Good Learning and Implicit Model Enumeration

MathSBML is an open-source, freely-downloadable Mathematica package that facilitates working with Systems Biology Markup Language (SBML) models. SBML is a toolneutral,computer-readable format for representing models of biochemical reaction networks, applicable to metabolic networks, cell-signaling pathways, genomic regulatory networks, and other modeling problems in systems biology that is widely supported by the systems biology community. SBML is based on XML, a standard medium for representing and transporting data that is widely supported on the internet as well as in computational biology and bioinformatics. Because SBML is tool-independent, it enables model transportability, reuse, publication and survival. In addition to MathSBML, a number of other tools that support SBML model examination and manipulation are provided on the sbml.org website, including libSBML, a C/C++ library for reading SBML models; an SBML Toolbox for MatLab; file conversion programs; an SBML model validator and visualizer; and SBML specifications and schemas. MathSBML enables SBML file import to and export from Mathematica as well as providing an API for model manipulation and simulation

Assessing aquitard integrity in a complex aquifer \u2013 aquitard system contaminated by chlorinated hydrocarbons

This study investigates for the first time the integrity of multiple stacked aquitards with different degrees of contaminant degradation. Aquitard integrity was assessed in a contaminated, multi-layered, alluvial aquifer-aquitard system (Ferrara, northern Italy). The system was contaminated by mixed organic contaminants of industrial origin (mostly chlorinated ethenes) that were illegally disposed in an urban dump four to five decades ago. High spatial resolution profiles of hydraulic head, geochemistry and chlorinated hydrocarbon concentrations were determined through the multi-layered system via discrete interval sampling of continuous cores and multilevel groundwater sampling, at three locations aligned along a transect adjacent to the buried waste to a maximum depth of 53 m below the water table. The profiles revealed that the two shallow aquitards had low integrity with respect to impeding downward migration of dense non-aqueous phase liquid (DNAPL), and provided little protection to the underlying aquifers against DNAPL contamination due to preferential pathways through imperceptible fractures and/or permeable micro-beds. However, both aquitards inhibited downward DNAPL migration to some extent due to DNAPL retention along its flow paths and accumulation at lower permeability interfaces, with decreasing peak concentrations at the top of successively deeper aquitard units. Moreover, both aquitards enhanced contaminant biodegradation due to the occurrence of organic rich sub-layers, influencing the contaminant plume composition, mobility and fate in the underlying and overlying aquifers. The deepest aquitard showed evidence of DNAPL accumulation at the top and slow diffusion-dominated transport consistent with 40 years of transport, suggesting higher integrity compared to the two shallower aquitards. However, the occurrence of micro-fractures and/or discontinuities in the aquitard upgradient under the dump (source) is the most likely explanation for contamination of the deepest aquifer. Analytical 1-D simulations of the diffusion profiles in the deepest aquitard revealed that DNAPL contamination down to the top of this aquitard occurred with minimal delay after DNAPL waste disposal began. The results highlight the necessity of high-resolution vertical profiling for assessing the presence of imperceptible features relevant to DNAPL migration and integrity of individual aquitards affecting organic contaminant source zone mass and phase distributions over decades

Asymmetric polar localization dynamics of the serine chemoreceptor protein Tsr in Escherichia coli

10.1371/journal.pone.0195887PLoS ONE135e019588