Detecting differential usage of exons from RNA-Seq data

RNA-Seq is a powerful tool for the study of alternative splicing and other forms of alternative isoform expression. Understanding the regulation of these processes requires comparisons between treatments, tissues or conditions. For the analysis of such experiments, we present _DEXSeq_, a statistical method to test for differential exon usage in RNA-Seq data. _DEXSeq_ employs generalized linear models and offers good detection power and reliable control of false discoveries by taking biological variation into account. An implementation is available as an R/Bioconductor package

Strategies to mitigate greenhouse gas and nitrogen emissions in Swiss agriculture: the application of an integrated sector model

Environmental impacts of agricultural production, such as greenhouse gas (GHG) and nitrogen emissions, are of major concern for scientists and policy makers throughout the world. Global agricultural activities account for about 60% of nitrous oxide and about 50% of methane emissions. From a global perspective, methane and nitrous oxide constitute crucial GHGs. They contribute substantially to climate change due to their high potential for effecting global warming compared to carbon dioxide. Emissions of these gases depend on the extent of agricultural production and applied technologies. Therefore, analysis of potential mitigation opportunities is challenging and requires an integrated approach in order to link agricultural economic perspectives to environmental aspects. In view of this, a mathematical programming model has been developed which enables assessment of cost-effective strategies for mitigating GHG and nitrogen emissions in the agricultural sector in Switzerland. This model is applied to improve understanding of the agricultural sector and its behavior with changing conditions in technology and policy. The presented recursive-dynamic model mimics the structure and inter- dependencies of Swiss agriculture and links that framework to core sources of GHG and nitrogen emissions. Calculated results for evaluation and application indicate that employed flexibility constraints provide a feasible approach to sufficiently validate the described model. Recursive-dynamic elements additionally enable adequate modeling of both an endogenous development of livestock dynamics and investments in buildings and machinery, also taking sunk costs into account. The presented findings reveal that the specified model approach is suitable to accurately estimate agricultural structure, GHG and nitrogen emissions within a tolerable range. The model performance can therefore be described as sufficiently robust and satisfactory. Thus, the model described here appropriately models strategies for GHG and nitrogen abatement in Swiss agriculture. The results indicate that there are limits to the ability of Swiss agriculture to contribute substantially to the mitigation of GHG and nitrogen emissions. There is only a limited level of mitigation available through technical approaches, and these approaches have high cost.resource use, environmental economics, greenhouse gas emission, nitrogen emission, integrated modeling

Knudsen Diffusion in Silicon Nanochannels

Measurements on helium and argon gas flow through an array of parallel, linear channels of 12 nm diameter and 200 micrometer length in a single crystalline silicon membrane reveal a Knudsen diffusion type transport from 10^2 to 10^7 in Knudsen number Kn. The classic scaling prediction for the transport diffusion coefficient on temperature and mass of diffusing species,D_He ~ sqrt(T), is confirmed over a T range from 40 K to 300 K for He and for the ratio of D_He/D_Ar ~ sqrt(m_Ar/m_He). Deviations of the channels from a cylindrical form, resolved with transmission electron microscopy down to subnanometer scales, quantitatively account for a reduced diffusivity as compared to Knudsen diffusion in ideal tubular channels. The membrane permeation experiments are described over 10 orders of magnitude in Kn, encompassing the transition flow regime, by the unified flow model of Beskok and Karniadakis.Comment: 4 pages, 3 figure

Hydraulic Transport Across Hydrophilic and Hydrophobic Nanopores: Flow Experiments with Water and n-Hexane

We experimentally explore pressure-driven flow of water and n-hexane across nanoporous silica (Vycor glass monoliths with 7 or 10 nm pore diameters, respectively) as a function of temperature and surface functionalization (native and silanized glass surfaces). Hydraulic flow rates are measured by applying hydrostatic pressures via inert gases (argon and helium, pressurized up to 70 bar) on the upstream side in a capacitor-based membrane permeability setup. For the native, hydrophilic silica walls, the measured hydraulic permeabilities can be quantitatively accounted for by bulk fluidity provided we assume a sticking boundary layer, i.e. a negative velocity slip length of molecular dimensions. The thickness of this boundary layer is discussed with regard to previous capillarity-driven flow experiments (spontaneous imbibition) and with regard to velocity slippage at the pore walls resulting from dissolved gas. Water flow across the silanized, hydrophobic nanopores is blocked up to a hydrostatic pressure of at least 70 bar. The absence of a sticking boundary layer quantitatively accounts for an enhanced n-hexane permeability in the hydrophobic compared to the hydrophilic nanopores.Comment: 15 pages, 7 figures, in press, Physical Review E 201

Capillary rise of water in hydrophilic nanopores

We report on the capillary rise of water in three-dimensional networks of hydrophilic silica pores with 3.5nm and 5nm mean radii, respectively (porous Vycor monoliths). We find classical square root of time Lucas-Washburn laws for the imbibition dynamics over the entire capillary rise times of up to 16h investigated. Provided we assume two preadsorbed strongly bound layers of water molecules resting at the silica walls, which corresponds to a negative velocity slip length of -0.5nm for water flow in silica nanopores, we can describe the filling process by a retained fluidity and capillarity of water in the pore center. This anticipated partitioning in two dynamic components reflects the structural-thermodynamic partitioning in strongly silica bound water layers and capillary condensed water in the pore center which is documented by sorption isotherm measurements.Comment: 4 pages, 3 figure