Customs of the Western Pyrenees

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Airborne Measurements of Gravity Wave Breaking at the Tropopause

2000 FLORIDA AVE NW, WASHINGTON, DC, 2000

Reverse genetics in Candida albicans predicts ARF cycling is essential for drug resistance and virulence

Peer reviewedPublisher PD

Almanac: MCMC-based signal extraction of power spectra and maps on the sphere

Inference in cosmology often starts with noisy observations of random fields on the celestial sphere, such as maps of the microwave background radiation, continuous maps of cosmic structure in different wavelengths, or maps of point tracers of the cosmological fields. Almanac uses Hamiltonian Monte Carlo sampling to infer the underlying all-sky noiseless maps of cosmic structures, in multiple redshift bins, together with their auto- and cross-power spectra. It can sample many millions of parameters, handling the highly variable signal-to-noise of typical cosmological signals, and it provides science-ready posterior data products. In the case of spin-weight 2 fields, Almanac infers $E$- and $B$-mode power spectra and parity-violating $EB$ power, and, by sampling the full posteriors rather than point estimates, it avoids the problem of $EB$-leakage. For theories with no $B$-mode signal, inferred non-zero $B$-mode power may be a useful diagnostic of systematic errors or an indication of new physics. Almanac's aim is to characterise the statistical properties of the maps, with outputs that are completely independent of the cosmological model, beyond an assumption of statistical isotropy. Inference of parameters of any particular cosmological model follows in a separate analysis stage. We demonstrate our signal extraction on a CMB-like experiment.Comment: 27 pages, 18 figures. v2 accepted for publication by The Open Journal of Astrophysics with minor changes. v3 no changes, missing acknowledgement adde

Beyond two-point statistics: using the minimum spanning tree as a tool for cosmology

Cosmological studies of large-scale structure have relied on two-point statistics, not fully exploiting the rich structure of the cosmic web. In this paper we show how to capture some of this cosmic web information by using the minimum spanning tree (MST), for the first time using it to estimate cosmological parameters in simulations. Discrete tracers of dark matter such as galaxies, N-body particles or haloes are used as nodes to construct a unique graph, the MST, that traces skeletal structure. We study the dependence of the MST on cosmological parameters using haloes from a suite of COmoving Lagrangian Acceleration (COLA) simulations with a box size of 250 h−1Mpc⁠, varying the amplitude of scalar fluctuations (As), matter density (Ωm), and neutrino mass (∑mν). The power spectrum P and bispectrum B are measured for wavenumbers between 0.125 and 0.5 hMpc−1⁠, while a corresponding lower cut of ∼12.6 h−1Mpc is applied to the MST. The constraints from the individual methods are fairly similar but when combined we see improved 1σ constraints of ∼17 per cent (⁠∼12 per cent⁠) on Ωm and ∼12 per cent (⁠∼10 per cent⁠) on As with respect to P (P + B) thus showing the MST is providing additional information. The MST can be applied to current and future spectroscopic surveys (BOSS, DESI, Euclid, PSF, WFIRST, and 4MOST) in 3D and photometric surveys (DES and LSST) in tomographic shells to constrain parameters and/or test systematics

Self-Regulation of Candida albicans Population Size during GI Colonization

Interactions between colonizing commensal microorganisms and their hosts play important roles in health and disease. The opportunistic fungal pathogen Candida albicans is a common component of human intestinal flora. To gain insight into C. albicans colonization, genes expressed by fungi grown within a host were studied. The EFH1 gene, encoding a putative transcription factor, was highly expressed during growth of C. albicans in the intestinal tract. Counterintuitively, an efh1 null mutant exhibited increased colonization of the murine intestinal tract, a model of commensal colonization, whereas an EFH1 overexpressing strain exhibited reduced colonization of the intestinal tract and of the oral cavity of athymic mice, the latter situation modeling human mucosal candidiasis. When inoculated into the bloodstream of mice, both efh1 null and EFH1 overexpressing strains caused lethal infections. In contrast, other mutants are attenuated in virulence following intravenous inoculation but exhibited normal levels of intestinal colonization. Finally, although expression of several genes is dependent on transcription factor Efg1p during laboratory growth, Efg1p-independent expression of these genes was observed during growth within the murine intestinal tract. These results show that expression of EFH1 regulated the level of colonizing fungi, favoring commensalism as opposed to candidiasis. Also, different genes are required in different host niches and the pathway(s) that regulates gene expression during host colonization can differ from well-characterized pathways used during laboratory growth

The impact of spectroscopic incompleteness in direct calibration of redshift distributions for weak lensing surveys

Obtaining accurate distributions of galaxy redshifts is a critical aspect of weak lensing cosmology experiments. One of the methods used to estimate and validate redshift distributions is to apply weights to a spectroscopic sample, so that their weighted photometry distribution matches the target sample. In this work, we estimate the selection bias in redshift that is introduced in this procedure. We do so by simulating the process of assembling a spectroscopic sample (including observer-assigned confidence flags) and highlight the impacts of spectroscopic target selection and redshift failures. We use the first year (Y1) weak lensing analysis in Dark Energy Survey (DES) as an example data set but the implications generalize to all similar weak lensing surveys. We find that using colour cuts that are not available to the weak lensing galaxies can introduce biases of up to Δz ∼ 0.04 in the weighted mean redshift of different redshift intervals (Δz ∼ 0.015 in the case most relevant to DES). To assess the impact of incompleteness in spectroscopic samples, we select only objects with high observer-defined confidence flags and compare the weighted mean redshift with the true mean. We find that the mean redshift of the DES Y1 weak lensing sample is typically biased at the Δz = 0.005−0.05 level after the weighting is applied. The bias we uncover can have either sign, depending on the samples and redshift interval considered. For the highest redshift bin, the bias is larger than the uncertainties in the other DES Y1 redshift calibration methods, justifying the decision of not using this method for the redshift estimations. We discuss several methods to mitigate this bias

Use of mRNA- and protein-destabilizing elements to develop a highly responsive reporter system

Reporter assays are widely used in applications that require measurement of changes in gene expression over time (e.g. drug screening). With standard reporter vectors, the measurable effect of a treatment or compound (altered reporter activity) is substantially diluted and delayed, compared with its true effect (altered transcriptional activity). This problem is caused by the relatively long half-lives of both the reporter protein and its mRNA. As a result, the activities of compounds, ligands or treatments that have a relatively minor effect, or a substantial but transient effect, often remain undetected. To circumvent this problem, we introduced modular protein- and mRNA-destabilizing elements into a range of commonly used reporters. Our data show that both elements are required for maximal responses to both increases and decreases in transcriptional activity. The double-destabilized reporter vectors showed markedly improved performance in drug screening, kinetic assays and dose–response titrations