Semantic Segmentation of Sorghum Using Hyperspectral Data Identifies Genetic Associations

This study describes the evaluation of a range of approaches to semantic segmentation of hyperspectral images of sorghum plants, classifying each pixel as either nonplant or belonging to one of the three organ types (leaf, stalk, panicle). While many current methods for segmentation focus on separating plant pixels from background, organ-specific segmentation makes it feasible to measure a wider range of plant properties. Manually scored training data for a set of hyperspectral images collected from a sorghum association population was used to train and evaluate a set of supervised classification models. Many algorithms show acceptable accuracy for this classification task. Algorithms trained on sorghum data are able to accurately classify maize leaves and stalks, but fail to accurately classify maize reproductive organs which are not directly equivalent to sorghum panicles. Trait measurements extracted from semantic segmentation of sorghum organs can be used to identify both genes known to be controlling variation in a previously measured phenotypes (e.g., panicle size and plant height) as well as identify signals for genes controlling traits not previously quantified in this population (e.g., stalk/leaf ratio). Organ level semantic segmentation provides opportunities to identify genes controlling variation in a wide range of morphological phenotypes in sorghum, maize, and other related grain crops

Morphometric discrimination of two sympatric sibling species in the Palaearctic region, Culicoides obsoletus Meigen and C-scoticus Downes & Kettle (Diptera: Ceratopogonidae), vectors of bluetongue and Schmallenberg viruses

Background Some Palaearctic biting midge species (subgenus Avaritia) have been implicated as vectors of bluetongue virus in northern Europe. Separation of two species (C. obsoletus and C. scoticus) is considered difficult morphologically and, often, these female specimens are grouped in entomological studies. However, species-specific identification is desirable to understand their life history characteristics, assess their roles in disease transmission or measure their abundance during arboviral outbreaks. This study aims to investigate whether morphometric identification techniques can be applied to female C. obsoletus and C. scoticus individuals trapped at different geographical regions and time periods during the vector season. Methods C. obsoletus and C. scoticus were collected using light-suction traps from the UK, France and Spain, with two geographical locations sampled per country. A total of 759 C. obsoletus/C. scoticus individuals were identified using a molecular assay based on the cytochrome c oxidase subunit I gene. Fifteen morphometric measurements were taken from the head, wings and abdomen of slide-mounted specimens, and ratios calculated between these measurements. Multivariate analyses explored whether a combination of morphometric variables could lead to accurate species identification. Finally, Culicoides spp. collected in France at the start, middle and end of the adult vector season were compared, to determine whether seasonal variation exists in any of the morphometric measurements. Results The principal component analyses revealed that abdominal characteristics: length and width of the smaller and larger spermathecae, and the length of the chitinous plates and width between them, are the most reliable morphometric characteristics to differentiate between the species. Seasonal variation in the size of each species was observed for head and wing measurements, but not abdominal measurements. Geographical variation in the size of Culicoides spp. was also observed and is likely to be related to temperature at the trapping sites, with smaller individuals trapped at more southern latitudes. Conclusions Our results suggest that female C. obsoletus and C. scoticus individuals can be separated under a stereomicroscope using abdominal measurements. Although we show the length and width of the spermathecae can be used to differentiate between the species, this can be time-consuming, so we recommend undertaking this using standardized subsampling of catches. (Résumé d'auteur

Near-forward Raman selection rules of the phonon-polariton created by alloying in (Zn,Be)Se

The Raman selection rules of the (ZnSe, BeSe) mixed phonon polariton created by alloying in the three mode (1ZnSe, 2BeSe) ZnBeSe system, whose dramatic S like dispersion covers the large frequency gap between the ZnSe and BeSe spectral ranges, is studied in its wave vector dependence by near forward scattering. Both the collapse regime away from the Brillouin zone centre and the reinforcement regime near the Brillouin zone centre are addressed, using appropriate laser lines and Be contents. We find that in both regimes the considered phonon polariton, in fact a transverse mode with mixed mechanical and electrical character, obeys the same nominal Raman selection rules as its purely mechanical variant commonly observed in the backscattering geometry. Besides, marked differences in the phonon polariton Raman lineshapes in the two regimes give a hint about how the phonon polariton electrical field E develops while descending the S like dispersion towards the Brillouin zone centre. In the reinforcement regime E is large, leading to intramode on top of intermode transfers of oscillator strength mediated by E between the two BeSe modes, that both exhibit a fine structure on account of the alloy disorder. In contrast, in the collapse regime E remains weak, as testified by the absence of intramode transfer. The discussion is supported by contour modeling of the multi phonon polariton Raman lineshapes in their wave vector dependence within the linear dielectric approach.Comment: 16 pages, 7 figure

Enquête auprès du public de la bibliothèque municipale de Bordeaux (2002)

Résultats de l\u27enquête de la Bibliothèque municipale de Bordeaux menée auprès du public en 2002. Questionnaire, résultats détaillés et analyse

Tumour invasiveness, the local and systemic environment and the basis of staging systems in colorectal cancer

background: The present study aimed to examine the relationship between tumour invasiveness (T stage), the local and systemic environment and cancer-specific survival (CSS) of patients with primary operable colorectal cancer. methods: The tumour microenvironment was examined using measures of the inflammatory infiltrate (Klintrup-Makinen (KM) grade and Immunoscore), tumour stroma percentage (TSP) and tumour budding. The systemic inflammatory environment was examined using modified Glasgow Prognostic Score (mGPS) and neutrophil:lymphocyte ratio (NLR). A 5-year CSS was examined. results: A total of 331 patients were included. Increasing T stage was associated with colonic primary, N stage, poor differentiation, margin involvement and venous invasion (P<0.05). T stage was significantly associated with KM grade (P=0.001), Immunoscore (P=0.016), TSP (P=0.006), tumour budding (P<0.001), and elevated mGPS and NLR (both P<0.05). In patients with T3 cancer, N stage stratified survival from 88 to 64%, whereas Immunoscore and budding stratified survival from 100 to 70% and from 91 to 56%, respectively. The Glasgow Microenvironment Score, a score based on KM grade and TSP, stratified survival from 93 to 58%. conclusions: Although associated with increasing T stage, local and systemic tumour environment characteristics, and in particular Immunoscore, budding, TSP and mGPS, are stage-independent determinants of survival and may be utilised in the staging of patients with primary operable colorectal cancer

Matrix Models and D-branes in Twistor String Theory

We construct two matrix models from twistor string theory: one by dimensional reduction onto a rational curve and another one by introducing noncommutative coordinates on the fibres of the supertwistor space P^(3|4)->CP^1. We comment on the interpretation of our matrix models in terms of topological D-branes and relate them to a recently proposed string field theory. By extending one of the models, we can carry over all the ingredients of the super ADHM construction to a D-brane configuration in the supertwistor space P^(3|4). Eventually, we present the analogue picture for the (super) Nahm construction.Comment: 1+37 pages, reference added, JHEP style, published versio

Comparison of climate change impacts on the recharge of two karst systems computing different modelling approaches

International audienceKarst systems constitute aquifers in which infiltration and groundwater flows are generally complex processes and are characterized by limited knowledge in terms of geometry and structure. Nonetheless, they often represent interesting groundwater resources, some of them being subjected to intensive exploitation and others non exploited due to their poor understanding. In the future, it is likely that climate change impact on water resources will increase the interest for such a kind of aquifers due to their strong infiltration and storage capacity, in a broad context of higher water scarcity.The Lez and the Lison karst systems in Southern and Eastern France, respectively, provide 2 examples of such systems of several km² under two contrasted climate conditions, the first one being heavily exploited. This study presents a comparative climate change assessment onboth karst systems. Nine climate scenarios corresponding to the Fourth assessment report of the IPCC (SRES A1B scenario), downscaled using weather-type methods by the CERFACS, have been applied to various recharge modelling approaches, as standard analytical solutions of recharge estimation and soil-water balance models. Results are compared and discussed in order to assess the influence on climate change impacts of i) the climate conditions(geographic location), ii) the groundwater exploitation and iii) the modelling approach

Competency-Based Learning Object Sequencing Using Particle Swarms

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