Deuterated formaldehyde in rho Ophiuchi A

From mapping observations of H2CO, HDCO, and D2CO, we have determined how the degree of deuterium fractionation changes over the central 3'x3' region of rho Oph A. The multi-transition data of the various H2CO isotopologues, as well as from other molecules (e.g., CH3OH and N2D+) present in the observed bands, were analysed using both the standard type rotation diagram analysis and, in selected cases, a more elaborate method of solving the radiative transfer for optically thick emission. In addition to molecular column densities, the analysis also estimates the kinetic temperature and H2 density. Toward the SM1 core in rho Oph A, the H2CO deuterium fractionation is very high. In fact, the observed D2CO/HDCO ratio is 1.34+/-0.19, while the HDCO/H2CO ratio is 0.107+/-0.015. This is the first time, to our knowledge, that the D2CO/HDCO abundance ratio is observed to be greater than 1. The kinetic temperature is in the range 20-30 K in the cores of rho Oph A, and the H2 density is (6-10)x10^5 cm-3. We estimate that the total H2 column density toward the deuterium peak is (1-4)x10^23 cm-2. As depleted gas-phase chemistry is not adequate, we suggest that grain chemistry, possibly due to abstraction and exchange reactions along the reaction chain H2CO -> HDCO -> D2CO, is at work to produce the very high deuterium levels observed.Comment: 17 pages, 11 figures, accepted for publication in Astronomy & Astrophysic

H2O line mapping at high spatial and spectral resolution - Herschel observations of the VLA1623 outflow

Apart from being an important coolant, H2O is known to be a tracer of high-velocity molecular gas. Recent models predict relatively high abundances behind interstellar shockwaves. The dynamical and physical conditions of the H2O emitting gas, however, are not fully understood yet. We aim to determine the abundance and distribution of H2O, its kinematics and the physical conditions of the gas responsible for the H2O emission. The observed line profile shapes help us understand the dynamics in molecular outflows. We mapped the VLA1623 outflow, in the ground-state transitions of o-H2O, with the HIFI and PACS instruments. We also present observations of higher energy transitions of o-H2O and p-H2O obtained with HIFI and PACS towards selected outflow positions. From comparison with non-LTE radiative transfer calculations, we estimate the physical parameters of the water emitting regions. The observed water emission line profiles vary over the mapped area. Spectral features and components, tracing gas in different excitation conditions, allow us to constrain the density and temperature of the gas. The H2O emission originates in a region where temperatures are comparable to that of the warm H2 gas (T\gtrsim200K). Thus, the H2O emission traces a gas component significantly warmer than the gas responsible for the low-J CO emission. The H2O column densities at the CO peak positions are low, i.e. N(H2O) \simeq (0.03-10)x10e14 cm-2. The H2O abundance with respect to H2 in the extended outflow is estimated at X(H2O)<1x10e-6, significantly lower than what would be expected from most recent shock models. The H2O emission traces a gas component moving at relatively high velocity compared to the low-J CO emitting gas. However, other dynamical quantities such as the momentum rate, energy and mechanical luminosity are estimated to be the same, independent of the molecular tracer used, CO or H2O.Comment: 14 pages, 13 figures, 4 table

Habitat structure: a fundamental concept and framework for urban soil ecology

Habitat structure is defined as the composition and arrangement of physical matter at a location. Although habitat structure is the physical template underlying ecological patterns and processes, the concept is relatively unappreciated and underdeveloped in ecology. However, it provides a fundamental concept for urban ecology because human activities in urban ecosystems are often targeted toward management of habitat structure. In addition, the concept emphasizes the fine-scale, on-the-ground perspective needed in the study of urban soil ecology. To illustrate this, urban soil ecology research is summarized from the perspective of habitat structure effects. Among the key conclusions emerging from the literature review are: (1) habitat structure provides a unifying theme for multivariate research about urban soil ecology; (2) heterogeneous urban habitat structures influence soil ecological variables in different ways; (3) more research is needed to understand relationships among sociological variables, habitat structure patterns and urban soil ecology. To stimulate urban soil ecology research, a conceptual framework is presented to show the direct and indirect relationships among habitat structure and ecological variables. Because habitat structure serves as a physical link between sociocultural and ecological systems, it can be used as a focus for interdisciplinary and applied research (e.g., pest management) about the multiple, interactive effects of urbanization on the ecology of soils

Control of star formation by supersonic turbulence

Understanding the formation of stars in galaxies is central to much of modern astrophysics. For several decades it has been thought that stellar birth is primarily controlled by the interplay between gravity and magnetostatic support, modulated by ambipolar diffusion. Recently, however, both observational and numerical work has begun to suggest that support by supersonic turbulence rather than magnetic fields controls star formation. In this review we outline a new theory of star formation relying on the control by turbulence. We demonstrate that although supersonic turbulence can provide global support, it nevertheless produces density enhancements that allow local collapse. Inefficient, isolated star formation is a hallmark of turbulent support, while efficient, clustered star formation occurs in its absence. The consequences of this theory are then explored for both local star formation and galactic scale star formation. (ABSTRACT ABBREVIATED)Comment: Invited review for "Reviews of Modern Physics", 87 pages including 28 figures, in pres

Multi-line detection of O2 toward rho Oph A

Models of pure gas-phase chemistry in well-shielded regions of molecular clouds predict relatively high levels of molecular oxygen, O2, and water, H2O. Contrary to expectation, the space missions SWAS and Odin found only very small amounts of water vapour and essentially no O2 in the dense star-forming interstellar medium. Only toward rho Oph A did Odin detect a weak line of O2 at 119 GHz in a beam size of 10 arcmin. A larger telescope aperture such as that of the Herschel Space Observatory is required to resolve the O2 emission and to pinpoint its origin. We use the Heterodyne Instrument for the Far Infrared aboard Herschel to obtain high resolution O2 spectra toward selected positions in rho Oph A. These data are analysed using standard techniques for O2 excitation and compared to recent PDR-like chemical cloud models. The 487.2GHz line was clearly detected toward all three observed positions in rho Oph A. In addition, an oversampled map of the 773.8GHz transition revealed the detection of the line in only half of the observed area. Based on their ratios, the temperature of the O2 emitting gas appears to vary quite substantially, with warm gas (> 50 K) adjacent to a much colder region, where temperatures are below 30 K. The exploited models predict O2 column densities to be sensitive to the prevailing dust temperatures, but rather insensitive to the temperatures of the gas. In agreement with these model, the observationally determined O2 column densities seem not to depend strongly on the derived gas temperatures, but fall into the range N(O2) = (3 to >6)e15/cm^2. Beam averaged O2 abundances are about 5e-8 relative to H2. Combining the HIFI data with earlier Odin observations yields a source size at 119 GHz of about 4 - 5 arcmin, encompassing the entire rho Oph A core.Comment: 10 pages, 8 figures intended for publication in A&

Complete Genome Sequence of the Complex Carbohydrate-Degrading Marine Bacterium, Saccharophagus degradans Strain 2-40T

The marine bacterium Saccharophagus degradans strain 2-40 (Sde 2-40) is emerging as a vanguard of a recently discovered group of marine and estuarine bacteria that recycles complex polysaccharides. We report its complete genome sequence, analysis of which identifies an unusually large number of enzymes that degrade >10 complex polysaccharides. Not only is this an extraordinary range of catabolic capability, many of the enzymes exhibit unusual architecture including novel combinations of catalytic and substrate-binding modules. We hypothesize that many of these features are adaptations that facilitate depolymerization of complex polysaccharides in the marine environment. This is the first sequenced genome of a marine bacterium that can degrade plant cell walls, an important component of the carbon cycle that is not well-characterized in the marine environment

Identification of 12 new susceptibility loci for different histotypes of epithelial ovarian cancer.

To identify common alleles associated with different histotypes of epithelial ovarian cancer (EOC), we pooled data from multiple genome-wide genotyping projects totaling 25,509 EOC cases and 40,941 controls. We identified nine new susceptibility loci for different EOC histotypes: six for serous EOC histotypes (3q28, 4q32.3, 8q21.11, 10q24.33, 18q11.2 and 22q12.1), two for mucinous EOC (3q22.3 and 9q31.1) and one for endometrioid EOC (5q12.3). We then performed meta-analysis on the results for high-grade serous ovarian cancer with the results from analysis of 31,448 BRCA1 and BRCA2 mutation carriers, including 3,887 mutation carriers with EOC. This identified three additional susceptibility loci at 2q13, 8q24.1 and 12q24.31. Integrated analyses of genes and regulatory biofeatures at each locus predicted candidate susceptibility genes, including OBFC1, a new candidate susceptibility gene for low-grade and borderline serous EOC

Altimetry for the future: Building on 25 years of progress

In 2018 we celebrated 25 years of development of radar altimetry, and the progress achieved by this methodology in the fields of global and coastal oceanography, hydrology, geodesy and cryospheric sciences. Many symbolic major events have celebrated these developments, e.g., in Venice, Italy, the 15th (2006) and 20th (2012) years of progress and more recently, in 2018, in Ponta Delgada, Portugal, 25 Years of Progress in Radar Altimetry. On this latter occasion it was decided to collect contributions of scientists, engineers and managers involved in the worldwide altimetry community to depict the state of altimetry and propose recommendations for the altimetry of the future. This paper summarizes contributions and recommendations that were collected and provides guidance for future mission design, research activities, and sustainable operational radar altimetry data exploitation. Recommendations provided are fundamental for optimizing further scientific and operational advances of oceanographic observations by altimetry, including requirements for spatial and temporal resolution of altimetric measurements, their accuracy and continuity. There are also new challenges and new openings mentioned in the paper that are particularly crucial for observations at higher latitudes, for coastal oceanography, for cryospheric studies and for hydrology. The paper starts with a general introduction followed by a section on Earth System Science including Ocean Dynamics, Sea Level, the Coastal Ocean, Hydrology, the Cryosphere and Polar Oceans and the ‘‘Green” Ocean, extending the frontier from biogeochemistry to marine ecology. Applications are described in a subsequent section, which covers Operational Oceanography, Weather, Hurricane Wave and Wind Forecasting, Climate projection. Instruments’ development and satellite missions’ evolutions are described in a fourth section. A fifth section covers the key observations that altimeters provide and their potential complements, from other Earth observation measurements to in situ data. Section 6 identifies the data and methods and provides some accuracy and resolution requirements for the wet tropospheric correction, the orbit and other geodetic requirements, the Mean Sea Surface, Geoid and Mean Dynamic Topography, Calibration and Validation, data accuracy, data access and handling (including the DUACS system). Section 7 brings a transversal view on scales, integration, artificial intelligence, and capacity building (education and training). Section 8 reviews the programmatic issues followed by a conclusion

AI is a viable alternative to high throughput screening: a 318-target study

: High throughput screening (HTS) is routinely used to identify bioactive small molecules. This requires physical compounds, which limits coverage of accessible chemical space. Computational approaches combined with vast on-demand chemical libraries can access far greater chemical space, provided that the predictive accuracy is sufficient to identify useful molecules. Through the largest and most diverse virtual HTS campaign reported to date, comprising 318 individual projects, we demonstrate that our AtomNet® convolutional neural network successfully finds novel hits across every major therapeutic area and protein class. We address historical limitations of computational screening by demonstrating success for target proteins without known binders, high-quality X-ray crystal structures, or manual cherry-picking of compounds. We show that the molecules selected by the AtomNet® model are novel drug-like scaffolds rather than minor modifications to known bioactive compounds. Our empirical results suggest that computational methods can substantially replace HTS as the first step of small-molecule drug discovery

A Probabilistic Model of Glenohumeral External Rotation Strength for Healthy Normals and Rotator Cuff Tear Cases

The reigning paradigm of musculoskeletal modeling is to construct deterministic models from parameters of an “average” subject and make predictions for muscle forces and joint torques with this model. This approach is limited because it does not perform well for outliers, and it does not model the effects of population parameter variability. The purpose of this study was to simulate variability in musculoskeletal parameters on glenohumeral external rotation strength in healthy normals, and in rotator cuff tear case using a Monte Carlo model. The goal was to determine if variability in musculoskeletal parameters could quantifiably explain variability in glenohumeral external rotation strength. Multivariate Gamma distributions for musculoskeletal architecture and moment arm were constructed from empirical data. Gamma distributions of measured joint strength were constructed. Parameters were sampled from the distributions and input to the model to predict muscle forces and joint torques. The model predicted measured joint torques for healthy normals, subjects with supraspinatus tears, and subjects with infraspinatus–supraspinatus tears with small error. Muscle forces for the three conditions were predicted and compared. Variability in measured torques can be explained by differences in parameter variability.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/44005/1/10439_2005_Article_9045.pd