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

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

Identification of Four Potential Epigenetic Modulators from the NCI Structural Diversity Library Using a Cell-Based Assay

Epigenetic pathways help control the expression of genes. In cancer and other diseases, aberrant silencing or overexpression of genes, such as those that control cell growth, can greatly contribute to pathogenesis. Access to these genes by the transcriptional machinery is largely mediated by chemical modifications of DNA or histones, which are controlled by epigenetic enzymes, making these enzymes attractive targets for drug discovery. Here we describe the characterization of a locus derepression assay, a fluorescence-based mammalian cellular system which was used to screen the NCI structural diversity library for novel epigenetic modulators using an automated imaging platform. Four structurally unique compounds were uncovered that, when further investigated, showed distinct activities. These compounds block the viability of lung cancer and melanoma cells, prevent cell cycle progression, and/or inhibit histone deacetylase activity, altering levels of cellular histone acetylation

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

Impact of the Method of G6PD Deficiency Assessment on Genetic Association Studies of Malaria Susceptibility

BACKGROUND:Clinical association studies have yielded varied results regarding the impact of glucose-6-phosphate dehydrogenase (G6PD) deficiency upon susceptibility to malaria. Analyses have been complicated by varied methods used to diagnose G6PD deficiency. METHODOLOGY/PRINCIPAL FINDINGS:We compared the association between uncomplicated malaria incidence and G6PD deficiency in a cohort of 601 Ugandan children using two different diagnostic methods, enzyme activity and G6PD genotype (G202A, the predominant East African allele). Although roughly the same percentage of males were identified as deficient using enzyme activity (12%) and genotype (14%), nearly 30% of males who were enzymatically deficient were wild-type at G202A. The number of deficient females was three-fold higher with assessment by genotype (21%) compared to enzyme activity (7%). Heterozygous females accounted for the majority (46/54) of children with a mutant genotype but normal enzyme activity. G6PD deficiency, as determined by G6PD enzyme activity, conferred a 52% (relative risk [RR] 0.48, 95% CI 0.31-0.75) reduced risk of uncomplicated malaria in females. In contrast, when G6PD deficiency was defined based on genotype, the protective association for females was no longer seen (RR = 0.99, 95% CI 0.70-1.39). Notably, restricting the analysis to those females who were both genotypically and enzymatically deficient, the association of deficiency and protection from uncomplicated malaria was again demonstrated in females, but not in males (RR = 0.57, 95% CI 0.37-0.88 for females). CONCLUSIONS/SIGNIFICANCE:This study underscores the impact that the method of identifying G6PD deficient individuals has upon association studies of G6PD deficiency and uncomplicated malaria. We found that G6PD-deficient females were significantly protected against uncomplicated malaria, but this protection was only seen when G6PD deficiency is described using enzyme activity. These observations may help to explain the discrepancy in some published association studies involving G6PD deficiency and uncomplicated malaria

Tidal evolution of exo-planetary systems: WASP-50, GJ 1214 and CoRoT-7

We perform numerical simulations to investigate tidal evolution of two single-planet systems, that is, WASP-50 and GJ 1214 and a two-planet system CoRoT-7. The results of orbital evolution show that tidal decay and circularization may play a significant role in shaping their final orbits, which is related to the initial orbital data in the simulations. For GJ 1214 system, different cases of initial eccentricity are also considered as only an upper limit of its eccentricity (0.27) is shown, and the outcome suggests a possible maximum initial eccentricity (0.4) in the adopted dynamical model. Moreover, additional runs with alternative values of dissipation factor $Q^\prime_1$ are carried out to explore tidal evolution for GJ 1214b, and these results further indicate that the real $Q^\prime_1$ of GJ 1214b may be much larger than its typical value, which may reasonably suggest that GJ 1214b bears a present-day larger eccentricity, undergoing tidal circularization at a slow rate. For the CoRoT-7 system, tidal forces make two planets migrating towards their host star as well as producing tidal circularization, and in this process tidal effects and mutual gravitational interactions are coupled with each other. Various scenarios of the initial eccentricity of the outer planet have also been done to investigate final planetary configuration. Tidal decay arising from stellar tides may still work for each system as the eccentricity decreases to zero, and this is in association with the remaining lifetime of each planet used to predict its future.Comment: 9 pages, 12 figures, accepted for publication in "SCIENCE CHINA Physics,Mechanics & Astronomy

On the construction of model Hamiltonians for adiabatic quantum computation and its application to finding low energy conformations of lattice protein models

In this report, we explore the use of a quantum optimization algorithm for obtaining low energy conformations of protein models. We discuss mappings between protein models and optimization variables, which are in turn mapped to a system of coupled quantum bits. General strategies are given for constructing Hamiltonians to be used to solve optimization problems of physical/chemical/biological interest via quantum computation by adiabatic evolution. As an example, we implement the Hamiltonian corresponding to the Hydrophobic-Polar (HP) model for protein folding. Furthermore, we present an approach to reduce the resulting Hamiltonian to two-body terms gearing towards an experimental realization.Comment: 35 pages, 8 figure

Non-Equilibrium Statistical Physics of Currents in Queuing Networks

We consider a stable open queuing network as a steady non-equilibrium system of interacting particles. The network is completely specified by its underlying graphical structure, type of interaction at each node, and the Markovian transition rates between nodes. For such systems, we ask the question ``What is the most likely way for large currents to accumulate over time in a network ?'', where time is large compared to the system correlation time scale. We identify two interesting regimes. In the first regime, in which the accumulation of currents over time exceeds the expected value by a small to moderate amount (moderate large deviation), we find that the large-deviation distribution of currents is universal (independent of the interaction details), and there is no long-time and averaged over time accumulation of particles (condensation) at any nodes. In the second regime, in which the accumulation of currents over time exceeds the expected value by a large amount (severe large deviation), we find that the large-deviation current distribution is sensitive to interaction details, and there is a long-time accumulation of particles (condensation) at some nodes. The transition between the two regimes can be described as a dynamical second order phase transition. We illustrate these ideas using the simple, yet non-trivial, example of a single node with feedback.Comment: 26 pages, 5 figure