Using sequence variants of a QTL region improves the accuracy of genomic evaluation in French Saanen goats

The enhanced availability of sequence data in livestock provides an opportunity for more accurate predictions in routine genomic evaluations. Such evaluations would therefore no longer rely only on the linkage disequilibrium between a chip marker and the causal mutation. The objective of this study was to assess the usefulness of sequence data in Saanen goats (n = 33) to better capture a quantitative trait locus (QTL) on chromosome 19 (CHI19) and improve the accuracy of predictions for 3 milk production traits, 5 type traits, and somatic cell scores. All 1,207 50K genotypes were imputed to the sequence level. Four scenarios, each using a subset of CHI19 imputed variants, were then tested. Sequence-derived information included all CHI19 variants (529,576), all variants in the QTL region (22,269), 178 variants selected in the QTL region and added to an updated chip, or 178 randomly selected variants on CHI19. Two genomic evaluation models were applied: single-step genomic BLUP and weighted single-step genomic BLUP. All scenarios were compared with single-step genomic BLUP using 50K genotypes. Best overall results were obtained using single-step genomic BLUP on 50K genotypes completed with all variants in the QTL region of chromosome 19 (6.2% average increase in accuracy for 9 traits) with the highest accuracy gain for fat yield (17.9%), significant increases for milk (13.7%) and protein yields (12.5%), and type traits associated with CHI19. Despite its association with the QTL region of chromosome 19, the somatic cell score showed decreased accuracy in every alternative scenario. Using all CHI19 variants led to an overall decrease of 4.8% in prediction accuracy. The updated chip was efficient and improved genomic evaluations by 3.1 to 6.4% on average, depending on the scenario. Indeed, information from only a few carefully selected variants increased accuracies for traits of interest when used in a single-step genomic BLUP model. In conclusion, using QTL region variants imputed from sequence data in single-step genomic evaluations represents a promising perspective for such evaluations in dairy goats. Furthermore, using only a limited number of selected variants in QTL regions, as available on SNP chip updates, significantly increases the accuracy for QTL-associated traits without deteriorating the evaluation accuracy for other traits. The latter approach is interesting, as it avoids time-consuming imputation and data formatting processes and provides reliable genotypes.     

Young infants' generalization of emotional expressions: Effects of familiarity.

From birth, infants are exposed to a wealth of emotional information in their interactions. Much research has been done to investigate the development of emotion perception, and factors influencing that development. The current study investigates the role of familiarity on 3.5-month-old infants' generalization of emotional expressions. Infants were assigned to one of two habituation sequences: in one sequence, infants were visually habituated to parental expressions of happy or sad. At test, infants viewed either a continuation of the habituation sequence, their mother depicting a novel expression, an unfamiliar female depicting the habituated expression, or an unfamiliar female depicting a novel expression. In the second sequence, a new sample of infants was matched to the infants in the first sequence. These infants viewed the same habituation and test sequences, but the actors were unfamiliar to them. Only those infants who viewed their own mothers and fathers during the habituation sequence increased looking. They dishabituated looking to maternal novel expressions, the unfamiliar female's novel expression, and the unfamiliar female depicting the habituated expression, especially when sad parental expressions were followed by an expression change to happy or to a change in person. Infants are guided in their recognition of emotional expressions by the familiarity of their parents, before generalizing to others. (PsycINFO Database Record (c) 2011 APA, all rights reserved)     

Incremental learning of Bayesian sensorimotor models: from low-level behaviours to large-scale structure of the environment

This paper concerns the incremental learning of hierarchies of representations of space in artificial or natural cognitive systems. We propose a mathematical formalism for defining space representations (Bayesian Maps) and modelling their interaction in hierarchies of representations (sensorimotor interaction operator).

We illustrate our formalism with a robotic experiment. Starting from a model based on the proximity to obstacles, we learn a new one related to the direction of the light source. It provides new behaviours, like phototaxis and photophobia. We then combine these two maps so as to identify parts of the environment where the way the two modalities interact is recognisable. This classification is a basis for learning a higher level of abstraction map that describes the large-scale structure of the environment.

In the final model, the perception–action cycle is modelled by a hierarchy of sensorimotor models of increasing time and space scales, which provide navigation strategies of increasing complexities.     

Endothelial Colony-Forming Cells Dysfunctions Are Associated with Arterial Hypertension in a Rat Model of Intrauterine Growth Restriction

Infants born after intrauterine growth restriction (IUGR) are at risk of developing arterial hypertension at adulthood. The endothelium plays a major role in the pathogenesis of hypertension. Endothelial colony-forming cells (ECFCs), critical circulating components of the endothelium, are involved in vasculo-and angiogenesis and in endothelium repair. We previously described impaired functionality of ECFCs in cord blood of low-birth-weight newborns. However, whether early ECFC alterations persist thereafter and could be associated with hypertension in individuals born after IUGR remains unknown. A rat model of IUGR was induced by a maternal low-protein diet during gestation versus a control (CTRL) diet. In six-month-old offspring, only IUGR males have increased systolic blood pressure (tail-cuff plethysmography) and microvascular rarefaction (immunofluorescence). ECFCs isolated from bone marrow of IUGR versus CTRL males displayed a decreased proportion of CD31+ versus CD146+ staining on CD45− cells, CD34 expression (flow cytometry, immunofluorescence), reduced proliferation (BrdU incorporation), and an impaired capacity to form capillary-like structures (Matrigel test), associated with an impaired angiogenic profile (immunofluorescence). These dysfunctions were associated with oxidative stress (increased superoxide anion levels (fluorescent dye), decreased superoxide dismutase protein expression, increased DNA damage (immunofluorescence), and stress-induced premature senescence (SIPS; increased beta-galactosidase activity, increased p16^INK4a, and decreased sirtuin-1 protein expression). This study demonstrated an impaired functionality of ECFCs at adulthood associated with arterial hypertension in individuals born after IUGR.     

IL-17A in Human Liver: Significant Source of Inflammation and Trigger of Liver Fibrosis Initiation

IL-17A is considered to guide liver inflammation and fibrosis. From twenty-two human liver samples of different fibrosis stages (F0 to F4), IL-17A, IL-22, and TGFβ1 protein expression in liver tissue lysates were analyzed. Ten paired samples of liver tissue (F0–F1 stage) and blood from the same patient were used to analyze intrahepatic and blood T-lymphoid IL-17A⁺ cells by flow cytometry. The analyses have been performed regardless of pathology, considering the stage of fibrosis. Human liver tissue was used for the primary human liver slice cultures, followed by subsequent cytokine stimulation and fibrotic markers’ analysis by ELISA. IL-17A production in human liver tissue was significantly higher in the early fibrotic stage compared with the advanced stage. Th17 T cells and, to a lesser extent, MAIT cells were the main sources of IL-17A in both compartments, the liver and the blood. Moreover, the presence of liver Th17IL-17A⁺INFγ⁺ cells was detected in the liver. IL-17A stimulation of human liver slice culture increased the expression of profibrotic and pro-inflammatory markers. IL-17A, secreted by Th17 and MAIT cells in the liver, triggered fibrosis by inducing the expression of IL-6 and profibrotic markers and could be a target for antifibrotic treatment. Further amplitude studies are needed to confirm the current results.     

Exploring conscious imitation of style with ready-made software

This article describes some approaches to imitation analysis and the use of ready-made software for this task. Devising computer-assisted techniques for exploring the conscious literary imitation of style is an application of particular relevance to contemporary Hispanic narrative and one that can be handled with a microcomputer and readily accessible software. The article describes some approaches to imitation analysis and the use of ready-made software to assess the effectiveness of stylistic imitation of eighteenth-century historical chronicle in La renuncia del héroe Baltasar (The Renunciation of the Hero Baltasar), by the Puerto Rican novelist Rodríguez Juliá. Even when employing familiar procedures of text analysis with computer, comparing a fictional text with a multiple and diverse corpus of authentic historical documents requires somewhat unique assumptions and hypotheses, since neither authorship, influence, or authenticity are in question.Estelle Irizarry is Professor of Spanish at Georgetown University, Washington, D. C., and author of 18 books and annotated editions dealing with modern Hispanic literature, art, and hoaxes.     

Bimodal Detection of Proteins by 129Xe NMR and Fluorescence Spectroscopy

A full understanding of biological phenomena involves sensitive and noninvasive detection. Herein, we report the optimization of a probe for intracellular proteins that combines the advantages of fluorescence and hyperpolarized ¹²⁹Xe NMR spectroscopy detection. The fluorescence detection part is composed of six residues containing a tetracysteine tag (−CCXXCC−) genetically incorporated into the protein of interest and of a small organic molecule, CrAsH. CrAsH becomes fluorescent if it binds to the tetracysteine tag. The part of the biosensor that enables detection by means of ¹²⁹Xe NMR spectroscopy, which is linked to the CrAsH moiety by a spacer, is based on a cryptophane core that is fully suited to reversibly host xenon. Three different peptides, containing the tetracysteine tag and four organic biosensors of different stereochemistry, are benchmarked to propose the best couple that is fully suited for the in vitro detection of proteins.     

Density measurement of fine aerosol fractions from wood combustion sources using ELPI distributions and image processing techniques

Aerosols from combustion sources are of high concern since they present a risk for health and environment. Particle size distribution of aerosols and in particular number size distribution are easily and quickly obtained using an Electrical Low Pressure Impactor (ELPI). However, this technique is depending of aerosol density; ρ, which may lead to biased particle size distributions. Aerosol density from combustion sources is usually not well known and depends on several parameters. Aerosol density cannot be measured with usual methods since there is generally not enough matter collected on each stage of the ELPI. Our approach uses electronic microscopy to evaluate ρ at each impaction stage in order to increase the accuracy of the number size distributions resulting from the ELPI measurements.Particles were collected on glass substrates deposited on each impaction stages. Images were obtained using a scanning electron microscope and image processing tools were applied.This method was first tested with silica particles resulting from a combustion process which have a constant density found to be comprised between 2.2 and 2.4 g cm⁻³ for stages 2 (57 and 95 nm) and 3 (95 and 158 nm), respectively. Once validated, this method was used to determine the density of wood combustion aerosols. The results match well for fly ashes from wood combustion with densities varying from 1.1 to 3.0 g cm⁻³ for particles of mean equivalent diameter ranging from 69 to 157 nm, respectively.