On Non-Topological Solutions for Planar Liouville Systems of Toda-Type

In this paper we determine the interaction of diagonal defect clusters in regions of an Aztec rectangle that scale to arbitrary points on its symmetry axis (in earlier work we treated the case when this point was the center of the scaled Aztec rectangle). We use the resulting formulas to determine the asymptotics of the correlation of defects that are macroscopically separated from one another and feel the influence of the boundary. In several of the treated situations this seems not to be accomplishable by previous methods. Our applications include the case of two long neutral strings, which turn out to interact by an analog of the Casimir force, two families of neutral doublets that turn out to interact completely independently of one another, a neutral doublet and a very long neutral string, a general collection of macroscopically separated monomer and separation defects, and the case of long strings consisting of consecutive monomers.     

Application of an ePix100 detector for coherent scattering using a hard X‐ray free‐electron laser

A prototype ePix100 detector was used in small‐angle scattering geometry to capture speckle patterns from a static sample using the Linac Coherent Light Source (LCLS) hard X‐ray free‐electron laser at 8.34 keV. The average number of detected photons per pixel per pulse was varied over three orders of magnitude from about 23 down to 0.01 to test the detector performance. At high average photon count rates, the speckle contrast was evaluated by analyzing the probability distribution of the pixel counts at a constant scattering vector for single frames. For very low average photon counts of less than 0.2 per pixel, the `droplet algorithm' was first applied to the patterns for correcting the effect of charge sharing, and then the pixel count statistics of multiple frames were analyzed collectively to extract the speckle contrast. Results obtained using both methods agree within the uncertainty intervals, providing strong experimental evidence for the validity of the statistical analysis. More importantly it confirms the suitability of the ePix100 detector for X‐ray coherent scattering experiments, especially at very low count rates with performances surpassing those of previously available LCLS detectors.     

A low-cost and low-tech electrochemical flow system for the evaluation of total phenolic content and antioxidant power of tea infusions

A disposable, small scale and low-cost electrochemical "wall-jet" flow-cell was build up together with a graphite lead mounted onto a pencil holder able to modulate the current response by the control of the surface area of the electrode. The total phenolic content of different types of tea infusions was determined and compared with the conventional Folin-Ciocolteau method. An index of antioxidant power was also proposed and data were compared with those obtained by the DPPH* assay.     

Comparison of the efficiency and the specificity of DNA-bound and free cationic porphyrin in photodynamic virus inactivation

The risk of transmitting infections by blood transfusion has been substantially reduced. However, alternative methods for inactivation of pathogens in blood and its components are needed. Application of photoactivated cationic porphyrins can offer an approach to remove non-enveloped viruses from aqueous media. Here we tested the virus inactivation capability of meso-Tetrakis(4-N-methylpyridyl)porphyrin (TMPyP) and meso-Tri-(4-N-methylpyridyl)monophenylporphyrin (TMPyMPP) in the dark and upon irradiation. T7 bacteriophage, as a surrogate on non-enveloped viruses was selected as a test system. TMPyP and TMPyMPP reduce the viability of T7 phage already in the dark, which can be explained by their selective binding to nucleic acid. Both compounds proved to be efficient photosensitizers of virus inactivation. The binding of porphyrin to phage DNA was not a prerequisite of phage photosensitization, moreover, photoinactivation was more efficiently induced by free than by DNA bound porphyrin. As optical melting studies and agarose gel electrophoresis of T7 nucleoprotein revealed, photoreactions of TMPyP and TMPyMPP affect the structural integrity of DNA and also of viral proteins, despite their selective DNA binding.     

DNA closed nanostructures: a structural and Monte Carlo simulation study

DNA nanoconstructs are obtained in solution by using six unique 42-mer DNA oligonucleotides, whose sequences have been designed to form a pseudohexagonal structure. The required flexibility is provided by the insertion of two non-base-paired thymines in the middle of each sequence that work as flexible hinges and constitute the corners of the nanostructure when formed. We show that hexagonally shaped nanostructures of about 7 nm diameter and their corresponding linear open constructs are formed by self-assembly of the specifically designed linear oligonucleotides. The structural and dynamical characterization of the nanostructure is obtained in situ for the first time by using dynamic light scattering (DLS), a noninvasive method that provides a fast dynamic and structural analysis and allows the characterization of the different synthetic DNA nanoconstructs in solution. A validation of the LS results is obtained through Monte Carlo (MC) simulations and atomic force microscopy (AFM). In particular, a mesoscale molecular model for DNA, developed by Knotts et al., is exploited to perform MC simulations and to obtain information about the conformations as well as the conformational flexibilities of these nanostructures, while AFM provides a very detailed particle analysis that yields an estimation of the particle size and size distribution. The structural features obtained by MC and AFM are in good agreement with DLS, showing that DLS is a fast and reliable tool for characterization of DNA nanostructures in solution.     

Optimum collision energies for proteomics: The impact of ion mobility separation

Ion mobility spectrometry (IMS) is a widespread separation technique used in various research fields. It can be coupled to liquid chromatography–mass spectrometry (LC–MS/MS) methods providing an additional separation dimension. During IMS, ions are subjected to multiple collisions with buffer gas, which may cause significant ion heating. The present project addresses this phenomenon from the bottom-up proteomics point of view. We performed LC–MS/MS measurements on a cyclic ion mobility mass spectrometer with varied collision energy (CE) settings both with and without IMS. We investigated the CE dependence of identification score, using Byonic search engine, for more than 1000 tryptic peptides from HeLa digest standard. We determined the optimal CE values—giving the highest identification score—for both setups (i.e., with and without IMS). Results show that lower CE is advantageous when IMS separation is applied, by 6.3 V on average. This value belongs to the one-cycle separation configuration, and multiple cycles may supposedly have even larger impact. The effect of IMS is also reflected in the trends of optimal CE values versus m/z functions. The parameters suggested by the manufacturer were found to be almost optimal for the setup without IMS; on the other hand, they are obviously too high with IMS. Practical consideration on setting up a mass spectrometric platform hyphenated to IMS is also presented. Furthermore, the two CID (collision induced dissociation) fragmentation cells of the instrument—located before and after the IMS cell—were also compared, and we found that CE adjustment is needed when the trap cell is used for activation instead of the transfer cell. Data have been deposited in the MassIVE repository (MSV000090944).     

Multiplier Hopf Monoids

The notion of multiplier Hopf monoid in any braided monoidal category is introduced as a multiplier bimonoid whose constituent fusion morphisms are isomorphisms. In the category of vector spaces over the complex numbers, Van Daele’s definition of multiplier Hopf algebra is re-obtained. It is shown that the key features of multiplier Hopf algebras (over fields) remain valid in this more general context. Namely, for a multiplier Hopf monoid A, the existence of a unique antipode is proved — in an appropriate, multiplier-valued sense — which is shown to be a morphism of multiplier bimonoids from a twisted version of A to A. For a regular multiplier Hopf monoid (whose twisted versions are multiplier Hopf monoids as well) the antipode is proved to factorize through a proper automorphism of the object A. Under mild further assumptions, duals in the base category are shown to lift to the monoidal categories of modules and of comodules over a regular multiplier Hopf monoid. Finally, the so-called Fundamental Theorem of Hopf modules is proved — which states an equivalence between the base category and the category of Hopf modules over a multiplier Hopf monoid.     

The mystery of the discolored flints. New molecules turn prehistoric lithic artifacts blue

Prehistoric artifacts turning blue in the store rooms of the Natural History Museum in Verona, Italy recently raised serious issues for heritage materials conservation. Our analytical investigation showed that the unusual discoloration process of the flint tools is caused by the surface presence of at least three previously unknown pigmenting molecules of the triphenylmetane dyes class: 6-(bis(2,2,4-trimethyl-1,2-dihydroquinolin-6-yl)methylene)-2,2,4-trimethyl-2,6-dihydroquinolinium and its hydrogenated derivatives 2,2,4-trimethyl-6-((2,2,4-trimethyl-1,2,3,4-tetrahydroquinolin-6-yl)(2,2,4-trimethyl-1,2-dihydroquinolin-6-yl)methylene)-2,6-dihydroquinolinium and 6-(bis(2,2,4-trimethyl-1,2,3,4-tetrahydroquinolin-6-yl)methylene)-2,2,4-trimethyl-2,6-dihydroquinolinium. The peculiar formation of the molecules is possibly catalyzed within the silica pore surface starting from a well-known rubber stabilizer 2,2,4-trimethyl-1,2-dihydroquinoline released by the plastic pads flooring the storing cabinets. The investigated reaction and its surprising blue product represent a case study of the application of modern materials science to conservation and a serious warning towards the unpredictable challenges faced in the preservation of our cultural heritage.     

Investigating the impact of internal standard heterogeneity on gold quantification with total reflection X-ray fluorescence: A simulation study

Total reflection X-ray Fluorescence (TXRF) is a powerful analytical tool with high detection sensitivity that has been applied to a variety of biological samples. While its ability to quantify gold nanoparticles (AuNPs) in cancer cells has been demonstrated, the extension to tissue slices would be of interest. To that end, the preservation of the underlying tissue microstructure requires samples to be measured as microtome slices. In this form, internal standard spiking is warranted. Thus, it is important to examine the impact of sample heterogeneity on the TXRF's quantification accuracy. To address these questions, a TXRF spectrometer along with 5 μm thin heterogeneous and homogeneous samples were modeled using TOPAS. The simulation model generated TXRF spectra which were then analyzed to obtain recovery rates of Au in both sample types. The results showed near 100% recovery regardless of the elemental spatial distribution in the samples. This provides insights into the quantification potential for AuNPs inside tumors that are histologically processed into thin tissue slices. In addition, this simulation toolkit provides the first practical means of modeling TXRF spectroscopy which will hopefully be of use to the TXRF community.