Status of MICE

Muon ionization cooling is the only practical method for preparing high-brilliance beams needed for a neutrino factory or muon collider. The muon ionization cooling experiment (MICE) under development at the Rutherford Appleton Laboratory comprises a dedicated beamline to generate a range of input emittance and momentum, with time-of-flight and Cherenkov detectors to ensure a pure muon beam. A first measurement of emittance is performed in the upstream magnetic spectrometer with a scintillating-fiber tracker. A cooling cell will then follow, alternating energy loss in liquid hydrogen with RF acceleration. A second spectrometer identical to the first and a particle identification system will measure the outgoing emittance. Plans for measurements of emittance and cooling are described.Comment: Poster presented at ICHEP08 Conference, Philadelphia, USA, July 2008. 3 pages, 3 figure

DNA methylation-associated colonic mucosal immune and defense responses in treatment-naïve pediatric ulcerative colitis

Inflammatory bowel diseases (IBD) are emerging globally, indicating that environmental factors may be important in their pathogenesis. Colonic mucosal epigenetic changes, such as DNA methylation, can occur in response to the environment and have been implicated in IBD pathology. However, mucosal DNA methylation has not been examined in treatment-naïve patients. We studied DNA methylation in untreated, left sided colonic biopsy specimens using the Infinium HumanMethylation450 BeadChip array. We analyzed 22 control (C) patients, 15 untreated Crohn’s disease (CD) patients, and 9 untreated ulcerative colitis (UC) patients from two cohorts. Samples obtained at the time of clinical remission from two of the treatment-naïve UC patients were also included into the analysis. UC-specific gene expression was interrogated in a subset of adjacent samples (5 C and 5 UC) using the Affymetrix GeneChip PrimeView Human Gene Expression Arrays. Only treatment-naïve UC separated from control. One-hundred-and-twenty genes with significant expression change in UC (> 2-fold, P < 0.05) were associated with differentially methylated regions (DMRs). Epigenetically associated gene expression changes (including gene expression changes in the IFITM1, ITGB2, S100A9, SLPI, SAA1, and STAT3 genes) were linked to colonic mucosal immune and defense responses. These findings underscore the relationship between epigenetic changes and inflammation in pediatric treatment-naïve UC and may have potential etiologic, diagnostic, and therapeutic relevance for IBD

ProCARs: Progressive Reconstruction of Ancestral Gene Orders

International audienceBackground: In the context of ancestral gene order reconstruction from extant genomes, there exist two main computational approaches: rearrangement-based, and homology-based methods. The rearrangement-based methods consist in minimizing a total rearrangement distance on the branches of a species tree. The homology-based methods consist in the detection of a set of potential ancestral contiguity features, followed by the assembling of these features into Contiguous Ancestral Regions (CARs). Results: In this paper, we present a new homology-based method that uses a progressive approach for both the detection and the assembling of ancestral contiguity features into CARs. The method is based on detecting a set of potential ancestral adjacencies iteratively using the current set of CARs at each step, and constructing CARs progressively using a 2-phase assembling method. We show the usefulness of the method through a reconstruction of the boreoeutherian ancestral gene order, and a comparison with three other homology-based methods: AnGeS, InferCARs and GapAdj. The program is written in Python, and the dataset used in this paper are available at http://bioinfo.lifl.fr/procars/

A study of fundamental limitations to statistical detection of redshifted H i from the epoch of reionization

In this paper, we explore for the first time the relative magnitudes of three fundamental sources of uncertainty, namely, foreground contamination, thermal noise, and sample variance, in detecting the H I power spectrum from the epoch of reionization (Eo

Tangent functional connectomes uncover more unique phenotypic traits

Functional connectomes (FCs) contain pairwise estimations of functional couplings based on pairs of brain regions activity. FCs are commonly represented as correlation matrices that are symmetric positive definite (SPD) lying on or inside the SPD manifold. Since the geometry on the SPD manifold is non-Euclidean, the inter-related entries of FCs undermine the use of Euclidean-based distances. By projecting FCs into a tangent space, we can obtain tangent functional connectomes (tangent-FCs). Tangent-FCs have shown a higher predictive power of behavior and cognition, but no studies have evaluated the effect of such projections with respect to fingerprinting. We hypothesize that tangent-FCs have a higher fingerprint than regular FCs. Fingerprinting was measured by identification rates (ID rates) on test-retest FCs as well as on monozygotic and dizygotic twins. Our results showed that identification rates are systematically higher when using tangent-FCs. Specifically, we found: (i) Riemann and log-Euclidean matrix references systematically led to higher ID rates. (ii) In tangent-FCs, Main-diagonal regularization prior to tangent space projection was critical for ID rate when using Euclidean distance, whereas barely affected ID rates when using correlation distance. (iii) ID rates were dependent on condition and fMRI scan length. (iv) Parcellation granularity was key for ID rates in FCs, as well as in tangent-FCs with fixed regularization, whereas optimal regularization of tangent-FCs mostly removed this effect. (v) Correlation distance in tangent-FCs outperformed any other configuration of distance on FCs or on tangent-FCs across the fingerprint gradient (here sampled by assessing test-retest, Monozygotic and Dizygotic twins). (vi)ID rates tended to be higher in task scans compared to resting-state scans when accounting for fMRI scan length.Comment: 29 pages, 10 figures, 2 table

Low-frequency observations of the moon with the murchison widefield array

A new generation of low-frequency radio telescopes is seeking to observe the redshifted 21cm signal from the epoch of reionization (EoR), requiring innovative methods of calibration and imaging to overcome the difficulties of wide-field low-frequency radio interferometry. Precise calibration will be required to separate the expected small EoR signal from the strong foreground emission at the frequencies of interest between 80 and 300MHz. The Moon may be useful as a calibration source for detection of the EoR signature, as it should have a smooth and predictable thermal spectrum across the frequency band of interest. Initial observations of the Moon with the Murchison Widefield Array 32 tile prototype show that the Moon does exhibit a similar trend to that expected for a cool thermally emitting body in the observed frequency range, but that the spectrum is corrupted by reflected radio emission from Earth. In particular, there is an abrupt increase in the observed flux density of the Moon within the internationally recognized frequency modulated (FM) radio band. The observations have implications for future low-frequency surveys and EoR detection experiments that will need to take this reflected emission from the Moon into account. The results also allow us to estimate the equivalent isotropic power emitted by the Earth in the FM band and to determine how bright the Earth might appear at meter wavelengths to an observer beyond our own solar system