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

Dynamic Behavior of Precast Concrete Beam-Column Sub-Assemblages with High Performance Connections Subjected to Sudden Column Removal Scenario

Unbonded posttensioned precast concrete (UPPC) structure has shown its excellent aseismic performance in laboratory tests and earthquake investigation. However, the progressive collapse behavior of UPPC subjected to column removal scenario is still unclear. To fill this knowledge gap, two 1/2 scaled UPPC beam-column sub-assemblages were tested under a penultimate column removal scenario. The dynamic test results indicated that UPPC sub-assemblages have desirable load redistribution capacity to mitigate progressive collapse. The failure modes of the sub-assemblages observed in dynamic test were quite similar to that in static counterparts

Investigating intra-host and intra-herd sequence diversity of foot-and-mouth disease virus

Due to the poor-fidelity of the enzymes involved in RNA genome replication, foot-and-mouth disease (FMD) virus samples comprise of unique polymorphic populations. In this study, deep sequencing was utilised to characterise the diversity of FMD virus (FMDV) populations in 6 infected cattle present on a single farm during the series of outbreaks in the UK in 2007. A novel RT–PCR method was developed to amplify a 7.6 kb nucleotide fragment encompassing the polyprotein coding region of the FMDV genome. Illumina sequencing of each sample identified the fine polymorphic structures at each nucleotide position, from consensus level changes to variants present at a 0.24% frequency. These data were used to investigate population dynamics of FMDV at both herd and host levels, evaluate the impact of host on the viral swarm structure and to identify transmission links with viruses recovered from other farms in the same series of outbreaks. In 7 samples, from 6 different animals, a total of 5 consensus level variants were identified, in addition to 104 sub-consensus variants of which 22 were shared between 2 or more animals. Further analysis revealed differences in swarm structures from samples derived from the same animal suggesting the presence of distinct viral populations evolving independently at different lesion sites within the same infected animal

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

Maser Oscillation in a Whispering-Gallery-Mode Microwave Resonator

We report the first observation of above-threshold maser oscillation in a whispering-gallery(WG)-mode resonator, whose quasi-transverse-magnetic, 17th azimuthal-order WG mode, at a frequency of approx. 12.038 GHz, with a loaded Q of several hundred million, is supported on a cylinder of mono-crystalline sapphire. An electron spin resonance (ESR) associated with Fe3+ ions, that are substitutively included within the sapphire at a concentration of a few parts per billion, coincides in frequency with that of the (considerably narrower) WG mode. By applying a c.w. `pump' to the resonator at a frequency of approx. 31.34 GHz, with no applied d.c. magnetic field, the WG (`signal') mode is energized through a three-level maser scheme. Preliminary measurements demonstrate a frequency stability (Allan deviation) of a few times 1e-14 for sampling intervals up to 100 s.Comment: REVTeX v.4, 3 pages, with a separate .bbl file and 3 .eps figure

The Effect of Harbor Developments on Future High-Tide Flooding in Miami, Florida

Little is known about the effect of tidal changes on minor flooding in most lagoonal estuaries, often due to a paucity of historical records that predate landscape changes. In this contribution, we recover and apply archival tidal range data to show that the mean tidal range in Miami, Florida, has almost doubled since 1900, from 0.32 to 0.61 m today. A likely cause is the dredging of a ∼15 m deep, 150 m wide harbor entrance channel beginning in the early 20th century, which changed northern Biscayne Bay from a choked inlet system to one with a tidal range close to coastal conditions. To investigate the implications for high-tide flooding, we develop and validate a tidal-inference based methodology that leverages estimates of pre-1900 tidal range to obtain historical tidal predictions and constituents. Next, water level predictions that represent historical and modern water level variations are projected forward in time using different sea level rise scenarios. Results show that the historical increase in tidal range hastened the occurrence of present-day flooding, and that the total integrated number of days with high-tide floods in the 2020–2100 period will be approximately O(103) more under present day tides compared to pre-development conditions. These results suggest that tidal change may be a previously under-appreciated factor in the increasing prevalence of high-tide flooding in lagoonal estuaries, and our methods open the door to improving our understanding of other heavily-altered systems

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