Alternative models for QTL detection in livestock. III. Heteroskedastic model and models corresponding to several distributions of the QTL effect

This paper describes two kinds of alternative models for QTL detection in livestock: an heteroskedastic model, and models corresponding to several hypotheses concerning the distribution of the QTL substitution effect among the sires: a fixed and limited number of alleles or an infinite number of alleles. The power of different tests built with these hypotheses were computed under different situations. The genetic variance associated with the QTL was shown in some situations. The results showed small power differences between the different models, but important differences in the quality of the estimations. In addition, a model was built in a simplified situation to investigate the gain in using possible linkage disequilibrium.Ce papier décrit deux types de modèles alternatifs pour la détection de QTL dans les populations animales : un modèle hétéroscédastique d’une part, et des modèles correspondants à différentes hypothèses sur la distribution de l’effet de substitution du QTL pour chaque mâle : un nombre fixe et limité d’allèles ou au contraire un nombre infini d’allèles. Les puissances des différents tests construits avec ces hypothèses sont calculées dans différentes situations. L’estimation de la variance génétique liée au QTL est donnée dans certaines situations. Les résultats montrent de faibles différences de puissance entre les différents modèles, mais des différences importantes dans la qualité des estimations. De plus, on construit un modèle dans une situation simplifiée pour étudier le gain que l’on peut obtenir en utilisant un éventuel déséquilibre de liaison

Alternative models for QTL detection in livestock. I. General introduction

In a series of papers, alternative models for QTL detection in livestock are proposed and their properties evaluated using simulations. This first paper describes the basic model used, applied to independent half-sib families, with marker phenotypes measured for a two or three generation pedigree and quantitative trait phenotypes measured only for the last generation. Hypotheses are given and the formulae for calculating the likelihood are fully described. Different alternatives to this basic model were studied, including variation in the performance modelling and consideration of full-sib families. Their main features are discussed here and their influence on the result illustrated by means of a numerical exampleDans une série d’articles scientifiques, des modèles alternatifs pour la détection de (QTLs chez les animaux de ferme sont proposés et leurs propriétés sont évaluées par simulation. Ce premier article décrit le modèle de base utilisé, qui concerne des familles indépendantes de demi-germains de père, avec des phénotypes marqueurs mesurés sur deux ou trois générations et des phénotypes quantitatifs mesurés seulement sur la dernière génération. Les hypothèses sont données et l’expression de la vraisemblance décrite en détail. À partir de ce modèle de base, différentes alternatives ont été étudiées, incluant diverses modélisations des performances et la prise en compte de structures familiales avec de vrais germains. Leurs principales caractéristiques sont décrites et une illustration est donné

Detecting Actions of Fruit Flies

In this thesis we describe a system that tracks fruit flies in video and automatically detects and classifies their actions. We introduce Caltech Fly-vs-Fly Interactions, a new dataset that contains hours of video showing pairs of fruit flies engaging in social interactions, and is published with complete expert annotations and articulated pose trajectory features. We compare experimentally the value of a frame-level feature representation with the more elaborate notion of bout features that capture the structure within actions. Similarly, we compare a simple sliding window classifier architecture with a more sophisticated structured output architecture, and find that window based detectors outperform the much slower structured counterparts, and approach human performance. In addition we test the top performing detector on the CRIM13 mouse dataset, finding that it matches the performance of the best published method. </p

Endemism increases species' climate change risk in areas of global biodiversity importance

Climate change affects life at global scales and across systems but is of special concern in areas that are disproportionately rich in biological diversity and uniqueness. Using a meta-analytical approach, we analysed >8000 risk projections of the projected impact of climate change on 273 areas of exceptional biodiversity, including terrestrial and marine environments. We found that climate change is projected to negatively impact all assessed areas, but endemic species are consistently more adversely impacted. Terrestrial endemics are projected to be 2.7 and 10 times more impacted than non-endemic natives and introduced species respectively, the latter being overall unaffected by climate change. We defined a high risk of extinction as a loss of >80% due to climate change alone. Of endemic species, 34% and 46% in terrestrial and marine ecosystems, and 100% and 84% of island and mountain species were projected to face high extinction risk respectively. A doubling of warming is projected to disproportionately increase extinction risks for endemic and non-endemic native species. Thus, reducing extinction risks requires both adaptation responses in biodiversity rich-spots and enhanced climate change mitigation

Semiconductor Spintronics

Spintronics refers commonly to phenomena in which the spin of electrons in a solid state environment plays the determining role. In a more narrow sense spintronics is an emerging research field of electronics: spintronics devices are based on a spin control of electronics, or on an electrical and optical control of spin or magnetism. This review presents selected themes of semiconductor spintronics, introducing important concepts in spin transport, spin injection, Silsbee-Johnson spin-charge coupling, and spindependent tunneling, as well as spin relaxation and spin dynamics. The most fundamental spin-dependent nteraction in nonmagnetic semiconductors is spin-orbit coupling. Depending on the crystal symmetries of the material, as well as on the structural properties of semiconductor based heterostructures, the spin-orbit coupling takes on different functional forms, giving a nice playground of effective spin-orbit Hamiltonians. The effective Hamiltonians for the most relevant classes of materials and heterostructures are derived here from realistic electronic band structure descriptions. Most semiconductor device systems are still theoretical concepts, waiting for experimental demonstrations. A review of selected proposed, and a few demonstrated devices is presented, with detailed description of two important classes: magnetic resonant tunnel structures and bipolar magnetic diodes and transistors. In most cases the presentation is of tutorial style, introducing the essential theoretical formalism at an accessible level, with case-study-like illustrations of actual experimental results, as well as with brief reviews of relevant recent achievements in the field.Comment: tutorial review; 342 pages, 132 figure

Alternative models for QTL detection in livestock. II. Likelihood approximations and sire marker genotype estimations

In this paper, we compare four different methods of dealing with the unknown linkage phase of sire markers which occurs in the detection of quantitative trait loci (QTL) in a half-sib family structure when no information is available on grand-parents. The methods are compared by considering a Gaussian approximation of the progeny likelihood instead of the mixture likelihood. In the first simulation study, the properties of the Gaussian model and of the mixture model were investigated, using the simplest method for sire gamete reconstruction. Both models lead to comparable results as regards the test power but the mean square error of sib QTL effect estimates was larger for the Gaussian likelihood than for the mixture likelihood, especially for maps with widely spaced markers. The second simulation study revealed that the simplest method for sire marker genotype estimation was as powerful as complicated methods and that the method including all the possible sire marker genotypes was never the most powerful

Idea Browsing on Digital Participation Platforms:A Mixed-methods Requirements Study

peer reviewedDigital participation platforms (DPP) are websites initiated by local governments through which citizens can post and react to ideas for their city. In practice, the majority of DPP users browse the posted ideas without contributing any. This activity, referred to as lurking, has widely recognized positive outcomes, especially in a citizen participation context. However, it has been devoted little attention. In practice, the idea browsing features available on current DPP are limited, and the literature has not evaluated the available approaches nor studied the requirements for idea browsing. In this paper, we report on an evaluation of the filterable list, which is the most common idea browsing approach on DPP. Our findings show that it lacks stimulation hedonic quality and call for a more stimulating approach. Thus, we conducted 11 semi-structured interviews to collect requirements and found that idea browsing on DPP should be supported by the combination of (1) a stimulating interactive representation such as circle packing or thematic trees displayed as entry point and (2) a filterable list for deeper exploration. This article is the first to study requirements for idea browsing features on DPP.Wal-E-Citie