On the Influence of Polynomial De-aliasing on Subgrid Scale Models

In this work we investigate the interplay of polynomial de-aliasing and sub-grid scale models for large eddy simulations based on discontinuous Galerkin discretizations. It is known that stability is a major concern when simulating underresolved turbulent flows with high order nodal collocation type discretizations. By changing the interpolatory character of the nodal collocation type discretization to a projection based discretization by increasing the number of quadrature points (polynomial de-aliasing), one is able to remove the aliasing induced stability problems. We focus on this effect and on the consequence for large eddy simulations with explicit subgrid scale models. Often, subgrid scale models have to achieve two possibly conflicting tasks in a single simulation: firstly stabilizing the numerics and secondly modeling the physical effect of the missing scales. Within a discontinuous Galerkin approach, it is possible to use either a fast (but potentially aliasing afflicted) nodal collocation discretization or a projection-based (but computationally costly) variant in combination with an explicit subgrid scale model. We use this framework to investigate the effect on the appropriate model parameter of a standard Smagorinsky subgrid scale model and of a Variational Multiscale Smagorinsky formulation. For this we first consider the 3-D viscous Taylor-Green vortex example to investigate the impact on the stability of the method and second the turbulent flow past a circular cylinder to investigate and compare the accuracy of the results. We show that the aliasing instabilities of collocative discretizations severely limit the choice of the model constant, in particular for high order schemes, while for de-aliased DG schemes, the closure model parameters can be chosen independently from the numerical scheme. For the cylinder flow, we also find that for the same model settings, the projection-based results are in better agreement with the reference DNS than those of the collocative scheme.     

An efficient synthesis of 3-alkyl-1,5,3-dioxazepanes and their use as electrophiles in double-Mannich reactions

An efficient synthesis of 3-alkyl 1,5,3-dioxazepanes was developed for subsequent use in double-Mannich reactions with a variety of carbon-based nucleophiles. It was found that addition of methyltrichlorosilane to the dioxazepane led to a long-lasting reactive species that reacted rapidly with acid-sensitive ketones and β-ketoesters to afford azabicyclo[3.3.1]nonanes in good yield.     

Site-specific C content by quantitative isotopic C Nuclear Magnetic Resonance spectrometry: A pilot inter-laboratory study

Isotopic ¹³C NMR spectrometry, which is able to measure intra-molecular ¹³C composition, is of emerging demand because of the new information provided by the ¹³C site-specific content of a given molecule. A systematic evaluation of instrumental behaviour is of importance to envisage isotopic ¹³C NMR as a routine tool. This paper describes the first collaborative study of intra-molecular ¹³C composition by NMR. The main goals of the ring test were to establish intra- and inter-variability of the spectrometer response. Eight instruments with different configuration were retained for the exercise on the basis of a qualification test. Reproducibility at the natural abundance of isotopic ¹³C NMR was then assessed on vanillin from three different origins associated with specific δ¹³C_i profiles. The standard deviation was, on average, between 0.9 and 1.2‰ for intra-variability. The highest standard deviation for inter-variability was 2.1‰. This is significantly higher than the internal precision but could be considered good in respect of a first ring test on a new analytical method. The standard deviation of δ¹³C_i in vanillin was not homogeneous over the eight carbons, with no trend either for the carbon position or for the configuration of the spectrometer. However, since the repeatability for each instrument was satisfactory, correction factors for each carbon in vanillin could be calculated to harmonize the results.     

Contamination of therapeutic human immunoglobulin preparations with apolipoprotein H (β2‐glycoprotein I)

Polyclonal immunoglobulin (Ig) concentrates are important biological medicinal products and the assurance of their quality and safety is crucial. In our present approach we used proteomic methods to check the purity of commercial Ig products of different origin. The experimental setup included nonreducing 2DE or DIGE combined with MALDI‐TOF and the thrombin generation assay, a routine safety test for pharmaceutical Ig preparations, and was complemented by a specific immunoassay. 2DE patterns displayed contaminations with trace amounts of human apolipoprotein H (Apo‐H), transferrin, albumin, and its fragments. In contrast to the latter, Apo‐H is a protein that is active in the coagulation cascade, and thus a potential involvement in thromboembolic events in vivo cannot be excluded. It was found by 2DE and MALDI‐TOF to be a contaminant of several Ig preparations. Spiking experiments of Ig preparations with pure Apo‐H demonstrated an Apo‐H concentration dependent increase in thrombin generation assay values. Traces of Apo‐H are possibly also contributing to unwanted side effects, as already known for factor XIa. The significance of Apo‐H contaminations for these side effects might be verified by detailed analyses of pharmacovigilance data.     

Analysis of monoclonal antibody by a novel CE‐UV/MALDI‐MS interface

mAbs are highly complex proteins that present a wide range of microheterogeneity that requires multiple analytical methods for full structure assessment and quality control. As a consequence, the characterization of mAbs on different levels is particularly product‐ and time‐consuming. CE‐MS couplings, especially to MALDI, appear really attractive methods for the characterization of biological samples. In this work, we report the last instrumental development and performance of the first totally automated off‐line CE‐UV/MALDI‐MS/MS. This interface is based on the removal of the original UV cell of the CE apparatus, modification of the spotting device geometry, and creation of an integrated delivery matrix system. The performance of the method was evaluated with separation of five intact proteins and a tryptic digest mixture of nine proteins. Intact protein application shows the acquisition of electropherograms with high resolution and high repeatability. In the peptide mapping approach, a total number of 154 unique identified peptides were characterized using MS/MS spectra corresponding to average sequence coverage of 64.1%. Comparison with NanoLC/MALDI‐MS/MS showed complementarity at the peptide level with an increase of 42% when using CE/MALDI‐MS coupling. Finally, this work represents the first analysis of intact mAb charge variants by CZE using an MS detection. Moreover, using a peptide mapping approach CE‐UV/MALDI‐MS/MS fragmentation allowed 100% sequence coverage of the light chain and 92% of the heavy chain, and the separation of four major glycosylated peptides and their structural characterization.     

The synthesis of luminescent lanthanide-based chemosensors for the detection of zinc ions

Herein, we report the synthesis of two lanthanide-based chemosensors, Tb-5 and Eu-6, designed to sense free zinc ions (Zn²⁺) in aqueous solutions. The Tb-5 complex features a bis(2-pyridinylmethyl)amine moiety as a zinc(II)-responsive lanthanide-sensitising ‘antenna’, while Eu-6 incorporates a quinoline-based moiety for this purpose. Luminescence enhancements of 210% and 340% are observed upon addition of Zn²⁺ ions to Tb-5 and Eu-6, respectively. Both sensors are selective for Zn²⁺ ions over several other cations of environmental significance.     

Synthesis and biological evaluation of the osteoblast proliferating cyclic peptides dianthins G and H

The first synthesis and osteoblast proliferative activity of the naturally occurring cyclic peptides dianthins G and H is described. The greater potency of naturally occurring dianthin G over dianthin H at physiological concentrations mirrored the osteoblast proliferative activity observed for synthetic dianthins G and H. Six alanine-scan analogues of the more potent dianthin G were also synthesised and osteoblast assays revealed that four of the six residues can be further modified for improved activity. We also confirmed by variable temperature ¹H NMR spectroscopic analysis that the sets of major and minor signals observed for dianthins G and H in DMSO-d₆ are in fact due to cis–trans rotational isomers of the proline ring.     

X-ray microfluorescence (μXRF) imaging of Aspergillus nidulans cell wall mutants reveals biochemical changes due to gene deletions

We used synchrotron X-ray fluorescence to create the first semiquantitative, submicron resolution, element distribution maps of P, S, K, and Ca, in situ, in fungal samples. Data collection was performed at the European Synchrotron Radiation Facility beam line ID21, Grenoble, France. We studied developing hyphae, septa, and conidiophores in Aspergillus nidulans, comparing wild type and two cell wall biosynthesis gene deletion strains. The latter encode sequential enzymes for biosynthesis of galactofuranose, a minor wall carbohydrate. Each gene deletion caused hyphal morphogenesis defects, and reduced both colony growth and sporulation 500-fold. Elemental imaging has helped elucidate biochemical changes in the phenotype induced by the gene deletions that were not apparent from morphological examination. Here, we examined S as a proxy for protein content, P for nucleic acid content, as well as Ca and K, which also have important metabolic roles. Element distributions in wild-type fungi reflect biological aspects already known or expected from other types of analysis; however, the application of X-ray fluorescence (XRF) imaging reveals aspects of gene deletion phenotypes that were not previously available. We have demonstrated that deleting a dispensable gene involved in galactose metabolism (ugeA) and one involved in biosynthesis of a minor cell wall component (ugmA) led to changes in hyphal elemental distribution that may have resulted from compromised wall composition.     

Combined Subcutaneous Fat Aspirate and Skin Tru-Cut Biopsy for Amyloid Screening in Patients with Suspected Systemic Amyloidosis

Screening for systemic amyloidosis is typically carried out with abdominal fat aspirates with varying reported sensitivities. Fat aspirates are preferred for use in primary screening instead of organ biopsies as they are less invasive and thereby minimize the potential risk of complications. At Odense Amyloidosis Center, we performed a prospective study on whether the combined use of fat aspirate and tru-cut skin biopsy could increase the diagnostic sensitivity. Both fat aspirates and skin biopsies were screened with Congo Red staining, and positive biopsies were subsequently subtyped using immunoelectron microscopy and mass spectrometry. Seventy-six patients were included. In total, 24 patients had systemic amyloidosis (11 AL, 12 wtATTR, 1 AA), and 6 patients had localized amyloidosis. Combined fat aspirate and skin biopsy were Congo Red-positive in 15 patients (overall sensitivity (OS) 62.5%). Fat aspirates were positive in 14 patients (OS 58.3%), and the skin biopsy was positive in 5 patients (OS 20.8%). In only one patient did the skin biopsy add extra diagnostic information. The sensitivity differed between AL and ATTR amyloidosis—81.8% and 41.7%, respectively. Using skin biopsy as the only screening method is not recommended.     

Lensless diffractive imaging using tabletop coherent high-harmonic soft-X-ray beams

We present the first experimental demonstration of lensless diffractive imaging using coherent soft x rays generated by a tabletop soft-x-ray source. A 29 nm high harmonic beam illuminates an object, and the subsequent diffraction is collected on an x-ray CCD camera. High dynamic range diffraction patterns are obtained by taking multiple exposures while blocking small-angle diffraction using beam blocks of varying size. These patterns reconstruct to images with 214 nm resolution. This work demonstrates a practical tabletop lensless microscope that promises to find applications in materials science, nanoscience, and biology.