Concordance between SIVA, IVAN, and VAMPIRE software tools for semi-automated analysis of retinal vessel caliber

We aimed to compare measurements from three of the most widely used software packages in the literature and to generate conversion algorithms for measurement of the central retinal artery equivalent (CRAE) and central retinal vein equivalent (CRVE) between SIVA and IVAN and between SIVA and VAMPIRE. We analyzed 223 retinal photographs from 133 human participants using both SIVA, VAMPIRE and IVAN independently for computing CRAE and CRVE. Agreement between measurements was assessed using Bland–Altman plots and intra-class correlation coefficients. A conversion algorithm between measurements was carried out using linear regression, and validated using bootstrapping and root-mean-square error. The agreement between VAMPIRE and IVAN was poor to moderate: The mean difference was 20.2 µm (95% limits of agreement, LOA, −12.2–52.6 µm) for CRAE and 21.0 µm (95% LOA, −17.5–59.5 µm) for CRVE. The agreement between VAMPIRE and SIVA was also poor to moderate: the mean difference was 36.6 µm (95% LOA, −12.8–60.4 µm) for CRAE, and 40.3 µm (95% LOA, 5.6–75.0 µm) for CRVE. The agreement between IVAN and SIVA was good to excellent: the mean difference was 16.4 µm (95% LOA, −4.25–37.0 µm) for CRAE, and 19.3 µm (95% LOA, 0.09–38.6 µm) for CRVE. We propose an algorithm converting IVAN and VAMPIRE measurements into SIVA-estimated measurements, which could be used to homogenize sets of vessel measurements obtained with different software packages

New pixelized Micromegas detector with low discharge rate for the COMPASS experiment

New Micromegas (Micro-mesh gaseous detectors) are being developed in view of the future physics projects planned by the COMPASS collaboration at CERN. Several major upgrades compared to present detectors are being studied: detectors standing five times higher luminosity with hadron beams, detection of beam particles (flux up to a few hundred of kHz/mm^{2}, 10 times larger than for the present Micromegas detectors) with pixelized read-out in the central part, light and integrated electronics, and improved robustness. Two solutions of reduction of discharge impact have been studied, with Micromegas detectors using resistive layers and using an additional GEM foil. Performance of such detectors has also been measured. A large size prototypes with nominal active area and pixelized read-out has been produced and installed at COMPASS in 2010. In 2011 prototypes featuring an additional GEM foil, as well as an resistive prototype, are installed at COMPASS and preliminary results from those detectors presented very good performance. We present here the project and report on its status, in particular the performance of large size prototypes with an additional GEM foil.Comment: 11 pages, 5 figures, proceedings to the Micro-Pattern Gaseous Detectors conference (MPGD2011), 29-31 August 2011, Kobe, Japa

FORECASTOR -- II. Simulating Galaxy Surveys with the Cosmological Advanced Survey Telescope for Optical and UV Research

The Cosmological Advanced Survey Telescope for Optical and UV Research (CASTOR) is a planned flagship space telescope, covering the blue-optical and UV part of the spectrum. Here we introduce the CASTOR image simulator, a Python GalSim package-based script capable of generating mock CASTOR images from an input catalogue. We generate example images from the CASTOR Wide, Deep, and Ultra-Deep surveys using simulated light-cones from the Santa Cruz Semi-Analytic Model. We make predictions for the performance of these surveys by comparing galaxies that are extracted from each image using Source Extractor to the input catalogue. We find that the Wide, Deep, and Ultra-Deep surveys will be complete to ~27, 29 and 30 mag, respectively, in the UV, u, and g filters, with the UV-split and u-split filters reaching a shallower depth. With a large area of ~2200 deg$^2$, the Wide survey will detect hundreds of millions of galaxies out to z~4, mostly with $M_\ast \gtrsim 10^9 M_\odot$. The Ultra-Deep survey will probe to z~5, detecting a large fraction of $M_\ast \simeq 10^8 M_\odot$ galaxies. These powerful samples will enable precision measurements of the distribution of star formation in the cosmic web, connecting the growth of stellar mass to the assembly of dark matter halos over two thirds of the history of the Universe, and other core goals of CASTOR's legacy surveys. These image simulations and the tools developed to generate them will be a vital planning tool to estimate CASTOR's performance and iterate the telescope and survey designs prior to launch.Comment: Submitted to A

Gut metagenome profile of the Nunavik Inuit youth is distinct from industrial and non-industrial counterparts

Comparative metagenomics studies have highlighted differences in microbiome community structure among human populations over diverse lifestyles and environments. With their unique environmental and historical backgrounds, Nunavik Inuit have a distinctive gut microbiome with undocumented health-related implications. Using shotgun metagenomics, we explored the taxonomic and functional structure of the gut microbiome from 275 Nunavik Inuit ranging from 16 to 30-year-old. Whole-metagenome analyses revealed that Nunavik Inuit youths have a more diverse microbiome than their non-industrialized and industrialized counterparts. A comparison of k-mer content illustrated the uniqueness of the Nunavik gut microbiome. Short-chain fatty acids producing species, and carbohydrates degradation pathways dominated Inuit metagenomes. We identified a taxonomic and functional signature unique to the Nunavik gut microbiome contrasting with other populations using a random forest classifier. Here, we show that the Nunavik Inuit gut microbiome exhibits high diversity and a distinct community structure

1814 en Chile: de la desobediencia a Lima a la ruptura con España

This article analyzes how the Chilean revolutionaries moved from the disobedience to Lima to the break with Spain in 1814. First, it studies the origins of the civil war that hit Chile since 1813. Then it studies the political factionalism within the revolutionary side and the importance of the Treaty of Lircay. Finally, it presents an account of the Americanist approach adopted by the Chilean rebels after signing a political and military alliance with José de San Martín.Este artículo interpreta el paso de la desobediencia a Lima a la ruptura definitiva con España durante el año 1814. Primero estudia los orígenes de la guerra civil en Chile comenzada en 1813. Luego presenta las causas del faccionalismo en el bando revolucionario y enfatiza la importancia del Tratado de Lircay. Finalmente, analiza la causa americanista seguida por los rebeldes chilenos después de firmar una alianza político-militar con José de San Martín

Longitudinal ambulatory measurements of gait abnormality in dystrophin-deficient dogs

Chantier qualité GAInternational audienceABSTRACT: BACKGROUND: This study aimed to measure the gait abnormalities in GRMD (Golden retriever muscular dystrophy) dogs during growth and disease progression using an ambulatory gait analyzer (3D-accelerometers) as a possible tool to assess the effects of a therapeutic intervention. METHODS: Six healthy and twelve GRMD dogs were evaluated twice monthly, from the age of two to nine months. The evolution of each gait variable previously shown to be modified in control and dystrophin-deficient adults was assessed using two-ways variance analysis (age, clinical status) with repeated measurements. A principal component analysis (PCA) was applied to perfect multivariate data interpretation. RESULTS: Speed, stride length, total power and force significantly already decreased (p < 0.01) at the age of 2 months. The other gait variables (stride frequency, relative power distributions along the three axes) became modified at later stages. Using the PCA analysis, a global gait index taking into account the main gait variables was calculated, and was also consistent to detect the early changes in the GRMD gait patterns, as well as the progressive degradation of gait quality. CONCLUSION: The gait variables measured by the accelerometers were sensitive to early detect and follow the gait disorders and mirrored the heterogeneity of clinical presentations, giving sense to monitor gait in GRMD dogs during progression of the disease and pre-clinical therapeutic trials

De novo assembly of the cattle reference genome with single-molecule sequencing.

BackgroundMajor advances in selection progress for cattle have been made following the introduction of genomic tools over the past 10-12 years. These tools depend upon the Bos taurus reference genome (UMD3.1.1), which was created using now-outdated technologies and is hindered by a variety of deficiencies and inaccuracies.ResultsWe present the new reference genome for cattle, ARS-UCD1.2, based on the same animal as the original to facilitate transfer and interpretation of results obtained from the earlier version, but applying a combination of modern technologies in a de novo assembly to increase continuity, accuracy, and completeness. The assembly includes 2.7 Gb and is &gt;250× more continuous than the original assembly, with contig N50 &gt;25 Mb and L50 of 32. We also greatly expanded supporting RNA-based data for annotation that identifies 30,396 total genes (21,039 protein coding). The new reference assembly is accessible in annotated form for public use.ConclusionsWe demonstrate that improved continuity of assembled sequence warrants the adoption of ARS-UCD1.2 as the new cattle reference genome and that increased assembly accuracy will benefit future research on this species

Internally Electrodynamic Particle Model: Its Experimental Basis and Its Predictions

The internally electrodynamic (IED) particle model was derived based on overall experimental observations, with the IED process itself being built directly on three experimental facts, a) electric charges present with all material particles, b) an accelerated charge generates electromagnetic waves according to Maxwell's equations and Planck energy equation and c) source motion produces Doppler effect. A set of well-known basic particle equations and properties become predictable based on first principles solutions for the IED process; several key solutions achieved are outlined, including the de Broglie phase wave, de Broglie relations, Schr\"odinger equation, mass, Einstein mass-energy relation, Newton's law of gravity, single particle self interference, and electromagnetic radiation and absorption; these equations and properties have long been broadly experimentally validated or demonstrated. A specific solution also predicts the Doebner-Goldin equation which emerges to represent a form of long-sought quantum wave equation including gravity. A critical review of the key experiments is given which suggests that the IED process underlies the basic particle equations and properties not just sufficiently but also necessarily.Comment: Presentation at the 27th Int Colloq on Group Theo Meth in Phys, 200