Discovery and validation of urinary exposure markers for different plant foods by untargeted metabolomics

While metabolomics is increasingly used to investigate the food metabolome and identify new markers of food exposure, limited attention has been given to the validation of such markers. The main objectives of the present study were to (1) discover potential food exposure markers (PEMs) for a range of plant foods in a study setting with a mixed dietary background and (2) validate PEMs found in a previous meal study. Three-day weighed dietary records and 24-h urine samples were collected three times during a 6-month parallel intervention study from 107 subjects randomized to two distinct dietary patterns. An untargeted UPLC-qTOF-MS metabolomics analysis was performed on the urine samples, and all features detected underwent strict data analyses, including an iterative paired t test and sensitivity and specificity analyses for foods. A total of 22 unique PEMs were identified that covered 7 out of 40 investigated food groups (strawberry, cabbages, beetroot, walnut, citrus, green beans and chocolate). The PEMs reflected foods with a distinct composition rather than foods eaten more frequently or in larger amounts. We found that 23 % of the PEMs found in a previous meal study were also valid in the present intervention study. The study demonstrates that it is possible to discover and validate PEMs for several foods and food classes in an intervention study with a mixed dietary background, despite the large variability in such a dataset. Final validation of PEMs for intake of foods should be performed by quantitative analysis.

Investigating Membrane-Mediated Antimicrobial Peptide Interactions with Synchrotron Radiation Far-Infrared Spectroscopy

Synchrotron radiation-based Fourier transform infrared spectroscopy enables access to vibrational information from mid over far infrared to even terahertz domains. This information may prove critical for the elucidation of fundamental bio-molecular phenomena including folding-mediated innate host defence mechanisms. Antimicrobial peptides (AMPs) represent one of such phenomena. These are major effector molecules of the innate immune system, which favour attack on microbial membranes. AMPs recognise and bind to the membranes whereupon they assemble into pores or channels destabilising the membranes leading to cell death. However, specific molecular interactions responsible for antimicrobial activities have yet to be fully understood. Herein we probe such interactions by assessing molecular specific variations in the near-THz 400–40 cm⁻¹ range for defined helical AMP templates in reconstituted phospholipid membranes. In particular, we show that a temperature-dependent spectroscopic analysis, supported by 2D correlative tools, provides direct evidence for the membrane-induced and folding-mediated activity of AMPs. The far-FTIR study offers a direct and information-rich probe of membrane-related antimicrobial interactions.     

Comparative 11A structure of two molluscan hemocyanins from 3D cryo-electron microscopy

Hemocyanins are giant extracellular proteins that transport oxygen in the hemolymph of many molluscs. Molluscan hemocyanins are cylindrical decamers or didecamers of a 350-400 kDa subunit that contains seven or eight different covalently linked globular functional units (FUs), arranged in a linear manner. Each FU carries a single copper active site and reversibly binds one dioxygen molecule. As a consequence, the decamer can carry up to 70 or 80 O(2) molecules. Although complete sequence information is now available from several molluscan hemocyanins, many details of the quaternary structure are still unclear, including the topology of the 10 subunits within the decamer. Here we show 3D reconstructions from cryo-electron micrographs of the hemocyanin decamer of Nautilus pompilius (Cephalopoda) and Haliotis tuberculata (Gastropoda) at a resolution of 11A (FSC(1/2-bit) criterion). The wall structure of both hemocyanins is very similar and shows, as in previous reconstructions, three tiers with 20 functional units each that encircle the cylinder wall, and the 10 oblique minor and major wall grooves. However, the six types of wall FUs of the polypeptide subunit, termed a-b-c-d-e-f, are now for the first time individually discernable by their specific orientation, shape, and connections. Also, the internal collar complex of the decamers shows superior resolution which, in this case, reveals striking differences between the two hemocyanins. The five arcs (FU-g pairs) of the central collar (in both hemocyanins) and the five slabs (FU-h pairs) of the peripheral collar (only present in Haliotis hemocyanin), as well as their connections to the wall and to each other are now more clearly defined. The arc is attached to the wall through a feature termed the anchor, a previously undescribed structural element of the hemocyanin wall.     

Pixel-by-pixel analysis of DCE MRI curve patterns and an illustration of its application to the imaging of the musculoskeletal system

Dynamic contrast enhanced (DCE) MRI is a widespread method that has found broad application in the imaging of the musculoskeletal (MSK) system. A common way of analyzing DCE MRI images is to look at the shape of the time-intensity curve (TIC) in pixels selected after drawing an ROI in a highly enhanced area. Although often applied to a number of MSK affections, shape analysis has so far not led to a unanimous correlation between these TIC patterns and pathology. We hypothesize that this might be a result of the subjective ROI approach. To overcome the shortcomings of the ROI approach (sampling error and interuser variability, among others), we created a method for a fast and simple classification of DCE MRI where time-curve enhancement shapes are classified pixel by pixel according to their shape. The result of the analysis is rendered in multislice, 2D color-coded images. With this approach, we show not only that differences on a short distance range of the TIC patterns are significant and cannot be appreciated with a conventional ROI analysis but also that the information that shape maps and conventional standard DCE MRI parameter maps convey are substantially different.     

Palladium nanoparticles on modified cellulose as a novel catalyst for low temperature gas reactions

Cellulose - Palladium was incorporated into carboxymethylated cellulose fibers as a support, thereby becoming an efficient and stable catalyst for low temperature gas phase reaction. Thus, NO was...     

Ultra‐Small Plutonium Oxide Nanocrystals: An Innovative Material in Plutonium Science

Apart from its technological importance, plutonium (Pu) is also one of the most intriguing elements because of its non‐conventional physical properties and fascinating chemistry. Those fundamental aspects are particularly interesting when dealing with the challenging study of plutonium‐based nanomaterials. Here we show that ultra‐small (3.2±0.9 nm) and highly crystalline plutonium oxide (PuO₂) nanocrystals (NCs) can be synthesized by the thermal decomposition of plutonyl nitrate ([PuO₂(NO₃)₂] ? 3 H₂O) in a highly coordinating organic medium. This is the first example reporting on the preparation of significant quantities (several tens of milligrams) of PuO₂ NCs, in a controllable and reproducible manner. The structure and magnetic properties of PuO₂ NCs have been characterized by a wide variety of techniques (powder X‐ray diffraction (PXRD), X‐ray absorption fine structure (XAFS), X‐ray absorption near edge structure (XANES), TEM, IR, Raman, UV/Vis spectroscopies, and superconducting quantum interference device (SQUID) magnetometry). The current PuO₂ NCs constitute an innovative material for the study of challenging problems as diverse as the transport behavior of plutonium in the environment or size and shape effects on the physics of transuranium elements.     

Numerical approach for generic three-phase flow based on cut-cell and ghost fluid methods

In this paper, we introduce numerical methods that can simulate complex multiphase flows. The finite volume method, applying Cartesian cut-cell is used in the computational domain, containing fluid and solid, to conserve mass and momentum. With this method, flows in and around any geometry can be simulated without complex and time consuming meshing. For the fluid region, which involves liquid and gas, the ghost fluid method is employed to handle the stiffness of the interface discontinuity problem. The interaction between each phase is treated simply by wall function models or jump conditions of pressure, velocity and shear stress at the interface. The sharp interface method “coupled level set (LS) and volume of fluid (VOF)” is used to represent the interface between the two fluid phases. This approach will combine some advantages of both interface tracking/capturing methods, such as the excellent mass conservation from the VOF method and good accuracy of interface normal computation from the LS function. The first coupled LS and VOF will be generated to reconstruct the interface between solid and the other materials. The second will represent the interface between liquid and gas.     

maxLik: A package for maximum likelihood estimation in R

This paper describes the package maxLik for the statistical environment R. The package is essentially a unified wrapper interface to various optimization routines, offering easy access to likelihood-specific features like standard errors or information matrix equality (BHHH method). More advanced features of the optimization algorithms, such as forcing the value of a particular parameter to be fixed, are also supported.