Human mobility and COVID-19 initial dynamics

Nonlinear Dynamics - Countries in Europe took different mobility containment measures to curb the spread of COVID-19. The European Commission asked mobile network operators to share on a...     

Computational maturation of a single-domain antibody against Aβ42 aggregation

The expansion of structural databases and the increase in computing power are enabling approaches for antibody discovery based on computational design. It has already been shown that it is possible to use this approach to generate antibodies for specific epitopes on challenging targets. Here we describe an application of this procedure for antibody maturation through the computational design of mutational variants of increased potency. We illustrate this procedure in the case of a single-domain antibody targeting an epitope in the N-terminal region of Aβ42, a peptide whose aggregation is closely associated with Alzheimer''s disease. We show that this approach enables the generation of an antibody variant with over 200-fold increased potency against the primary nucleation process in Aβ42 aggregation. Our results thus demonstrate that potentiated antibody variants can be obtained by computational maturation.

A computational maturation method enables the generation of an antibody variant with over 200-fold increased potency against the primary nucleation process in Aβ42 aggregation.     

Auger electron emission in proton-induced interactions in living matter: A TILDA-V Monte Carlo tracking

The present work focuses on studying the contribution of the Auger electron emission in proton-induced interactions in biological matter. The Monte Carlo track-structure code, TILDA-V, was then used for modeling the protons beams of 10 keV to 100 MeV in biological matter, namely, water vapor and hydrated DNA. The main ionizing processes are described by means of an extensive set of ab initio differential and total cross sections computed within a quantum-mechanical CDW-EIS approximation.     

Emission of volatile sesquiterpenes and monoterpenes in grapevine genotypes following Plasmopara viticola inoculation in vitro

The grapevine (Vitis vinifera) is one of the most widely cultivated fruit crops globally, and one of its most important diseases in terms of economic losses is downy mildew, caused by Plasmopara viticola. Several wild Vitis species have been found to be resistant to this pathogen and have been used in breeding programs to introduce resistance traits to susceptible cultivars. Plant defense is based on different mechanisms, and volatile organic compounds (VOCs) play a major role in the response to insects and pathogens. Although grapevine resistance mechanisms and the production of secondary metabolites have been widely characterized in resistant genotypes, the emission of VOCs has not yet been investigated following P. viticola inoculation. A Proton Transfer Reaction‐Time of Flight‐Mass Spectrometer (PTR‐ToF‐MS) was used to analyze the VOCs emitted by in vitro‐grown plants of grapevine genotypes with different levels of resistance. Downy mildew inoculation significantly increased the emission of monoterpenes and sesquiterpenes by the resistant SO4 and Kober 5BB genotypes, but not by the susceptible V. vinifera Pinot noir. Volatile terpenes were implicated in plant defense responses against pathogens, suggesting that they could play a major role in the resistance against downy mildew by direct toxicity or by inducing grapevine resistance. The grapevine genotypes differed in terms of the VOC emission pattern of both inoculated and uninoculated plants, indicating that PTR‐ToF‐MS could be used to screen hybrids with different levels of downy mildew resistance. Copyright © 2015 John Wiley & Sons, Ltd.     

Multi‐responses Methodology Applied in the Electroanalytical Determination of Hair Dye by Using Printed Carbon Electrode Modified with Graphene

This paper describes a rapid and sensitive method for determination of the hair dye Basic Blue 41 in wastewater samples using screen‐printed carbon electrodes modified with graphene (SPCE/Gr). The method is based on the reversible reduction of azo groups of the dye at potential of ?0.23 V/?0.26 V, where both the anodic and cathodic currents increased 1,300 % when compared to screen‐printed carbon (SPCE) and glassy carbon electrodes (GCE). The optimization of a square wave voltammetric method was performed by means of 2³ factorial design, Doehlert matrix and multi‐response assays, and the best parameters were: frequency (54.8 Hz), step potential (6 mV), pulse amplitude (43.7 mV) and pH 4.5. The analytical curve was constructed from 3.00×10^?8 to 2.01×10^?6 mol L^?1, with detection and quantification limits of 5.00×10^?9 and 1.70×10^?8 mol L^?1, respectively. The repeatability of the method evaluated for 10 consecutive measurements at concentrations of 1.70×10^?7 mol L^?1 and 1.70×10^?6 mol L^?1, showed relative standard deviation of 3.56 and 0.57 %, respectively. The sensor based in SPCE/Gr was successfully applied in wastewater samples collected from a drinking water treatment plant and validated by comparison with HPLC‐DAD method with good accuracy.     

Analysis of polycyclic aromatic hydrocarbons (PAHs) in environmental samples: a critical review of gas chromatographic (GC) methods

Polycyclic aromatic hydrocarbons (PAHs) are frequently measured in the atmosphere for air quality assessment, in biological tissues for health-effects monitoring, in sediments and mollusks for environmental monitoring, and in foodstuffs for safety reasons. In contemporary analysis of these complex matrices, gas chromatography (GC), rather than liquid chromatography (LC), is often the preferred approach for separation, identification, and quantification of PAHs, largely because GC generally affords greater selectivity, resolution, and sensitivity than LC. This article reviews modern-day GC and state-of-the-art GC techniques used for the determination of PAHs in environmental samples. Standard test methods are discussed. GC separations of PAHs on a variety of capillary columns are examined, and the properties and uses of selected mass spectrometric (MS) techniques are presented. PAH literature on GC with MS techniques, including chemical ionization, ion-trap MS, time-of-flight MS (TOF-MS), and isotope-ratio mass spectrometry (IRMS), is reviewed. Enhancements to GC, for example large-volume injection, thermal desorption, fast GC, and coupling of GC to LC, are also discussed with regard to the determination of PAHs in an effort to demonstrate the vigor and robustness GC continues to achieve in the analytical sciences.     

Spectroscopic properties in the liquid phase: combining high-level ab initio calculations and classical molecular dynamics.

We present an integrated computational tool, rooted in density functional theory, the polarizable continuum model, and classical molecular dynamics employing spherical boundary conditions, to study the spectroscopic observables of molecules in solution. As a test case, a modified OPLS-AA force field has been developed and used to compute the UV and NMR spectra of acetone in aqueous solution. The results show that provided the classical force fields are carefully reparameterized and validated, the proposed approach is robust and effective, and can also be used by nonspecialists to provide a general and powerful complement to experimental techniques.     

Two new marine sediment standard reference materials (SRMs) for the determination of organic contaminants

Two new marine sediment standard reference materials (SRMs), SRM 1941b Organics in Marine Sediment and SRM 1944 New York/New Jersey Waterway Sediment, have been recently issued by the National Institute of Standards and Technology (NIST) for the determination of organic contaminants including polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyl (PCB) congeners, and chlorinated pesticides. Both sediment SRMs were analyzed using multiple analytical methods including gas chromatography/mass spectrometry (GC/MS) on columns with different selectivity, reversed-phase liquid chromatography with fluorescence detection (for PAHs only), and GC with electron capture detection (for PCBs and pesticides only). SRM 1941b has certified concentrations for 24 PAHs, 29 PCB congeners, and 7 pesticides, and SRM 1944 has certified concentrations for 24 PAHs, 29 PCB congeners, and 4 pesticides. Reference concentrations are also provided for an additional 58 (SRM 1941b) and 39 (SRM 1944) PAHs, PCB congeners, and pesticides. SRM 1944, which was collected from multiple sites within New York/New Jersey coastal waterways, has contaminant concentrations that are generally a factor of 10–20 greater than SRM 1941b, which was collected in the Baltimore (Maryland) harbor. These two SRMs represent the most extensively characterized marine sediment certified reference materials available for the determination of organic contaminants.Electronic Supplementary Material Supplementary material is available in the online version of this article at . A link in the frame on the left on that page takes you directly to the supplementary material.     

Phase shifting photoelasticity in white light

The availability of image acquisition systems has led to the development of digital photoelasticity both in monochromatic and white light. In particular white light has been used mainly with the following methods: Spectral Content Analysis, RGB photoelasticity and phase shifting photoelasticity. Phase shifting photoelasticity in the colour domain has been used effectively for the determination of the isoclinic parameter in order to reduce the influence of the isochromatic fringes. The method has been also proposed for the determination of the isochromatic fringe order. This paper concerns the general characteristics of phase shifting photoelasticity in the colour domain. Special attention is drawn towards the influence of spectral content of the light source, the spectral response of the colour camera filters, the dispersion of the birefringence and the error of quarter wave plates.     

An approximation scheme for the two-stage,two-dimensional knapsack problem

We present an approximation scheme for the two-dimensional version of the knapsack problem which requires packing a maximum-area set of rectangles in a unit square bin, with the further restrictions that packing must be orthogonal without rotations and done in two stages. Achieving a solution which is close to the optimum modulo a small additive constant can be done by taking wide inspiration from an existing asymptotic approximation scheme for two-stage two-dimensional bin packing. On the other hand, getting rid of the additive constant to achieve a canonical approximation scheme appears to be widely nontrivial.