On the bond distance in methane

The equilibrium bond distance in methane was optimized using coupled-pair functional and contracted CI wave functions, and a Gaussian basis that includes g-type functions on carbon and d-type functions on hydrogen. The resulting bond distance, when corrected for core-valence correlation effects, agrees with the experimental value of 2.052 a(0) to within the experimental uncertainty of 0.002 a(0). The main source of error in the best previous studies, which showed discrepancies with experiment of 0.007 a(0) is shown to be basis set incompleteness. In particular, it is important that the basis set be close to saturation, at least for the lower angular quantum numbers

POPE—a tool to aid high-throughput phylogenetic analysis

Summary: POPE (Phylogeny, Ortholog and Paralog Extractor) provides an integrated platform for automatic ortholog identification. Intermediate steps can be visualized, modified and analyzed in order to assess and improve the underlying quality of orthology and paralogy assignments

First ice core records of NO3− stable isotopes from Lomonosovfonna, Svalbard

Samples from two ice cores drilled at Lomonosovfonna, Svalbard, covering the period 1957–2009, and 1650–1995, respectively, were analyzed for NO3− concentrations, and NO3− stable isotopes (δ15N and δ18O). Post-1950 δ15N has an average of (−6.9 ± 1.9) ‰, which is lower than the isotopic signal known for Summit, Greenland, but agrees with values observed in recent Svalbard snow and aerosol. Pre-1900 δ15N has an average of (4.2 ± 1.6) ‰ suggesting that natural sources, enriched in the 15 N-isotope, dominated before industrialization. The post-1950 δ18O average of (75.1 ± 4.1) ‰ agrees with data from low and polar latitudes, suggesting similar atmospheric NOy (NOy = NO + NO2 + HNO3) processing pathways. The combination of anthropogenic source δ15N and transport isotope effect was estimated as −29.1 ‰ for the last 60 years. This value is below the usual range of NOx (NOx = NO + NO2) anthropogenic sources which is likely the result of a transport isotope effect of –32 ‰. We suggest that the δ15N recorded at Lomonosovfonna is influenced mainly by fossil fuel combustion, soil emissions and forest fires; the first and second being responsible for the marked decrease in δ15N observed in the post-1950s record with soil emissions being associated to the decreasing trend in δ15N observed up to present time, and the third being responsible for the sharp increase of δ15N around 2000

Structural Kinetic Modeling of Metabolic Networks

To develop and investigate detailed mathematical models of cellular metabolic processes is one of the primary challenges in systems biology. However, despite considerable advance in the topological analysis of metabolic networks, explicit kinetic modeling based on differential equations is still often severely hampered by inadequate knowledge of the enzyme-kinetic rate laws and their associated parameter values. Here we propose a method that aims to give a detailed and quantitative account of the dynamical capabilities of metabolic systems, without requiring any explicit information about the particular functional form of the rate equations. Our approach is based on constructing a local linear model at each point in parameter space, such that each element of the model is either directly experimentally accessible, or amenable to a straightforward biochemical interpretation. This ensemble of local linear models, encompassing all possible explicit kinetic models, then allows for a systematic statistical exploration of the comprehensive parameter space. The method is applied to two paradigmatic examples: The glycolytic pathway of yeast and a realistic-scale representation of the photosynthetic Calvin cycle.Comment: 14 pages, 8 figures (color

Hydrodynamic modelling of the microbial water quality in a drinking water source as input for risk reduction management

To mitigate the faecal contamination of drinking water sources and, consequently, to prevent waterborne disease outbreaks, an estimation of the contribution from different sources to the total faecal contamination at the raw water intake of a drinking water treatment plant is needed. The aim of this article was to estimate how much different sources contributed to the faecal contamination at the water intake in a drinking water source, Lake Rådasjön in Sweden. For this purpose, the fate and transport of faecal indicator Escherichia coli within Lake Rådasjön were simulated by a three-dimensional hydrodynamic model. The calibrated hydrodynamic model described the measured data on vertical temperature distribution in the lake well (the Pearson correlation coefficient was 0.99). The data on the E. coli load from the identified contamination sources were gathered and the fate and transport of E. coli released from these sources within the lake were simulated using the developed hydrodynamic model, taking the decay of the E. coli into account. The obtained modelling results were compared to the observed E. coli concentrations at the water intake. The results illustrated that the sources that contributed the most to the faecal contamination at the water intake in Lake Rådasjön were the discharges from the on-site sewers and the main inflow to the lake – the river Mölndalsån. Based on the modelling results recommendations for water producers were formulated. The study demonstrated that this modelling approach is a useful tool for estimating the contribution from different sources to the faecal contamination at the water intake of a drinking water treatment plant and provided decision-support information for the reduction of risks posed to the drinking water source

The link between neuroinflammation and the neurovascular unit in synucleinopathies.

The neurovascular unit (NVU) is composed of vascular cells, glial cells, and neurons. As a fundamental functional module in the central nervous system, the NVU maintains homeostasis in the microenvironment and the integrity of the blood-brain barrier. Disruption of the NVU and interactions among its components are involved in the pathophysiology of synucleinopathies, which are characterized by the pathological accumulation of α-synuclein. Neuroinflammation contributes to the pathophysiology of synucleinopathies, including Parkinson's disease, multiple system atrophy, and dementia with Lewy bodies. This review aims to summarize the neuroinflammatory response of glial cells and vascular cells in the NVU. We also review neuroinflammation in the context of the cross-talk between glial cells and vascular cells, between glial cells and pericytes, and between microglia and astroglia. Last, we discuss how α-synuclein affects neuroinflammation and how neuroinflammation influences the aggregation and spread of α-synuclein and analyze different properties of α-synuclein in synucleinopathies