Response to letter regarding “Evidence of natural occurence of the banned antibiotic chloramphenicol in herbs and grass”

# The Author(s) 2011. This article is published with open access at Springerlink.com We were surprised to read that the natural occurrence of chloramphenicol (CAP) was reported as long ago as 2003 by Hanekamp et al. [1]. We missed that information, probably because their findings were not published in a peer-reviewed journal. In our paper [2], we did not claim to be the first to suggest the natural occurrence of CAP; on the contrary, we included several references from earlier studies. We stated that our paper was the first to describe the detection of CAP in plant materials, sample material which had not been addressed before. Furthermore, there is an important issue which is not raised by Hanekamp et al. and that is the issue of ‘criteria for confirmation of the identity of a compound’. InEU legislation, viz. Commission Decision 2002/657/EC, it i

Colloidal carbon particles as a new label for rapid immunochemical test methods: quantitative computer image analysis of results

Colloidal carbon particles can serve as label in sol particle immunoassays. The universal applicability of these particles in qualitative and (semi)quantitative immunoassays has been demonstrated. Sol particle and/or dipstick immunoassays, not yet optimized in terms of sensitivity, are discussed.\ud \ud The colloidal label has been used successfully in a mouse immunoglobulin isotyping kit. Human serum albumin spotted onto nitrocellulose in a concentration range of 7.8 to 1000 ng could be detected using anti-albumin antibody adsorbed onto colloidal carbon particles. It was also possible to perform a competitive assay with this conjugate for a concentration range of free human serum albumin varying from 0.25 to 6.75 ¿g. The Kunitz-type trypsin inhibitor from soybean was determined by a colloidal carbon based immunoassay in a range of 2.5 to 160 ng. In this assay, free and colloidal carbon-bound inhibitor competed for binding specific antibodies spotted onto a nitrocellulose membrane.\ud \ud An image- and data-processing procedure has been developed that enables a rapid and simple quantification of colloidal carbon sol particle immunoassays. The average grey level of a spot is taken as a measure for quantitative purposes. This so-called Sol-particle Image Processed ImmunoAssay (SIPIA) procedure is equally well applicable to assays using other colloidal particles

A Deep Learning Framework for Unsupervised Affine and Deformable Image Registration

Image registration, the process of aligning two or more images, is the core technique of many (semi-)automatic medical image analysis tasks. Recent studies have shown that deep learning methods, notably convolutional neural networks (ConvNets), can be used for image registration. Thus far training of ConvNets for registration was supervised using predefined example registrations. However, obtaining example registrations is not trivial. To circumvent the need for predefined examples, and thereby to increase convenience of training ConvNets for image registration, we propose the Deep Learning Image Registration (DLIR) framework for \textit{unsupervised} affine and deformable image registration. In the DLIR framework ConvNets are trained for image registration by exploiting image similarity analogous to conventional intensity-based image registration. After a ConvNet has been trained with the DLIR framework, it can be used to register pairs of unseen images in one shot. We propose flexible ConvNets designs for affine image registration and for deformable image registration. By stacking multiple of these ConvNets into a larger architecture, we are able to perform coarse-to-fine image registration. We show for registration of cardiac cine MRI and registration of chest CT that performance of the DLIR framework is comparable to conventional image registration while being several orders of magnitude faster.Comment: Accepted: Medical Image Analysis - Elsevie

Cooling rate, heating rate and aging effects in glassy water

We report a molecular dynamics simulation study of the properties of the potential energy landscape sampled by a system of water molecules during the process of generating a glass by cooling, and during the process of regenerating the equilibrium liquid by heating the glass. We study the dependence of these processes on the cooling/heating rates as well as on the role of aging (the time elapsed in the glass state). We compare the properties of the potential energy landscape sampled during these processes with the corresponding properties sampled in the liquid equilibrium state to elucidate under which conditions glass configurations can be associated with equilibrium liquid configurations.Comment: to be published in Phys. Rev. E (rapid comunication

Wetting and contact-line effects for spherical and cylindrical droplets on graphene layers: A comparative molecular-dynamics investigation

In Molecular Dynamics (MD) simulations, interactions between water molecules and graphitic surfaces are often modeled as a simple Lennard-Jones potential between oxygen and carbon atoms. A possible method for tuning this parameter consists of simulating a water nanodroplet on a flat graphitic surface, measuring the equilibrium contact angle, extrapolating it to the limit of a macroscopic droplet and finally matching this quantity to experimental results. Considering recent evidence demonstrating that the contact angle of water on a graphitic plane is much higher than what was previously reported, we estimate the oxygen-carbon interaction for the recent SPC/Fwwater model. Results indicate a value of about 0.2 kJ/mol, much lower than previous estimations. We then perform simulations of cylindrical water filaments on graphitic surfaces, in order to compare and correlate contact angles resulting from these two different systems. Results suggest that modified Young's equation does not describe the relation between contact angle and drop size in the case of extremely small systems and that contributions different from the one deriving from contact line tension should be taken into account.Comment: To be published on Physical Review E (http://pre.aps.org/

Perspective: How good is DFT for water?

Kohn-Sham density functional theory (DFT) has become established as an indispensable tool for investigating aqueous systems of all kinds, including those important in chemistry, surface science, biology and the earth sciences. Nevertheless, many widely used approximations for the exchange-correlation (XC) functional describe the properties of pure water systems with an accuracy that is not fully satisfactory. The explicit inclusion of dispersion interactions generally improves the description, but there remain large disagreements between the predictions of different dispersion-inclusive methods. We present here a review of DFT work on water clusters, ice structures and liquid water, with the aim of elucidating how the strengths and weaknesses of different XC approximations manifest themselves across this variety of water systems. Our review highlights the crucial role of dispersion in describing the delicate balance between compact and extended structures of many different water systems, including the liquid. By referring to a wide range of published work, we argue that the correct description of exchange-overlap interactions is also extremely important, so that the choice of semi-local or hybrid functional employed in dispersion-inclusive methods is crucial. The origins and consequences of beyond-2-body errors of approximate XC functionals are noted, and we also discuss the substantial differences between different representations of dispersion. We propose a simple numerical scoring system that rates the performance of different XC functionals in describing water systems, and we suggest possible future developments

Formation energy and interaction of point defects in two-dimensional colloidal crystals

The manipulation of individual colloidal particles using optical tweezers has allowed vacancies to be created in two-dimensional (2d) colloidal crystals, with unprecedented possibility of real-time monitoring the dynamics of such defects (Nature {\bf 413}, 147 (2001)). In this Letter, we employ molecular dynamics (MD) simulations to calculate the formation energy of single defects and the binding energy between pairs of defects in a 2d colloidal crystal. In the light of our results, experimental observations of vacancies could be explained and then compared to simulation results for the interstitial defects. We see a remarkable similarity between our results for a 2d colloidal crystal and the 2d Wigner crystal (Phys. Rev. Lett. {\bf 86}, 492 (2001)). The results show that the formation energy to create a single interstitial is $12$ lower than that of the vacancy. Because the pair binding energies of the defects are strongly attractive for short distances, the ground state should correspond to bound pairs with the interstitial bound pairs being the most probable.Comment: 5 pages, 2 figure

Polarization forces in water deduced from single molecule data

Intermolecular polarization interactions in water are determined using a minimal atomic multipole model constructed with distributed polarizabilities. Hydrogen bonding and other properties of water-water interactions are reproduced to fine detail by only three multipoles $\mu_H$, $\mu_O$, and $\theta_O$ and two polarizabilities $\alpha_O$ and $\alpha_H$, which characterize a single water molecule and are deduced from single molecule data.Comment: 4 revtex pages, 3 embedded color PS figure