Version control of pathway models using XML patches

<p>Background: Computational modelling has become an important tool in understanding biological systems such as signalling pathways. With an increase in size complexity of models comes a need for techniques to manage model versions and their relationship to one another. Model version control for pathway models shares some of the features of software version control but has a number of differences that warrant a specific solution.</p> <p>Results: We present a model version control method, along with a prototype implementation, based on XML patches. We show its application to the EGF/RAS/RAF pathway.</p> <p>Conclusion: Our method allows quick and convenient storage of a wide range of model variations and enables a thorough explanation of these variations. Trying to produce these results without such methods results in slow and cumbersome development that is prone to frustration and human error.</p&gt

Variability of Internally Generated Turbulence in an Estuary, from 100 Days of Continuous Observations

We present detailed observations of internally generated turbulence in a sheared, stratified natural flow, as well as an analysis of the external factors leading to its generation and temporal variability. Multi-month time series of vertical profiles of velocity, acoustic backscatter (0.5 Hz), and turbulence parameters were collected with two moored acoustic Doppler current profilers (ADCPs) in the Hudson River estuary, and estuary-long transects of water density were collected 30 times. ADCP backscatter is used for visualization of coherent turbulent structures and evaluation of surface wave biases to the turbulence measurements. Benefits of the continuous long-term turbulence record include our capturing: (1) the seasonality of turbulence due to changing riverflow, (2) hysteresis in stratification and turbulence over the fortnightly cycle of tidal range, and (3) intermittent events such as breaking internal waves. Internal mixing layers (IMLs) are defined as turbulent regions above the logarithmic velocity layer, and the bottom boundary layer (BBL) is defined as the continuously turbulent range of heights above the bed. A cross-correlation analysis reveals how IML and BBL turbulence vary with stratification and external forcing from tidal range, river flow, and winds. Turbulence in both layers is maximal at spring tide and minimal when most stratified, with one exception IML turbulence at a site with changing channel depth and width is maximal at times of maximum stratification and freshwater input

Evaluation of modelling approaches for predicting the spatial distribution of soil organic carbon stocks at the national scale

Soil organic carbon (SOC) plays a major role in the global carbon budget. It can act as a source or a sink of atmospheric carbon, thereby possibly influencing the course of climate change. Improving the tools that model the spatial distributions of SOC stocks at national scales is a priority, both for monitoring changes in SOC and as an input for global carbon cycles studies. In this paper, we compare and evaluate two recent and promising modelling approaches. First, we considered several increasingly complex boosted regression trees (BRT), a convenient and efficient multiple regression model from the statistical learning field. Further, we considered a robust geostatistical approach coupled to the BRT models. Testing the different approaches was performed on the dataset from the French Soil Monitoring Network, with a consistent cross-validation procedure. We showed that when a limited number of predictors were included in the BRT model, the standalone BRT predictions were significantly improved by robust geostatistical modelling of the residuals. However, when data for several SOC drivers were included, the standalone BRT model predictions were not significantly improved by geostatistical modelling. Therefore, in this latter situation, the BRT predictions might be considered adequate without the need for geostatistical modelling, provided that i) care is exercised in model fitting and validating, and ii) the dataset does not allow for modelling of local spatial autocorrelations, as is the case for many national systematic sampling schemes

Saturn's atmospheric temperature structure and heat budget

The effective temperature of Saturn from 30°S to 10°N is 96.5 ± 2.5 K. This value is 1.9 K higher than our preliminary estimate (Ingersoll et al., 1980). The atmospheric mole fraction of H_2 relative to H_2 + He is 90 ± 3%. This value is derived by comparing infrared and radio occultation data (Kliore et al., this issue) for the same latitude. The high value of the effective temperature suggests that Saturn has an additional energy source besides cooling and contraction. The high mole fraction of H_2 suggests that separation of heavier He toward the core may be supplying the additional energy. Atmospheric temperatures in the 60- to 600-mbar range are 2.5 K lower within 7° of the equator than at higher latitudes. An almost isothermal layer exists between 60 and 160 mbar at all latitudes

EVOLUTION OF THE STRATOSPHERIC TEMPERATURE AND CHEMICAL COMPOSITION OVER ONE TITANIAN YEAR

Since the Voyager 1 (V1) flyby in 1980, Titans exploration from space and the ground has been ongoing for more than a full revolution of Saturn around the Sun (one Titan year or 29.5 Earth years was completed in May 2010). In this study we search for temporal variations affecting Titans atmospheric thermal and chemical structure within that year. We process Cassini CIRS data taken during the Titan flybys from 2006-2013 and compare them to the 1980 V1IRIS spectra (re-analyzed here). We also consider data from Earth-based and -orbiting observatories (such as from the ISO, re-visited). When we compare the CIRS 2010 and the IRIS data we find limited inter-annual variations, below the 25 or35 levels for the lower and middle, or the high latitudes, respectively. A return to the 1980 stratospheric temperatures and abundances is generally achieved from 50degN to 50degS, indicative of the solar radiation being the dominating energy source at 10 AU, as for the Earth, as predicted by GCM and photochemical models. However, some exceptions exist among the most complex hydrocarbons (C4H2 and C3H4), especially in the North. In the Southern latitudes, since 2012, we see a trend for an increase of several trace gases, possibly indicative of a seasonal atmospheric reversal. At the Northern latitudes we found enhanced abundances around the period of the northern spring equinox in mid-2009 (as in Bampasidis et al. 2012), which subsequently decreased (from 2010-2012) returning to values similar to those found in the V1 epoch a Titanian year before

Calibration of the Herschel SPIRE Fourier Transform Spectrometer

The Herschel SPIRE instrument consists of an imaging photometric camera and an imaging Fourier Transform Spectrometer (FTS), both operating over a frequency range of 450-1550 GHz. In this paper, we briefly review the FTS design, operation, and data reduction, and describe in detail the approach taken to relative calibration (removal of instrument signatures) and absolute calibration against standard astronomical sources. The calibration scheme assumes a spatially extended source and uses the Herschel telescope as primary calibrator. Conversion from extended to point-source calibration is carried out using observations of the planet Uranus. The model of the telescope emission is shown to be accurate to within 6% and repeatable to better than 0.06% and, by comparison with models of Mars and Neptune, the Uranus model is shown to be accurate to within 3%. Multiple observations of a number of point-like sources show that the repeatability of the calibration is better than 1%, if the effects of the satellite absolute pointing error (APE) are corrected. The satellite APE leads to a decrement in the derived flux, which can be up to ~10% (1 sigma) at the high-frequency end of the SPIRE range in the first part of the mission, and ~4% after Herschel operational day 1011. The lower frequency range of the SPIRE band is unaffected by this pointing error due to the larger beam size. Overall, for well-pointed, point-like sources, the absolute flux calibration is better than 6%, and for extended sources where mapping is required it is better than 7%.Comment: 20 pages, 18 figures, accepted for publication in MNRA

Assessing the Time Variability of Jupiter's Tropospheric Properties from 1996 to 2011

We acquired and analyzed mid-infrared images of Jupiter's disk at selected wavelengths from NASA's Infrared Telescope Facility (IRTF) from 1996 to 2011, including a period of large-scale changes of cloud color and albedo. We derived the 100-300 mbar temperature structure, together with tracers of vertical motion: the thickness of a 600- mbar cloud layer, the 300-mbar abundance of the condensable gas NH3, and the 400- mbar para- vs. ortho-H2 ratio. The biggest visual change was detected in the normally dark South Equatorial Belt (SEB) that 'faded' to a light color in 2010, during which both cloud thickness and NH3 abundance rose; both returned to their pre-fade levels in 2011, as the SEB regained its normal dark color. The cloud thickness in Jupiter's North Temperate Belt (NTB) increased in 2002, coincident with its visible brightening, and its NH3 abundance spiked in 2002-2003. Jupiter's Equatorial Zone (EZ), a region marked by more subtle but widespread color and albedo change, showed high cloud thickness variability between 2007 and 2009. In Jupiter's North Equatorial Belt (NEB), the cloud thickened in 2005, then slowly decreased to a minimum value in 2010-2011. No temperature variations were associated with any of these changes, but we discovered temperature oscillations of approx.2-4 K in all regions, with 4- or 8-year periods and phasing that was dissimilar in the different regions. There was also no detectable change in the para- vs. ortho-H2 ratio over time, leading to the possibility that it is driven from much deeper atmospheric levels and may be time-invariant. Our future work will continue to survey the variability of these properties through the Juno mission, which arrives at Jupiter in 2016, and to connect these observations with those made using raster-scanned images from 1980 to 1993 (Orton et al. 1996 Science 265, 625)

Hazard Assessment from Storm Tides and Rainfall on a Tidal River Estuary

Here, we report on methods and results for a model-based flood hazard assessment we have conducted for the Hudson River from New York City to Troy/Albany at the head of tide. Our recent work showed that neglecting freshwater flows leads to underestimation of peak water levels at up-river sites and neglecting stratification (typical with two-dimensional modeling) leads to underestimation all along the Hudson. As a result, we use a three-dimensional hydrodynamic model and merge streamflows and storm tides from tropical and extratropical cyclones (TCs, ETCs), as well as wet extratropical cyclone (WETC) floods (e.g. freshets, rain-on-snow events). We validate the modeled flood levels and quantify error with comparisons to 76 historical events. A Bayesian statistical method is developed for tropical cyclone streamflows using historical data and consisting in the evaluation of (1) the peak discharge and its pdf as a function of TC characteristics, and (2) the temporal trend of the hydrograph as a function of temporal evolution of the cyclone track, its intensity and the response characteristics of the specific basin. A k-nearest-neighbors method is employed to determine the hydrograph shape. Out of sample validation tests demonstrate the effectiveness of the method. Thus, the combined effects of storm surge and runoff produced by tropical cyclones hitting the New York area can be included in flood hazard assessment. Results for the upper Hudson (Albany) suggest a dominance of WETCs, for the lower Hudson (at New York Harbor) a case where ETCs are dominant for shorter return periods and TCs are more important for longer return periods (over 150 years), and for the middle-Hudson (Poughkeepsie) a mix of all three flood events types is important. However, a possible low-bias for TC flood levels is inferred from a lower importance in the assessment results, versus historical event top-20 lists, and this will be further evaluated as these preliminary methods and results are finalized. Future funded work will quantify the influences of sea level rise and flood adaptation plans (e.g. surge barriers). It would also be valuable to examine how streamflows from tropical cyclones and wet cool-season storms will change, as this factor will dominate at upriver locations

Optimizing protection for rear seat occupants: assessing booster performance with realistic belt geometry using the Hybrid III 6YO ATD

A series of sled tests was conducted to examine the performance of booster seats under belt geometries representing the range found in the rear seats of current vehicles. Twelve tests were performed with the standard 6YO Hybrid III ATD and 29 tests were performed with a modified version of the 6YO ATD. The modified dummy has a pelvis with more realistic shape and flesh stiffness, a gel abdomen with biomechanically-based stiffness characteristics, and a custom neoprene jacket. Shoulder belt upper anchorage was set at the FMVSS No. 213 belt anchorage location and 64 mm inboard and outboard from this location. Lap belt anchorage locations were chosen to span the range of lap belt angles permitted under FMVSS 210, using the FMVSS No. 213 belt anchorage locations and forward belt anchorage locations that produce a much steeper lap belt angle. Four booster seats that provide a range of static belt fit were used. The ATDs were positioned using either the standard FMVSS No. 213 seating procedure or an alternate UMTRI procedure that produces postures closer to those of similar-size children. Kinematic results for the standard and modified dummies under the same test conditions were more similar than expected. The current version of the modified 6YO is less sensitive to lap belt geometry than the prototype version of the dummy. The seating procedure had a greater affect on kinematic results. The UMTRI seating procedure produced greater knee-head excursion differences and less forward torso rotation than the FMVSS No. 213 procedure. Shifting the shoulder belt upper anchorage 128 mm laterally produced minimal variations in kinematics for a given booster seat/lap belt condition, likely because the belt-routing features of the booster seats limited the differences in static shoulder belt score to less than 10 mm. Moving the lap belt geometry from rearward (shallow angle) to forward (steep angle) produced less desirable kinematics with all booster seats tested. The forward position of the lap belt anchorage allows greater forward translation of the booster and ATD before the belt engages the pelvis. Steeper belt angles are associated with better lap belt fit for children sitting without boosters, so designing rear seat belts for children who sit with and without boosters may involve a performance tradeoff.National Highway Traffic Safety Administrationhttp://deepblue.lib.umich.edu/bitstream/2027.42/90973/1/102860.pd

Time invariance violating nuclear electric octupole moments

The existence of a nuclear electric octupole moment (EOM) requires both parity and time invariance violation. The EOMs of odd $Z$ nuclei that are induced by a particular T- and P-odd interaction are calculated. We compare such octupole moments with the collective EOMs that can occur in nuclei having a static octupole deformation. A nuclear EOM can induce a parity and time invariance violating atomic electric dipole moment, and the magnitude of this effect is calculated. The contribution of a nuclear EOM to such a dipole moment is found, in most cases, to be smaller than that of other mechanisms of atomic electric dipole moment production.Comment: Uses RevTex, 25 page