Assessing non-linear models for galaxy clustering II: model validation and forecasts for Stage IV surveys

Accurate modelling of non-linear scales in galaxy clustering will be crucial for data analysis of Stage IV galaxy surveys. A selection of competing non-linear models must be made based on validation studies. We provide a comprehensive set of forecasts of two different models for the halo redshift space power spectrum, namely the commonly applied TNS model and an effective field theory of large scale structure (EFTofLSS) inspired model. Using simulation data and a least-χ2 analysis, we determine ranges of validity for the models. We then conduct an exploratory Fisher analysis using the full anisotropic power spectrum to investigate parameter degeneracies. We proceed to perform an MCMC analysis utilising the monopole, quadrupole, and hexadecapole spectra, with a restricted range of scales for the latter in order to avoid biasing our growth rate, f, constraint. We find that the TNS model with a Lorentzian damping and standard Eulerian perturbative modelling outperforms other variants of the TNS model. Our MCMC analysis finds that the EFTofLSS-based model may provide tighter marginalised constraints on f at z = 0.5 and z = 1 than the TNS model, despite having additional nuisance parameters. However this depends on the range of scales used as well as the fiducial values and priors on the EFT nuisance parameters. Finally, we extend previous work to provide a consistent comparison between the Fisher matrix and MCMC forecasts using the multipole expansion formalism, and find good agreement between them

Artifacts with uneven sampling of red noise

The vast majority of sampling systems operate in a standard way: at each tick of a fixed-frequency master clock a digitizer reads out a voltage that corresponds to the value of some physical quantity and translates it into a bit pattern that is either transmitted, stored, or processed right away. Thus signal sampling at evenly spaced time intervals is the rule: however this is not always the case, and uneven sampling is sometimes unavoidable. While periodic or quasi-periodic uneven sampling of a deterministic signal can reasonably be expected to produce artifacts, it is much less obvious that the same happens with noise: here I show that this is indeed the case only for long-memory noise processes, i.e., power-law noises $1/f^\alpha$ with $\alpha > 2$. The resulting artifacts are usually a nuisance although they can be eliminated with a proper processing of the signal samples, but they could also be turned to advantage and used to encode information.Comment: 5 figure

DEXAMETHASONE AND PENTOXIFYLLINE INHIBIT ENDOTOXIN-INDUCED CACHECTIN TUMOR-NECROSIS-FACTOR SYNTHESIS AT SEPARATE POINTS IN THE SIGNALING PATHWAY

The induction of cachectin/tumor necrosis factor (TNF) synthesis by bacterial endotoxins is a process that entails activation at several levels. Cachectin/TNF gene transcription is accelerated, leading to rapid accumulation of mRNA within the macrophage cytosol. In addition, translational derepression occurs, leading to far more efficient message utilization. Through the use of posttranscriptional reporter constructs, we now demonstrate that certain agents capable of inhibiting cachectin/TNF biosynthesis operate through different mechanisms. In RAW 264.7 macrophages, pentoxifylline blocks cachectin/TNF mRNA accumulation but has no effect upon the efficiency of reporter mRNA translation. Dexamethasone, on the other hand, has only a modest effect on cachectin/TNF mRNA accumulation, but strongly impedes translational derepression. Combined application of dexamethasone and pentoxifylline to macrophages causes a greater suppression of cachectin/TNF biosynthesis that can be achieved by either agent alone. These findings suggest that the signaling pathway activated by endotoxin is branched, and that selective inhibition of different parts of the pathway may be achieved through the use of distinct agents

Heterozygous mis-sense mutations in Prkcb as a critical determinant of anti-polysaccharide antibody formation

To identify rate-limiting steps in T cell-independent type 2 (TI-2) antibody production against polysaccharide antigens, we performed a genome-wide screen by immunizing several hundred pedigrees of C57BL/6 mice segregating ENU-induced mis-sense mutations. Two independent mutations, Tilcara and Untied, were isolated that semi-dominantly diminished antibody against polysaccharide but not protein antigens. Both mutations resulted from single amino acid substitutions within the kinase domain of Protein Kinase C Beta (PKCβ). In Tilcara, a Ser552>Pro mutation occurred in helix G, in close proximity to a docking site for the inhibitory N-terminal pseudosubstrate domain of the enzyme, resulting in almost complete loss of active, autophosphorylated PKCβI whereas the amount of alternatively spliced PKCβII protein was not markedly reduced. Circulating B cell subsets were normal and acute responses to BCR-stimulation such as CD25 induction and initiation of DNA synthesis were only measurably diminished in Tilcara homozygotes, whereas the fraction of cells that had divided multiple times was decreased to an intermediate degree in heterozygotes. These results, coupled with evidence of numerous mis-sense PRKCB mutations in the human genome, identify Prkcb as a genetically sensitive step likely to contribute substantially to population variability in anti-polysaccharide antibody levels

Reporters for Single-Cell Analysis of Colicin Ib Expression in Salmonella enterica Serovar Typhimurium

Colicins are toxins that mediate interference competition in microbial ecosystems. They serve as a "common good" for the entire producer population but are synthesized by only few members which pay the costs of colicin production. We have previously shown that production of colicin Ib (cib),a group B colicin, confers a competitive advantage to Salmonella enterica serovar Typhimurium (S. Tm) over commensal E. coli strains. Here, we studied regulation of S. Tm cib expression at the single cell level. Comparative analysis of a single-and a multicopy gfp-reporter for the colicin Ib promoter (Pcib) revealed that the latter yielded optimal signal intensity for a diverse range of applications. We further validated this reporter and showed that gfp expression correlated well with colicin Ib (ColIb) protein levels in individual cells. Pcib is negatively controlled by two repressors, LexA and Fur. Only a small fraction of S. Tm expressed cib under non-inducing conditions. We studied Pcib activity in response to mitomycin C mediated DNA damage and iron limitation. Both conditions, if applied individually, lead to an increase in the fraction of GFP(+) S. Tm, albeit an overall low fluorescence intensity. When both conditions were applied simultaneously, the majority of S. Tm turned GFP(+) and displayed high fluorescence intensity. Thus, both repressors individually confine cib expression to a subset of the population. Taken together, we provide the first thorough characterization of a conventional gfp-reporter to study regulation of a group B colicin at the single cell level. This reporter will be useful to further investigate the costs and benefits of ColIb production in human pathogenic S. Tm and analyze cib expression under environmental conditions encountered in the mammalian gut

Negaton and Positon Solutions of the KDV Equation

We give a systematic classification and a detailed discussion of the structure, motion and scattering of the recently discovered negaton and positon solutions of the Korteweg-de Vries equation. There are two distinct types of negaton solutions which we label $[S^{n}]$ and $[C^{n}]$, where $(n+1)$ is the order of the Wronskian used in the derivation. For negatons, the number of singularities and zeros is finite and they show very interesting time dependence. The general motion is in the positive $x$ direction, except for certain negatons which exhibit one oscillation around the origin. In contrast, there is just one type of positon solution, which we label $[\tilde C^n]$. For positons, one gets a finite number of singularities for $n$ odd, but an infinite number for even values of $n$. The general motion of positons is in the negative $x$ direction with periodic oscillations. Negatons and positons retain their identities in a scattering process and their phase shifts are discussed. We obtain a simple explanation of all phase shifts by generalizing the notions of ``mass" and ``center of mass" to singular solutions. Finally, it is shown that negaton and positon solutions of the KdV equation can be used to obtain corresponding new solutions of the modified KdV equation.Comment: 20 pages plus 12 figures(available from authors on request),Latex fil

Automated reliability assessment for spectroscopic redshift measurements

We present a new approach to automate the spectroscopic redshift reliability assessment based on machine learning (ML) and characteristics of the redshift probability density function (PDF). We propose to rephrase the spectroscopic redshift estimation into a Bayesian framework, in order to incorporate all sources of information and uncertainties related to the redshift estimation process, and produce a redshift posterior PDF that will be the starting-point for ML algorithms to provide an automated assessment of a redshift reliability. As a use case, public data from the VIMOS VLT Deep Survey is exploited to present and test this new methodology. We first tried to reproduce the existing reliability flags using supervised classification to describe different types of redshift PDFs, but due to the subjective definition of these flags, soon opted for a new homogeneous partitioning of the data into distinct clusters via unsupervised classification. After assessing the accuracy of the new clusters via resubstitution and test predictions, unlabelled data from preliminary mock simulations for the Euclid space mission are projected into this mapping to predict their redshift reliability labels.Comment: Submitted on 02 June 2017 (v1). Revised on 08 September 2017 (v2). Latest version 28 September 2017 (this version v3