A High-Level Programming Language for Modelling the Earth

Computational models based on the solution of partial differential equations (PDEs) play a key role in Earth systems simulations. The software implementing these models depends on the discretisation method, data structures and the computer architecture. For this reason, it is difficult for scientists to implement new models without strong software engineering skills. In this paper, we present a computational modeling language (escript) based on the object-oriented scripting language (Python). This language, is designed to implement PDE-based models with a high degree of abstraction from the underlying discretization techniques and their implementation. The main components of escript are the Data class objects which handle data with a spatial distribution and the linearPDE class which define linear PDEs to be solved in each step of a time integration or non-linear iteration scheme. As an example we will discuss the solution of the Lame equation and the implementation of a quasi-static model for crustal fault systems

Chalcogen-hyperdoped germanium for short-wavelength infrared photodetection

Obtaining short-wavelength-infrared (SWIR; 1.4 μm–3.0 μm) room-temperature photodetection in a low-cost, group IV semiconductor is desirable for numerous applications. We demonstrate a non-equilibrium method for hyperdoping germanium with selenium or tellurium for dopant-mediated SWIR photodetection. By ion-implanting Se or Te into Ge wafers and restoring crystallinity with pulsed laser melting induced rapid solidification, we obtain single crystalline materials with peak Se and Te concentrations of 1020 cm−3 (104 times the solubility limits). These hyperdoped materials exhibit sub-bandgap absorption of light up to wavelengths of at least 3.0 μm, with their sub-bandgap optical absorption coefficients comparable to those of commercial SWIR photodetection materials. Although previous studies of Ge-based photodetectors have reported a sub-bandgap optoelectronic response only at low temperature, we report room-temperature sub-bandgap SWIR photodetection at wavelengths as long as 3.0 μm from rudimentary hyperdoped Ge:Se and Ge:Te photodetectors

Au-rich filamentary behavior and associated subband gap optical absorption in hyperdoped Si

Au-hyperdoped Si, synthesized by ion implantation and pulsed laser melting, is known to exhibit a strong sub-band gap photoresponse that scales monotonically with the Au concentration. However, there is thought to be a limit to this behavior since ultrahigh Au concentrations (>1 x 10(20) cm(-3)) are expected to induce cellular breakdown during the rapid resolidification of Si, a process that is associated with significant lateral impurity precipitation. This work shows that the cellular morphology observed in Au-hyperdoped Si differs from that in conventional, steady-state cellular breakdown. In particular, Rutherford backscattering spectrometry combined with channeling and transmission electron microscopy revealed an inhomogeneous Au distribution and a subsurface network of Au-rich filaments, within which the Au impurities largely reside on substitutional positions in the crystalline Si lattice, at concentrations as high as similar to 3 at. %. The measured substitutional Au dose, regardless of the presence of Au-rich filaments, correlates strongly with the sub-band gap optical absorptance. Upon subsequent thermal treatment, the supersaturated Au forms precipitates, while the Au substitutionality and the sub-band gap optical absorption both decrease. These results offer insight into a metastable filamentary regime in Au-hyperdoped Si that has important implications for Si-based infrared optoelectronics.The US Army (Contract No. FA5209-16-P-0104) for partial financial support of this project

Dark Matter Candidates: A Ten-Point Test

An extraordinarily rich zoo of non-baryonic Dark Matter candidates has been proposed over the last three decades. Here we present a 10-point test that a new particle has to pass, in order to be considered a viable DM candidate: I.) Does it match the appropriate relic density? II.) Is it {\it cold}? III.) Is it neutral? IV.) Is it consistent with BBN? V.) Does it leave stellar evolution unchanged? VI.) Is it compatible with constraints on self-interactions? VII.) Is it consistent with {\it direct} DM searches? VIII.) Is it compatible with gamma-ray constraints? IX.) Is it compatible with other astrophysical bounds? X.) Can it be probed experimentally?Comment: 29 pages, 12 figure

The WiggleZ Dark Energy Survey: final data release and the metallicity of UV-luminous galaxies

The WiggleZ Dark Energy Survey measured the redshifts of over 200 000 ultraviolet (UV)- selected (NUV < 22.8 mag) galaxies on the Anglo-Australian Telescope. The survey detected the baryon acoustic oscillation signal in the large-scale distribution of galaxies over the redshift range 0.2 < z < 1.0, confirming the acceleration of the expansion of the Universe and measuring the rate of structure growth within it. Here, we present the final data release of the survey: a catalogue of 225 415 galaxies and individual files of the galaxy spectra. We analyse the emission-line properties of these UV-luminous Lyman-break galaxies by stacking the spectra in bins of luminosity, redshift, and stellar mass. The most luminous (-25 mag < MFUV < -22 mag) galaxies have very broad Hβ emission from active nuclei, as well as a broad second component to the [OIII] (495.9 nm, 500.7 nm) doublet lines that is blueshifted by 100 km s-1, indicating the presence of gas outflows in these galaxies. The composite spectra allow us to detect and measure the temperature-sensitive [O III] (436.3 nm) line and obtain metallicities using the direct method. The metallicities of intermediate stellar mass (8.8 < log (M*/M⊙) < 10)WiggleZ galaxies are consistent with normal emission-line galaxies at the samemasses. In contrast, the metallicities of high stellarmass (10 < log (M*/M⊙) < 12) WiggleZ galaxies are significantly lower than for normal emission-line galaxies at the same masses. This is not an effect of evolution as the metallicities do not vary with redshift; it is most likely a property specific to the extremely UV-luminous WiggleZ galaxies

Disease-Related Cardiac Troponins Alter Thin Filament Ca2+ Association and Dissociation Rates

The contractile response of the heart can be altered by disease-related protein modifications to numerous contractile proteins. By utilizing an IAANS labeled fluorescent troponin C, , we examined the effects of ten disease-related troponin modifications on the Ca2+ binding properties of the troponin complex and the reconstituted thin filament. The selected modifications are associated with a broad range of cardiac diseases: three subtypes of familial cardiomyopathies (dilated, hypertrophic and restrictive) and ischemia-reperfusion injury. Consistent with previous studies, the majority of the protein modifications had no effect on the Ca2+ binding properties of the isolated troponin complex. However, when incorporated into the thin filament, dilated cardiomyopathy mutations desensitized (up to 3.3-fold), while hypertrophic and restrictive cardiomyopathy mutations, and ischemia-induced truncation of troponin I, sensitized the thin filament to Ca2+ (up to 6.3-fold). Kinetically, the dilated cardiomyopathy mutations increased the rate of Ca2+ dissociation from the thin filament (up to 2.5-fold), while the hypertrophic and restrictive cardiomyopathy mutations, and the ischemia-induced truncation of troponin I decreased the rate (up to 2-fold). The protein modifications also increased (up to 5.4-fold) or decreased (up to 2.5-fold) the apparent rate of Ca2+ association to the thin filament. Thus, the disease-related protein modifications alter Ca2+ binding by influencing both the association and dissociation rates of thin filament Ca2+ exchange. These alterations in Ca2+ exchange kinetics influenced the response of the thin filament to artificial Ca2+ transients generated in a stopped-flow apparatus. Troponin C may act as a hub, sensing physiological and pathological stimuli to modulate the Ca2+-binding properties of the thin filament and influence the contractile performance of the heart

A framework for human microbiome research

A variety of microbial communities and their genes (the microbiome) exist throughout the human body, with fundamental roles in human health and disease. The National Institutes of Health (NIH)-funded Human Microbiome Project Consortium has established a population-scale framework to develop metagenomic protocols, resulting in a broad range of quality-controlled resources and data including standardized methods for creating, processing and interpreting distinct types of high-throughput metagenomic data available to the scientific community. Here we present resources from a population of 242 healthy adults sampled at 15 or 18 body sites up to three times, which have generated 5,177 microbial taxonomic profiles from 16S ribosomal RNA genes and over 3.5 terabases of metagenomic sequence so far. In parallel, approximately 800 reference strains isolated from the human body have been sequenced. Collectively, these data represent the largest resource describing the abundance and variety of the human microbiome, while providing a framework for current and future studies

Structure, function and diversity of the healthy human microbiome

Author Posting. © The Authors, 2012. This article is posted here by permission of Nature Publishing Group. The definitive version was published in Nature 486 (2012): 207-214, doi:10.1038/nature11234.Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and vagina. Much of this diversity remains unexplained, although diet, environment, host genetics and early microbial exposure have all been implicated. Accordingly, to characterize the ecology of human-associated microbial communities, the Human Microbiome Project has analysed the largest cohort and set of distinct, clinically relevant body habitats so far. We found the diversity and abundance of each habitat’s signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals. The project encountered an estimated 81–99% of the genera, enzyme families and community configurations occupied by the healthy Western microbiome. Metagenomic carriage of metabolic pathways was stable among individuals despite variation in community structure, and ethnic/racial background proved to be one of the strongest associations of both pathways and microbes with clinical metadata. These results thus delineate the range of structural and functional configurations normal in the microbial communities of a healthy population, enabling future characterization of the epidemiology, ecology and translational applications of the human microbiome.This research was supported in part by National Institutes of Health grants U54HG004969 to B.W.B.; U54HG003273 to R.A.G.; U54HG004973 to R.A.G., S.K.H. and J.F.P.; U54HG003067 to E.S.Lander; U54AI084844 to K.E.N.; N01AI30071 to R.L.Strausberg; U54HG004968 to G.M.W.; U01HG004866 to O.R.W.; U54HG003079 to R.K.W.; R01HG005969 to C.H.; R01HG004872 to R.K.; R01HG004885 to M.P.; R01HG005975 to P.D.S.; R01HG004908 to Y.Y.; R01HG004900 to M.K.Cho and P. Sankar; R01HG005171 to D.E.H.; R01HG004853 to A.L.M.; R01HG004856 to R.R.; R01HG004877 to R.R.S. and R.F.; R01HG005172 to P. Spicer.; R01HG004857 to M.P.; R01HG004906 to T.M.S.; R21HG005811 to E.A.V.; M.J.B. was supported by UH2AR057506; G.A.B. was supported by UH2AI083263 and UH3AI083263 (G.A.B., C. N. Cornelissen, L. K. Eaves and J. F. Strauss); S.M.H. was supported by UH3DK083993 (V. B. Young, E. B. Chang, F. Meyer, T. M. S., M. L. Sogin, J. M. Tiedje); K.P.R. was supported by UH2DK083990 (J. V.); J.A.S. and H.H.K. were supported by UH2AR057504 and UH3AR057504 (J.A.S.); DP2OD001500 to K.M.A.; N01HG62088 to the Coriell Institute for Medical Research; U01DE016937 to F.E.D.; S.K.H. was supported by RC1DE0202098 and R01DE021574 (S.K.H. and H. Li); J.I. was supported by R21CA139193 (J.I. and D. S. Michaud); K.P.L. was supported by P30DE020751 (D. J. Smith); Army Research Office grant W911NF-11-1-0473 to C.H.; National Science Foundation grants NSF DBI-1053486 to C.H. and NSF IIS-0812111 to M.P.; The Office of Science of the US Department of Energy under Contract No. DE-AC02-05CH11231 for P.S. C.; LANL Laboratory-Directed Research and Development grant 20100034DR and the US Defense Threat Reduction Agency grants B104153I and B084531I to P.S.C.; Research Foundation - Flanders (FWO) grant to K.F. and J.Raes; R.K. is an HHMI Early Career Scientist; Gordon&BettyMoore Foundation funding and institutional funding fromthe J. David Gladstone Institutes to K.S.P.; A.M.S. was supported by fellowships provided by the Rackham Graduate School and the NIH Molecular Mechanisms in Microbial Pathogenesis Training Grant T32AI007528; a Crohn’s and Colitis Foundation of Canada Grant in Aid of Research to E.A.V.; 2010 IBM Faculty Award to K.C.W.; analysis of the HMPdata was performed using National Energy Research Scientific Computing resources, the BluBioU Computational Resource at Rice University