The Genomedata format for storing large-scale functional genomics data

Summary: We present a format for efficient storage of multiple tracks of numeric data anchored to a genome. The format allows fast random access to hundreds of gigabytes of data, while retaining a small disk space footprint. We have also developed utilities to load data into this format. We show that retrieving data from this format is more than 2900 times faster than a naive approach using wiggle files

XMM-Newton Surveys of the Canada-France Redshift Survey Fields - III: The Environments of X-ray Selected AGN at 0.4<z<0.6

The environmental properties of a sample of 31 hard X-ray selected AGN are investigated, from scales of 500 kpc down to 30 kpc, and are compared to a control sample of inactive galaxies. The AGN all lie in the redshift range 0.4<z<0.6. The accretion luminosity-density of the Universe peaks close to this redshift range, and the AGN in the sample have X-ray luminosities close to the knee in the hard X-ray luminosity function, making them representative of the population which dominated this important phase of energy conversion. Using both the spatial clustering amplitude and near neighbour counts it is found that the AGN have environments that are indistinguishable from normal, inactive galaxies over the same redshift range and with similar optical properties. Typically, the environments are of sub-cluster richness, in contrast to similar studies of high-z quasars, which are often found in clusters with comparable richness to the Abell R>=0 clusters. It is suggested that minor mergers with low mass companions is a likely candidate for the mechanism by which these modest luminosity AGN are fuelled.Comment: 12 pages, 6 figures, accepted by MNRA

Globally sparse PLS regression

Volume 56 ; Print ISBN : 978-1-4614-8282-6Partial least squares (PLS) regression combines dimensionality reduction and prediction using a latent variable model. It provides better predictive ability than principle component analysis by taking into account both the independent and re- sponse variables in the dimension reduction procedure. However, PLS suffers from over-fitting problems for few samples but many variables. We formulate a new criterion for sparse PLS by adding a structured sparsity constraint to the global SIMPLS optimization. The constraint is a sparsity-inducing norm, which is useful for selecting the important variables shared among all the components. The optimization is solved by an augmented Lagrangian method to obtain the PLS components and to perform variable selection simultaneously. We propose a novel greedy algorithm to overcome the computation difficulties. Experiments demonstrate that our approach to PLS regression attains better performance with fewer selected predictor

Alternative global Cretaceous paleogeography

Plate tectonic reconstructions for the Cretaceous have assumed that the major continental blocks—Eurasia, Greenland, North America, South America, Africa, India, Australia, and Antarctica—had separated from one another by the end of the Early Cretaceous, and that deep ocean passages connected the Pacific, Tethyan, Atlantic, and Indian Ocean basins. North America, Eurasia, and Africa were crossed by shallow meridional seaways. This classic view of Cretaceous paleogeography may be incorrect. The revised view of the Early Cretaceous is one of three large continental blocks— North America–Eurasia, South America–Antarctica-India-Madagascar-Australia; and Africa—with large contiguous land areas surrounded by shallow epicontinental seas. There was a large open Pacific basin, a wide eastern Tethys, and a circum- African Seaway extending from the western Tethys (“Mediterranean”) region through the North and South Atlantic into the juvenile Indian Ocean between Madagascar-India and Africa. During the Early Cretaceous the deep passage from the Central Atlantic to the Pacific was blocked by blocks of northern Central America and by the Caribbean plate. There were no deep-water passages to the Arctic. Until the Late Cretaceous the Atlantic-Indian Ocean complex was a long, narrow, sinuous ocean basin extending off the Tethys and around Africa. Deep passages connecting the western Tethys with the Central Atlantic, the Central Atlantic with the Pacific, and the South Atlantic with the developing Indian Ocean appeared in the Late Cretaceous. There were many island land areas surrounded by shallow epicontinental seas at high sea-level stands

JHK Observations of Faint Standard Stars in the Mauna Kea Near-Infrared Photometric System

JHK photometry in the Mauna Kea Observatory (MKO) near-IR system is presented for 115 stars. Of these, 79 are UKIRT standards and 42 are LCO standards. The average brightness is 11.5 mag, with a range of 10 to 15. The average number of nights each star was observed is 4, and the average of the internal error of the final results is 0.011 mag. These JHK data agree with those reported by other groups to 0.02 mag. The measurements are used to derive transformations between the MKO JHK photometric system and the UKIRT, LCO and 2MASS systems. The 2MASS-MKO data scatter by 0.05 mag for redder stars: 2MASS-J includes H2O features in dwarfs and MKO-K includes CO features in giants. Transformations derived for stars whose spectra contain only weak features cannot give accurate transformations for objects with strong absorption features within a filter bandpasses. We find evidence of systematic effects at the 0.02 mag level in the photometry of stars with J<11 and H,K<10.5. This is due to an underestimate of the linearity correction for stars observed with the shortest exposure times; very accurate photometry of stars approaching the saturation limits of infrared detectors which are operated in double-read mode is difficult to obtain. Four stars in the sample, GSPC S705-D, FS 116 (B216-b7), FS 144 (Ser-EC84) and FS 32 (Feige 108), may be variable. 84 stars in the sample have 11< J< 15 and 10.5<H,K<15, are not suspected to be variable, and have magnitudes with an estimated error <0.027 mag; 79 of these have an error of <0.020 mag. These represent the first published high-accuracy JHK stellar photometry in the MKO photometric system; we recommend these objects be employed as primary standards for that system [abridged].Comment: Accepted for publication in MNRAS, 14 pages, 5 Figure

Evolution of trace gases and particles emitted by a chaparral fire in California

Biomass burning (BB) is a major global source of trace gases and particles. Accurately representing the production and evolution of these emissions is an important goal for atmospheric chemical transport models. We measured a suite of gases and aerosols emitted from an 81 hectare prescribed fire in chaparral fuels on the central coast of California, US on 17 November 2009. We also measured physical and chemical changes that occurred in the isolated downwind plume in the first ~4 h after emission. The measurements were carried out onboard a Twin Otter aircraft outfitted with an airborne Fourier transform infrared spectrometer (AFTIR), aerosol mass spectrometer (AMS), single particle soot photometer (SP2), nephelometer, LiCor CO_2 analyzer, a chemiluminescence ozone instrument, and a wing-mounted meteorological probe. Our measurements included: CO_2; CO; NO_x; NH_3; non-methane organic compounds; organic aerosol (OA); inorganic aerosol (nitrate, ammonium, sulfate, and chloride); aerosol light scattering; refractory black carbon (rBC); and ambient temperature, relative humidity, barometric pressure, and three-dimensional wind velocity. The molar ratio of excess O_3 to excess CO in the plume (ΔO_3/ΔCO) increased from −5.13 (±1.13) × 10^(−3) to 10.2 (±2.16) × 10^(−2) in ~4.5 h following smoke emission. Excess acetic and formic acid (normalized to excess CO) increased by factors of 1.73 ± 0.43 and 7.34 ± 3.03 (respectively) over the same time since emission. Based on the rapid decay of C_2H_4 we infer an in-plume average OH concentration of 5.27 (±0.97) × 10^6 molec cm^(−3), consistent with previous studies showing elevated OH concentrations in biomass burning plumes. Ammonium, nitrate, and sulfate all increased over the course of 4 h. The observed ammonium increase was a factor of 3.90 ± 2.93 in about 4 h, but accounted for just ~36% of the gaseous ammonia lost on a molar basis. Some of the gas phase NH_3 loss may have been due to condensation on, or formation of, particles below the AMS detection range. NO_x was converted to PAN and particle nitrate with PAN production being about two times greater than production of observable nitrate in the first ~4 h following emission. The excess aerosol light scattering in the plume (normalized to excess CO_2) increased by a factor of 2.50 ± 0.74 over 4 h. The increase in light scattering was similar to that observed in an earlier study of a biomass burning plume in Mexico where significant secondary formation of OA closely tracked the increase in scattering. In the California plume, however, ΔOA/ΔCO_2 decreased sharply for the first hour and then increased slowly with a net decrease of ~20% over 4 h. The fraction of thickly coated rBC particles increased up to ~85% over the 4 h aging period. Decreasing OA accompanied by increased scattering/particle coating in initial aging may be due to a combination of particle coagulation and evaporation processes. Recondensation of species initially evaporated from the particles may have contributed to the subsequent slow rise in OA. We compare our results to observations from other plume aging studies and suggest that differences in environmental factors such as smoke concentration, oxidant concentration, actinic flux, and RH contribute significantly to the variation in plume evolution observations

Brown carbon in tar balls from smoldering biomass combustion

We report the direct observation of laboratory production of spherical, carbonaceous particles- tar balls -from smoldering combustion of two commonly occurring dry mid-latitude fuels. Real-time measurements of spectrally varying absorption Ångström coefficients (AAC) indicate that a class of light absorbing organic carbon (OC) with wavelength dependent imaginary part of its refractive index-optically defined as brown carbon -is an important component of tar balls. The spectrum of the imaginary parts of their complex refractive indices can be described with a Lorentzian-like model with an effective resonance wavelength in the ultraviolet (UV) spectral region. Sensitivity calculations for aerosols containing traditional OC (no absorption at visible and UV wavelengths) and brown carbon suggest that accounting for near-UV absorption by brown carbon leads to an increase in aerosol radiative forcing efficiency and increased light absorption. Since particles from smoldering combustion account for nearly three-fourths of the total carbonaceous aerosol mass emitted globally, inclusion of the optical properties of tar balls into radiative forcing models has significance for the Earth\u27s radiation budget, optical remote sensing, and understanding of anomalous UV absorption in the troposphere

The genotype-phenotype relationship in multicellular pattern-generating models - the neglected role of pattern descriptors

Background: A deep understanding of what causes the phenotypic variation arising from biological patterning processes, cannot be claimed before we are able to recreate this variation by mathematical models capable of generating genotype-phenotype maps in a causally cohesive way. However, the concept of pattern in a multicellular context implies that what matters is not the state of every single cell, but certain emergent qualities of the total cell aggregate. Thus, in order to set up a genotype-phenotype map in such a spatiotemporal pattern setting one is actually forced to establish new pattern descriptors and derive their relations to parameters of the original model. A pattern descriptor is a variable that describes and quantifies a certain qualitative feature of the pattern, for example the degree to which certain macroscopic structures are present. There is today no general procedure for how to relate a set of patterns and their characteristic features to the functional relationships, parameter values and initial values of an original pattern-generating model. Here we present a new, generic approach for explorative analysis of complex patterning models which focuses on the essential pattern features and their relations to the model parameters. The approach is illustrated on an existing model for Delta-Notch lateral inhibition over a two-dimensional lattice. Results: By combining computer simulations according to a succession of statistical experimental designs, computer graphics, automatic image analysis, human sensory descriptive analysis and multivariate data modelling, we derive a pattern descriptor model of those macroscopic, emergent aspects of the patterns that we consider of interest. The pattern descriptor model relates the values of the new, dedicated pattern descriptors to the parameter values of the original model, for example by predicting the parameter values leading to particular patterns, and provides insights that would have been hard to obtain by traditional methods. Conclusion: The results suggest that our approach may qualify as a general procedure for how to discover and relate relevant features and characteristics of emergent patterns to the functional relationships, parameter values and initial values of an underlying pattern-generating mathematical model

Predicting Crystal Structures with Data Mining of Quantum Calculations

Predicting and characterizing the crystal structure of materials is a key problem in materials research and development. It is typically addressed with highly accurate quantum mechanical computations on a small set of candidate structures, or with empirical rules that have been extracted from a large amount of experimental information, but have limited predictive power. In this letter, we transfer the concept of heuristic rule extraction to a large library of ab-initio calculated information, and demonstrate that this can be developed into a tool for crystal structure prediction.Comment: 4 pages, 3 pic

Results of a climate model for Triassic Pangaea

We have used a new General Circulation Model, GENESIS Version 1.02, derived from the U. S. National Center for Atmospheric Research Community Climate Model I (NCAR-CCM I) to simulate the climate of an Earth with realistic Pangaean geography. The climate model was run assuming that the ocean heat flux was similar to that of today, atmospheric C02 content was four times that of today, the solar constant was 2 % less than today, and the Earth's orbit was circular, with mean obliquity 23.4°. Models were run for paleogeographies at 245 Ma (Scythian) and 225 Ma (Carnian). The results indicate that no ice cap would develop over the land, and there is no permanent sea ice. The seasonal temperature Variation in the interior of the continent is in the order of 50 °C. The Continental areas are very dry except for a few Coastal areas and along uplifts. The models both suggest an extreme seasonal monsoonal circulation, with strong westerly winds parallel to the entire coast of Gondwana and the east coast of Laurasia during the northern hemisphere summet. In both hemispheres, the effect is to cause coastal upwelling. The model also predicts permafrost in the deeper soil layers poleward of 50° N and S. The effects of topographic uplifts on the atmospheric circulation are pervasive. Topography strongly affects the monsoonal circulation causing major deviations of the wind Systems suggested in model runs with idealized geographies. Topography also plays a crucial role in concentrating rainfall in a few small areas. It is evident that in order to have a realistic Simulation of paleoclimate, an accurate representation of the paleotopography is essential. It is also evident that the paleoclimate models may be useful in suggesting geological criteria that can confirm or reject the predicted paleoclimatic conditions