Alas, the dark matter structures were not that trivial

The radial density profile of dark matter structures has been observed to have an almost universal behaviour in numerical simulations, however, the physical reason for this behaviour remains unclear. It has previously been shown that if the pseudo phase-space density, rho/sigma_d^epsilon, is a beautifully simple power-law in radius, with the "golden values" epsilon=3 and d=r (i.e., the phase-space density is only dependent on the radial component of the velocity dispersion), then one can analytically derive the radial variation of the mass profile, dispersion profile etc. That would imply, if correct, that we just have to explain why rho/sigma^3_r ~r^{-alpha}, and then we would understand everything about equilibrated DM structures. Here we use a set of simulated galaxies and clusters of galaxies to demonstrate that there are no such golden values, but that each structure instead has its own set of values. Considering the same structure at different redshifts shows no evolution of the phase-space parameters towards fixed points. There is also no clear connection between the halo virialized mass and these parameters. This implies that we still do not understand the origin of the profiles of dark matter structures.Comment: 4 pages, 3 figures, accepted for publication in ApJ

Viewpoint consistency in Z and LOTOS: A case study

Specification by viewpoints is advocated as a suitable method of specifying complex systems. Each viewpoint describes the envisaged system from a particular perspective, using concepts and specification languages best suited for that perspective. Inherent in any viewpoint approach is the need to check or manage the consistency of viewpoints and to show that the different viewpoints do not impose contradictory requirements. In previous work we have described a range of techniques for consistency checking, refinement, and translation between viewpoint specifications, in particular for the languages LOTOS and Z. These two languages are advocated in a particular viewpoint model, viz. that of the Open Distributed Processing (ODP) reference model. In this paper we present a case study which demonstrates how all these techniques can be combined in order to show consistency between a viewpoint specified in LOTOS and one specified in Z. Keywords: Viewpoints; Consistency; Z; LOTOS; ODP

Dark energy and dark matter from cosmological observations

The present status of our knowledge about the dark matter and dark energy is reviewed. Bounds on the content of cold and hot dark matter from cosmological observations are discussed in some detail. I also review current bounds on the physical properties of dark energy, mainly its equation of state and effective speed of sound.Comment: 12 pages, 4 figures, to appear in Lepton-Photon 2005 proceedings, added figure and typos correcte

Correlating microbial community profiles with geochemical data in highly stratified sediments from the Arctic Mid-Ocean Ridge

Microbial communities and their associated metabolic activity in marine sediments have a profound impact on global biogeochemical cycles. Their composition and structure are attributed to geochemical and physical factors, but finding direct correlations has remained a challenge. Here we show a significant statistical relationship between variation in geochemical composition and prokaryotic community structure within deep-sea sediments. We obtained comprehensive geochemical data from two gravity cores near the hydrothermal vent field Loki’s Castle at the Arctic Mid-Ocean Ridge, in the Norwegian- Greenland Sea. Geochemical properties in the rift valley sediments exhibited strong centimeter-scale stratigraphic variability. Microbial populations were profiled by pyrosequencing from 15 sediment horizons (59,364 16S rRNA gene tags), quantitatively assessed by qPCR, and phylogenetically analyzed. Although the same taxa were generally present in all samples, their relative abundances varied substantially among horizons and fluctuated between Bacteria- and Archaea-dominated communities. By independently summarizing covariance structures of the relative abundance data and geochemical data, using principal components analysis, we found a significant correlation between changes in geochemical composition and changes in community structure. Differences in organic carbon and mineralogy shaped the relative abundance of microbial taxa. We used correlations to build hypotheses about energy metabolisms, particularly of the Deep Sea Archaeal Group, specific Deltaproteobacteria, and sediment lineages of potentially anaerobic Marine Group I Archaea. We demonstrate that total prokaryotic community structure can be directly correlated to geochemistry within these sediments, thus enhancing our understanding of biogeochemical cycling and our ability to predict metabolisms of uncultured microbes in deep-sea sediments

Computational protein profile similarity screening for quantitative mass spectrometry experiments

Motivation: The qualitative and quantitative characterization of protein abundance profiles over a series of time points or a set of environmental conditions is becoming increasingly important. Using isobaric mass tagging experiments, mass spectrometry-based quantitative proteomics deliver accurate peptide abundance profiles for relative quantitation. Associated data analysis workflows need to provide tailored statistical treatment that (i) takes the correlation structure of the normalized peptide abundance profiles into account and (ii) allows inference of protein-level similarity. We introduce a suitable distance measure for relative abundance profiles, derive a statistical test for equality and propose a protein-level representation of peptide-level measurements. This yields a workflow that delivers a similarity ranking of protein abundance profiles with respect to a defined reference. All procedures have in common that they operate based on the true correlation structure that underlies the measurements. This optimizes power and delivers more intuitive and efficient results than existing methods that do not take these circumstances into account. Results: We use protein profile similarity screening to identify candidate proteins whose abundances are post-transcriptionally controlled by the Anaphase Promoting Complex/Cyclosome (APC/C), a specific E3 ubiquitin ligase that is a master regulator of the cell cycle. Results are compared with an established protein correlation profiling method. The proposed procedure yields a 50.9-fold enrichment of co-regulated protein candidates and a 2.5-fold improvement over the previous method

Loss of chromosome 11q21–23.1 and 17p and gain of chromosome 6p are independent prognostic indicators in B-cell non-Hodgkin's lymphoma

Comparative genomic hybridization (CGH) was employed to study chromosomal aberrations in relation to cell proliferation, apoptosis, and patient survival in 94 cases of B-cell non-Hodgkin's lymphoma diagnosed between 1983 and 1993. Eighty cases had aberrations by CGH. Chromosomal regions 1p21–31.1 (10%), 6cen-q24 (12%), 8p (11%), 9p21-ter (14%), 11q21–23.1 (11%), 13q13–21.1 (12%), and 17p (15%) were frequently lost. Gains were found at 3q21-ter (22%), 6p (11%), 7p (12%), 8q23-ter (13%), 12cen-q15 (17%), 17q24-ter (13%), and 18q13.3–21 (20%). A high number of aberrations (≥ 4, 33 cases) was associated (P ≤ 0.001) with the mantle cell and diffuse large B-cell lymphoma subtypes, a high fraction of tumour cells in S phase, and short survival (RR (relative risk) = 3.7). Loss of 1p21–31.1, 8p, 9p21-ter, 11q21–23.1, and 13q13–21.1 were associated with mantle cell lymphoma (P ≤ 0.03), while gain of 6p and 12cen-q15 were more frequent in diffuse large B-cell and small lymphocytic lymphoma, respectively (P = 0.04). Loss of 8p and 17p, and gain of 3q21-ter, 6p, 7p, and 8q23-ter were associated with a high S phase fraction (P ≤ 0.03), but none of the aberrations were associated with tumour apoptotic fraction (P ≥ 0.13). The most important prognostic CGH parameters (P < 0.001) were losses of 11q21–23.1 (RR = 3.8) and 17p (RR = 4.4), and gain of 6p (RR = 4.2). The latter parameters and IPI were the only ones with independent prognostic value (RR = 10, 5.0, 6.7, and 3.7, respectively; P < 0.001) when assessed together with lymphoma sub-type, primary versus relapse cases, treatment, B symptoms, S phase fraction, and presence of BCL1 and BCL2 translocations. A combined CGH/IPI binary parameter had high prognostic value for patients receiving different treatments, with various lymphoma sub-types, and for primary as well as relapse cases.© 2001 Cancer Research Campaign http://www.bjcancer.co

An alternative to grids and glasses: Quaquaversal pre-initial conditions for N-body simulations

N-body simulations sample their initial conditions on an initial particle distribution, which for cosmological simulations is usually a glass or grid, whilst a Poisson distribution is used for galaxy models, spherical collapse etc. These pre-initial conditions have inherent correlations, noise due to discreteness and preferential alignments, whilst the glass distribution is poorly defined and computationally expensive to construct. We present a novel particle distribution which can be useful as a pre-initial condition for N-body simulations, using a simple construction based on a ``quaquaversal'' tiling of space. This distribution has little preferred orientation (i.e. is statistically isotropic), has a rapidly vanishing large scale power-spectrum (P(k) ~ k^4), and is trivial to create. It should be particularly useful for warm dark matter and cold collapse simulations.Comment: 8 pages, 6 figures, extended discussion of level of isotropy, matches version accepted in Ap