Comparison between predicted and observed sand waves and sand banks in the North Sea

For the first time a prediction model of regular morphological patterns on the seabed was tested against observations of sand wave and sand bank occurrence in the entire North Sea. The model, which originates from first physical principles, predicts this occurrence via two dimensionless parameters on the basis of the water depth, the tidal velocity amplitude, the level of zero intercept above the seabed (z0), and a viscosity variation parameter alt epsilon. The latter two quantities were varied in a number of predictions for the entire North Sea, whereas for the first two, local values were used. The range of realistic values of alt epsilon and z0 was large enough to let these two parameters distinguish between the possible (combinations of) bed forms, as is shown in the shallower southern bight of the North Sea. The results were more sensitive to variations in z0 than in alt epsilon. A slightly more detailed approach focused on sand waves only in the southern North Sea and estimated local values for z0 using depth information. Quantification of the results showed that the model was able to predict the contours of the sand wave patches, but it could not account for the absence of the bed features within this area. The type of bed deposit partly explains the smaller-scale variation. The work confirms the validity of the theoretical bed form prediction model and verifies the hypothesis that the large-scale seabed features are formed as free instabilities of tide-topography interactions

Hydrogen Fluoride in High-Mass Star-forming Regions

Hydrogen fluoride has been established to be an excellent tracer of molecular hydrogen in diffuse clouds. In denser environments, however, the HF abundance has been shown to be approximately two orders of magnitude lower. We present Herschel/HIFI observations of HF J=1-0 toward two high-mass star formation sites, NGC6334 I and AFGL 2591. In NGC6334 I the HF line is seen in absorption in foreground clouds and the source itself, while in AFGL 2591 HF is partially in emission. We find an HF abundance with respect to H2 of 1.5e-8 in the diffuse foreground clouds, whereas in the denser parts of NGC6334 I, we derive a lower limit on the HF abundance of 5e-10. Lower HF abundances in dense clouds are most likely caused by freeze out of HF molecules onto dust grains in high-density gas. In AFGL 2591, the view of the hot core is obstructed by absorption in the massive outflow, in which HF is also very abundant 3.6e-8) due to the desorption by sputtering. These observations provide further evidence that the chemistry of interstellar fluorine is controlled by freeze out onto gas grains.Comment: accepted in Ap

Controlled Assembly of Macromolecular β-Sheet Fibrils

Construction of functional molecular devices by directed assembly processes is one of the main challenges in the field of nanotechnology. Many approaches to this challenge use biological assembly as a source of inspiration for the build up of new materials with controlled organization at the nanoscale. In particular, the self-assembly properties of β-sheet peptides have been used in the design of supramolecular materials, such as tapes, nanotubes, and fibrils

Влияние параметров одномассной системы с упругими ограничителями на характер ее колебаний

У статті розглянуто одномасну систему з пружними обмежувачами. Побудовано області існування різних режимів коливань системи, а також визначено вплив параметрів системи на межі цих областей.A one-mass system with elastic constraints is studied. Areas of existing of different oscillation modes are built. Also an influence of system parameters on limits of these areas is determined

Improved detection of artifactual viral minority variants in high-throughput sequencing data

textabstractHigh-throughput sequencing (HTS) of viral samples provides important information on the presence of viral minority variants. However, detection and accurate quantification is limited by the capacity to distinguish biological from artificial variation. In this study, errors related to the Illumina HiSeq2000 library generation and HTS process were investigated by determining minority variant frequencies in an influenza A/WSN/1933(H1N1) virus reverse-genetics plasmid pool. Errors related to amplification and sequencing were determined using the same plasmid pool, by generation of infectious virus using reverse genetics followed by in duplo reverse-transcriptase PCR (RT-PCR) amplification and HTS in the same sequence run. Results showed that after "best practice" quality control (QC), within the plasmid pool, one minority variant with a frequency >0.5% was identified, while 84 and 139 were identified in the RT-PCR amplified samples, indicating RT-PCR amplification artificially increased variation. Detailed analysis showed that artifactual minority variants could be identified by two major technical characteristics: their predominant presence in a single read orientation and uneven distribution of mismatches over the length of the reads. We demonstrate that by addition of two QC steps 95% of the artifactual minority variants could be identified. When our analysis approach was applied to three clinical samples 68% of the initially identified minority variants were identified as artifacts. Our study clearly demonstrated that, without additional QC steps, overestimation of viral minority variants is very likely to occur, mainly as a consequence of the required RT-PCR amplification step. The improved ability to detect and correct for artifactual minority variants, increases data resolution and could aid both past and future studies incorporating HTS. The source code has been made available through Sourceforge (https://sourceforge.net/projects/mva-ngs)

Deficiency of the first mannosylation step in the N-glycosylation pathway causes congenital disorder of glycosylation type Ik

Defects of N-linked glycosylation represent diseases with multiple organ involvements that are classified as congenital disorders of glycosylation (CDG). In recent years, several CDG types have been attributed to defects of dolichol-linked oligosaccharide assembly in the endoplasmic reticulum. The profiling of [3H]mannose-labeled lipid-linked oligosaccharides was instrumental in identifying most of these glycosylation disorders. However, this method is poorly suited for the identification of short lipid-linked oligosaccharide biosynthesis defects. To adequately resolve deficiencies affecting the first steps of lipid-linked oligosaccharide formation, we have used a non-radioactive procedure employing the fluorescence detection of 2-aminobenzamide-coupled oligosaccharides after HPLC separation. By applying this method, we have detected the accumulation of dolichylpyrophosphate-GlcNAc2 in a previously untyped CDG patient. The accumulation pattern suggested a deficiency of the ALG1 β1,4 mannosyltransferase, which adds the first mannose residue to lipid-linked oligosaccharides. This was supported by the finding that this CDG patient was compound heterozygous for three mutations in the ALG1 gene, leading to the amino acid substitutions S150R and D429E on one allele and S258L on the other. The detrimental effect of these mutations on ALG1 protein function was demonstrated in a complementation assay using alg1 Saccharomyces cerevisiae yeast mutants. The ALG1 mannosyltransferase defect described here represents a novel type of CDG, which should be referred to as CDG-I