The Accuracy of Subhalo Detection

With the ever increasing resolution of N-body simulations, accurate subhalo detection is becoming essential in the study of the formation of structure, the production of merger trees and the seeding of semi-analytic models. To investigate the state of halo finders, we compare two different approaches to detecting subhaloes; the first based on overdensities in a halo and the second being adaptive mesh refinement. A set of stable mock NFW dark matter haloes were produced and a subhalo was placed at different radii within a larger halo. SUBFIND (a Friends-of-Friends based finder) and AHF (an adaptive mesh based finder) were employed to recover the subhalo. As expected, we found that the mass of the subhalo recovered by SUBFIND has a strong dependence on the radial position and that neither halo finder can accurately recover the subhalo when it is very near the centre of the halo. This radial dependence is shown to be related to the subhalo being truncated by the background density of the halo and originates due to the subhalo being defined as an overdensity. If the subhalo size is instead determined using the peak of the circular velocity profile, a much more stable value is recovered. The downside to this is that the maximum circular velocity is a poor measure of stripping and is affected by resolution. For future halo finders to recover all the particles in a subhalo, a search of phase space will need to be introduced.Comment: 9 pages, 7 figures, accepted for publication in MNRA

Identification and correction of systematic error in high-throughput sequence data

A feature common to all DNA sequencing technologies is the presence of base-call errors in the sequenced reads. The implications of such errors are application specific, ranging from minor informatics nuisances to major problems affecting biological inferences. Recently developed “next-gen” sequencing technologies have greatly reduced the cost of sequencing, but have been shown to be more error prone than previous technologies. Both position specific (depending on the location in the read) and sequence specific (depending on the sequence in the read) errors have been identified in Illumina and Life Technology sequencing platforms. We describe a new type of _systematic_ error that manifests as statistically unlikely accumulations of errors at specific genome (or transcriptome) locations. We characterize and describe systematic errors using overlapping paired reads form high-coverage data. We show that such errors occur in approximately 1 in 1000 base pairs, and that quality scores at systematic error sites do not account for the extent of errors. We identify motifs that are frequent at systematic error sites, and describe a classifier that distinguishes heterozygous sites from systematic error. Our classifier is designed to accommodate data from experiments in which the allele frequencies at heterozygous sites are not necessarily 0.5 (such as in the case of RNA-Seq). Systematic errors can easily be mistaken for heterozygous sites in individuals, or for SNPs in population analyses. Systematic errors are particularly problematic in low coverage experiments, or in estimates of allele-specific expression from RNA-Seq data. Our characterization of systematic error has allowed us to develop a program, called SysCall, for identifying and correcting such errors. We conclude that correction of systematic errors is important to consider in the design and interpretation of high-throughput sequencing experiments

Feasibility study on the design of a probe for rectal cancer detection

Rectal examination techniques are considered in terms of detection capability, patient acceptance, and cost reduction. A review of existing clinical techniques are considered in terms of detection capability, patient acceptance, and cost reduction. A review of existing clinical techniques and of relevant aerospace technology included evaluation of the applicability of visual, thermal, ultrasound, and radioisotope modalities of examination. The desired improvements can be obtained by redesigning the proctosigmoidoscope to have reduced size, additional visibility, and the capability of readily providing a color photograph of the entire rectosigmoid mucosa in a single composite view

Galaxies going MAD: The Galaxy-Finder Comparison Project

With the ever increasing size and complexity of fully self-consistent simulations of galaxy formation within the framework of the cosmic web, the demands upon object finders for these simulations has simultaneously grown. To this extent we initiated the Halo Finder Comparison Project that gathered together all the experts in the field and has so far led to two comparison papers, one for dark matter field haloes (Knebe et al. 2011), and one for dark matter subhaloes (Onions et al. 2012). However, as state-of-the-art simulation codes are perfectly capable of not only following the formation and evolution of dark matter but also account for baryonic physics (e.g. hydrodynamics, star formation, feedback) object finders should also be capable of taking these additional processes into consideration. Here we report on a comparison of codes as applied to the Constrained Local UniversE Simulation (CLUES) of the formation of the Local Group which incorporates much of the physics relevant for galaxy formation. We compare both the properties of the three main galaxies in the simulation (representing the MW, M31, and M33) as well as their satellite populations for a variety of halo finders ranging from phase-space to velocity-space to spherical overdensity based codes, including also a mere baryonic object finder. We obtain agreement amongst codes comparable to (if not better than) our previous comparisons, at least for the total, dark, and stellar components of the objects. However, the diffuse gas content of the haloes shows great disparity, especially for low-mass satellite galaxies. This is primarily due to differences in the treatment of the thermal energy during the unbinding procedure. We acknowledge that the handling of gas in halo finders is something that needs to be dealt with carefully, and the precise treatment may depend sensitively upon the scientific problem being studied.Comment: 14 interesting pages, 17 beautiful figures, and 2 informative tables accepted for publication in MNRAS (matches published version

Streams Going Notts: The tidal debris finder comparison project

While various codes exist to systematically and robustly find haloes and subhaloes in cosmological simulations (Knebe et al., 2011, Onions et al., 2012), this is the first work to introduce and rigorously test codes that find tidal debris (streams and other unbound substructure) in fully cosmological simulations of structure formation. We use one tracking and three non-tracking codes to identify substructure (bound and unbound) in a Milky Way type simulation from the Aquarius suite (Springel et al., 2008) and post-process their output with a common pipeline to determine the properties of these substructures in a uniform way. By using output from a fully cosmological simulation, we also take a step beyond previous studies of tidal debris that have used simple toy models. We find that both tracking and non-tracking codes agree well on the identification of subhaloes and more importantly, the {\em unbound tidal features} associated with them. The distributions of basic properties of the total substructure distribution (mass, velocity dispersion, position) are recovered with a scatter of $\sim20$. Using the tracking code as our reference, we show that the non-tracking codes identify complex tidal debris with purities of $\sim40$. Analysing the results of the substructure finders, we find that the general distribution of {\em substructures} differ significantly from the distribution of bound {\em subhaloes}. Most importantly, both bound and unbound {\em substructures} together constitute $\sim18$ of the host halo mass, which is a factor of $\sim2$ higher than the fraction in self-bound {\em subhaloes}. However, this result is restricted by the remaining challenge to cleanly define when an unbound structure has become part of the host halo. Nevertheless, the more general substructure distribution provides a more complete picture of a halo's accretion history.Comment: 19 pages, 12 figures, accepted for publication in MNRA

Stagnation and mass loss on a Himalayan debris-covered glacier: processes, patterns and rates

This research was supported financially by the University Centre in Svalbard (UNIS), National Geographic Society GRANT #W135-10, The Natural Environmental Research Council and the European Commission FP7-MC-IEF.The ablation areas of debris-covered glaciers typically consist of a complex mosaic of surface features with contrasting processes and rates of mass loss. This greatly complicates glacier response to climate change, and increases the uncertainty of predictive models. In this paper we present a series of high-resolution DEMs and repeat lake bathymetric surveys on Ngozumpa Glacier, Nepal, to study processes and patterns of mass loss on a Himalayan debris-covered glacier in unprecedented detail. Most mass loss occurs by melt below supraglacial debris, and melt and calving of ice cliffs (backwasting). Although ice cliffs cover only ∼5% of the area of the lower tongue, they account for 40% of the ablation. The surface debris layer is subject to frequent re-distribution by slope processes, resulting in large spatial and temporal differences in debris-layer thickness, enhancing or inhibiting local ablation rates and encouraging continuous topographic inversion. A moraine-dammed lake on the lower glacier tongue (Spillway Lake) underwent a period of rapid expansion from 2001 to 2009, but later experienced a reduction of area and volume as a result of lake level lowering and sediment redistribution. Rapid lake growth will likely resume in the near future, and may eventually become up to 7 km long.Publisher PDFPeer reviewe