Halo assembly bias and its effects on galaxy clustering

The clustering of dark halos depends not only on their mass but also on their assembly history, a dependence we term `assembly bias'. Using a galaxy formation model grafted onto the Millennium Simulation of the LCDM cosmogony, we study how assembly bias affects galaxy clustering. We compare the original simulation to `shuffled' versions where the galaxy populations are randomly swapped among halos of similar mass, thus isolating the effects of correlations between assembly history and environment at fixed mass. Such correlations are ignored in the halo occupation distribution models often used populate dark matter simulations with galaxies, but they are significant in our more realistic simulation. Assembly bias enhances 2-point correlations by 10% for galaxies with M_bJ-5logh brighter than -17, but suppresses them by a similar amount for galaxies brighter than -20. When such samples are split by colour, assembly bias is 5% stronger for red galaxies and 5% weaker for blue ones. Halo central galaxies are differently affected by assembly bias than are galaxies of all types. It almost doubles the correlation amplitude for faint red central galaxies. Shuffling galaxies among halos of fixed formation redshift or concentration in addition to fixed mass produces biases which are not much smaller than when mass alone is fixed. Assembly bias must reflect a correlation of environment with aspects of halo assembly which are not encoded in either of these parameters. It induces effects which could compromise precision measurements of cosmological parameters from large galaxy surveys.Comment: 8 pages, 4 figures, accepted for publication in MNRA

454-Pyrosequencing: A Molecular Battiscope for Freshwater Viral Ecology

Viruses, the most abundant biological entities on the planet, are capable of infecting organisms from all three branches of life, although the majority infect bacteria where the greatest degree of cellular diversity lies. However, the characterization and assessment of viral diversity in natural environments is only beginning to become a possibility. Through the development of a novel technique for the harvest of viral DNA and the application of 454 pyrosequencing, a snapshot of the diversity of the DNA viruses harvested from a standing pond on a cattle farm has been obtained. A high abundance of viral genotypes (785) were present within the virome. The absolute numbers of lambdoid and Shiga toxin (Stx) encoding phages detected suggested that the depth of sequencing had enabled recovery of only ca. 8% of the total virus population, numbers that agreed within less than an order of magnitude with predictions made by rarefaction analysis. The most abundant viral genotypes in the pond were bacteriophages (93.7%). The predominant viral genotypes infecting higher life forms found in association with the farm were pathogens that cause disease in cattle and humans, e.g. members of the Herpesviridae. The techniques and analysis described here provide a fresh approach to the monitoring of viral populations in the aquatic environment, with the potential to become integral to the development of risk analysis tools for monitoring the dissemination of viral agents of animal, plant and human diseases

SparkFlow : towards high-performance data analytics for Spark-based genome analysis

The recent advances in DNA sequencing technology triggered next-generation sequencing (NGS) research in full scale. Big Data (BD) is becoming the main driver in analyzing these large-scale bioinformatic data. However, this complicated process has become the system bottleneck, requiring an amalgamation of scalable approaches to deliver the needed performance and hide the deployment complexity. Utilizing cutting-edge scientific workflows can robustly address these challenges. This paper presents a Spark-based alignment workflow called SparkFlow for massive NGS analysis over singularity containers. SparkFlow is highly scalable, reproducible, and capable of parallelizing computation by utilizing data-level parallelism and load balancing techniques in HPC and Cloud environments. The proposed workflow capitalizes on benchmarking two state-of-art NGS workflows, i.e., BaseRecalibrator and ApplyBQSR. SparkFlow realizes the ability to accelerate large-scale cancer genomic analysis by scaling vertically (HyperThreading) and horizontally (provisions on-demand). Our result demonstrates a trade-off inevitably between the targeted applications and processor architecture. SparkFlow achieves a decisive improvement in NGS computation performance, throughput, and scalability while maintaining deployment complexity. The paper’s findings aim to pave the way for a wide range of revolutionary enhancements and future trends within the High-performance Data Analytics (HPDA) genome analysis realm.Postprin

Red Galaxy Growth and the Halo Occupation Distribution

We have traced the past 7 Gyr of red galaxy stellar mass growth within dark matter halos. We have determined the halo occupation distribution, which describes how galaxies reside within dark matter halos, using the observed luminosity function and clustering of 40,696 0.2<z<1.0 red galaxies in Bootes. Half of 10^{11.9} Msun/h halos host a red central galaxy, and this fraction increases with increasing halo mass. We do not observe any evolution of the relationship between red galaxy stellar mass and host halo mass, although we expect both galaxy stellar masses and halo masses to evolve over cosmic time. We find that the stellar mass contained within the red population has doubled since z=1, with the stellar mass within red satellite galaxies tripling over this redshift range. In cluster mass halos most of the stellar mass resides within satellite galaxies and the intra-cluster light, with a minority of the stellar mass residing within central galaxies. The stellar masses of the most luminous red central galaxies are proportional to halo mass to the power of a third. We thus conclude that halo mergers do not always lead to rapid growth of central galaxies. While very massive halos often double in mass over the past 7 Gyr, the stellar masses of their central galaxies typically grow by only 30%.Comment: Accepted for publication in the ApJ. 34 pages, 22 Figures, 5 Table

The mouse genetics toolkit: revealing function and mechanism

Large-scale projects are providing rapid global access to a wealth of mouse genetic resources to help discover disease genes and to manipulate their function

Integrating pest population models with biophysical crop models to better represent the farming system

Farming systems frameworks such as the Agricultural Production Systems simulator (APSIM) represent fluxes through the soil, plant and atmosphere of the system well, but do not generally consider the biotic constraints that function within the system. We designed a method that allowed population models built in DYMEX to interact with APSIM. The simulator engine component of the DYMEX population-modelling platform was wrapped within an APSIM module allowing it to get and set variable values in other APSIM models running in the simulation. A rust model developed in DYMEX is used to demonstrate how the developing rust population reduces the crop's green leaf area. The success of the linking process is seen in the interaction of the two models and how changes in rust population on the crop's leaves feedback to the APSIM crop modifying the growth and development of the crop's leaf area. This linking of population models to simulate pest populations and biophysical models to simulate crop growth and development increases the complexity of the simulation, but provides a tool to investigate biotic constraints within farming systems and further moves APSIM towards being an agro-ecological framework

Integrating pest population models with biophysical crop models to better represent the farming system

Farming systems frameworks such as the Agricultural Production Systems simulator (APSIM) represent fluxes through the soil, plant and atmosphere of the system well, but do not generally consider the biotic constraints that function within the system. We designed a method that allowed population models built in DYMEX to interact with APSIM. The simulator engine component of the DYMEX population-modelling platform was wrapped within an APSIM module allowing it to get and set variable values in other APSIM models running in the simulation. A rust model developed in DYMEX is used to demonstrate how the developing rust population reduces the crop's green leaf area. The success of the linking process is seen in the interaction of the two models and how changes in rust population on the crop's leaves feedback to the APSIM crop modifying the growth and development of the crop's leaf area. This linking of population models to simulate pest populations and biophysical models to simulate crop growth and development increases the complexity of the simulation, but provides a tool to investigate biotic constraints within farming systems and further moves APSIM towards being an agro-ecological framework

Whole system radar modelling::Simulation and validation

The ever-expanding horizon of radar applications demands solutions with high-end radar functionalities and technologies and is often limited by the available radar equipment, cost and time. A practical method to tackle the situation is to rely on the modelling and simulation of radar systems based on the user requirements. The comprehensive system-level modelling of a pulsed Doppler radar in MATLAB/Simulink consisting of all the fundamental blocks in the transmit chain, the environment, the receive chain, and the data processing chain is presented in this article. The first half of the article discusses the high-fidelity simulation of each building block in the radar model. In the second half of the article, the range-Doppler plot generated from the high-fidelity radar model is compared and validated using the range-Doppler plot from a real radar trial. The radar phase noise plays a crucial role in the detection of slowly moving, low radar cross-section targets in the presence of strong clutter. The article also briefly discusses the effects of radar oscillator phase noise in the range-Doppler plot. The validated, fully flexible radar model has the advantage of supporting the addition of further building blocks and optimising the parameters based on user requirements

AEGIS: Chandra Observation of DEEP2 Galaxy Groups and Clusters

We present a 200 ksec Chandra observation of seven spectroscopically selected, high redshift (0.75 < z < 1.03) galaxy groups and clusters discovered by the DEEP2 Galaxy Redshift Survey in the Extended Groth Strip (EGS). X-ray emission at the locations of these systems is consistent with background. The 3-sigma upper limits on the bolometric X-ray luminosities (L_X) of these systems put a strong constraint on the relation between L_X and the velocity dispersion of member galaxies sigma_gal at z~1; the DEEP2 systems have lower luminosity than would be predicted by the local relation. Our result is consistent with recent findings that at high redshift, optically selected clusters tend to be X-ray underluminous. A comparison with mock catalogs indicates that it is unlikely that this effect is entirely caused by a measurement bias between sigma_gal and the dark matter velocity dispersion. Physically, the DEEP2 systems may still be in the process of forming and hence not fully virialized, or they may be deficient in hot gas compared to local systems. We find only one possibly extended source in this Chandra field, which happens to lie outside the DEEP2 coverage.Comment: 5 pages, 3 figures. Accepted for publication in AEGIS ApJ Letters special editio

A List of Galaxies for Gravitational Wave Searches

We present a list of galaxies within 100 Mpc, which we call the Gravitational Wave Galaxy Catalogue (GWGC), that is currently being used in follow-up searches of electromagnetic counterparts from gravitational wave searches. Due to the time constraints of rapid follow-up, a locally available catalogue of reduced, homogenized data is required. To achieve this we used four existing catalogues: an updated version of the Tully Nearby Galaxy Catalog, the Catalog of Neighboring Galaxies, the V8k catalogue and HyperLEDA. The GWGC contains information on sky position, distance, blue magnitude, major and minor diameters, position angle, and galaxy type for 53,255 galaxies. Errors on these quantities are either taken directly from the literature or estimated based on our understanding of the uncertainties associated with the measurement method. By using the PGC numbering system developed for HyperLEDA, the catalogue has a reduced level of degeneracies compared to catalogues with a similar purpose and is easily updated. We also include 150 Milky Way globular clusters. Finally, we compare the GWGC to previously used catalogues, and find the GWGC to be more complete within 100 Mpc due to our use of more up-to-date input catalogues and the fact that we have not made a blue luminosity cut.Comment: Accepted for publication in Classical and Quantum Gravity, 13 pages, 7 figure