years of embryo cultures, half of the considered clonal lines were found to be « mantled ». Finally, 40 % were found to be normal over 15 years of in vitro conservation. Clonal conformity of ramets resulting from the re-cloning of somaplants depended, on one hand, on the floral status of the mother plant at the time of sampling and, on the other hand, on its origin. Re-cloning of abnormal regenerants led, in all cases, to 100 % abnormal offspring. The age of the ramet used as mother palm at the time of sampling was found to be critical for true-to-type regeneration. There is a high risk of obtaining variant regenerant palms if the clonal mother palm is sampled at nursery stage. Field observations carried out on palms originating from somatic embryos cryopreserved at -196 °C showed floral conformity rates comparable to those obtained from standard not-cryopreserved clonal palms, for 6 out of the 8 clonal lines studied. From the 2 remaining clonal lines, a few regenerant palms originating from standard batch were found to be « mantled », whereas those resulting from cryopreserved embryos were all normal. The assumption of changes in levels of genomic DNA methylation during preservation was discussed, together with the capacity of our cryopreservation protocol to select embryogenic cells which were only suited to trueto- type regeneration.Trois approches de conservation des ressources génétiques clonales de palmier à huile (Elaeis guineensis Jacq.) ont été testées et leurs incidences sur l\'induction de la variation somaclonale « mantled » ont été évaluées. La conservation in vitro à long terme des souches d\'embryons somatiques a montré qu\'après 5 ans de culture, 75 % des clones étaient encore normaux. Entre 8 et 13 ans de culture, la moitié des clones a présenté des plants à floraison anormale « mantled ». Finalement, 40 % des clones étaient toujours normaux même après 15 ans de conservation in vitro. La conformité florale des plants issus de reclonage de vitroplants dépend, d\'une part, du statut floral du palmier donneur au moment de son utilisation et, d\'autre part ,de l\'origine de la lignée clonale à laquelle il appartient. Le reclonage de régénérants anormaux a conduit, dans tous les cas, à 100 % de descendances anormales. L\'âge du vitro plant donneur au moment de son prélèvement semble être essentiel pour l\'obtention d\'une régénération conforme. Un grand risque d\'obtention de régénérants variants existe si le plant utilisé est prélevé au stade pépinière. Les observations réalisées sur les palmiers issus d\'embryons cryoconservés à -196 °C ont montré des taux de conformité florale comparables à ceux issus d\'embryons témoins non congelés, pour 6 des 8 clones étudiés. Pour les 2 autres clones, quelques plants issus d\'embryons témoins ont présenté la variation florale « mantled », alors que ceux issus d\'embryons cryo-conservés ont tous été normaux. L\'hypothèse d\'une modification du niveau de méthylation de l\'ADN génomique au cours de la durée de la conservation a été discutée et la capacité de notre protocole de cryoconservation à sélectionner les cellules embryogènes aptes à une régénération conforme de plants. Keywords:In situ preservation, « mantled » floral abnormality, somaclonal variation, somatic embryogenesis, oil palm, Côte d\'IvoireAgronomie Africaine Vol. 18 (3) 2006: pp. 187-20