Implementation of traceability – needs and perspective of the in-vitro-diagnosticum industry

Manufacturers support the concept of traceability. However, only a small number of the medically relevant measurands can be traced to the highest metrological order. In many cases, the measured substances are heterogeneous mixtures where traceability can be established only to either an international conventional reference measurement procedure or to a manufacturers own in-house reference system. The traceability concept needs to be seen in the context that the results of medical laboratories are not an aim per se, but are meant to provide useful medical information to clinicians, and that pre- and post-analytical steps may also contribute significantly to errors. There is a need for the further development of suitable reference measurement systems, but in view of the multitude of tasks and limited resources, priorities need to be set.Presented at BERM-9 – 9^th International Symposium on Biological and Environmental Reference Materials, 15–19 June 2003, Berlin, Germany     

Explorative data analysis of two-dimensional electrophoresis gels

Methods for classification of two-dimensional (2-DE) electrophoresis gels based on multivariate data analysis are demonstrated. Two-dimensional gels of ten wheat varieties are analyzed and it is demonstrated how to classify the wheat varieties in two qualities and a method for initial screening of gels is presented. First, an approach is demonstrated in which no prior knowledge of the separated proteins is used. Alignment of the gels followed by a simple transformation of data makes it possible to analyze the gels in an automated explorative manner by principal component analysis, to determine if the gels should be further analyzed. A more detailed approach is done by analyzing spot volume lists by principal components analysis and partial least square regression. The use of spot volume data offers a mean to investigate the spot pattern and link the classified protein patterns to distinct spots on the gels for further investigation. The explorative approach in analysis of 2-D gels makes it possible, in a fast and convenient way, to screen many gels in order to determine the protein patterns that form clusters and could be selected for further examination.     

A multi-shear perfusion bioreactor for investigating shear stress effects in endothelial cell constructs

Tissue engineering research is increasingly relying on the use of advanced cultivation technologies that provide rigorously-controlled cell microenvironments. Herein, we describe the features of a micro-fabricated Multi-Shear Perfusion Bioreactor (MSPB) designed to deliver up to six different levels of physiologically-relevant shear stresses (1-13 dyne cm(-2)) to six cell constructs simultaneously, during a single run. To attain a homogeneous fluid flow within each construct, flow-distributing nets photo-etched with a set of openings for fluid flow were placed up- and down-stream from each construct. Human umbilical vein endothelial cells (HUVECs) seeded in alginate scaffolds within the MSPB and subjected to three different levels of shear stress for 24 h, responded accordingly by expressing three different levels of the membranal marker Intercellular Adhesion Molecule 1 (ICAM-1) and the phosphorylated endothelial nitric oxide synthetase (eNOS). A longer period of cultivation, 17 d, under two different levels of shear stress resulted in different lengths of cell sprouts within the constructs. Collectively, the HUVEC behaviour within the different constructs confirms the feasibility of using the MSPB system for simultaneously imposing different shear stress levels, and for validating the flow regime in the bioreactor vessel as assessed by the computational fluid dynamic (CFD) model.     

Improved self-consistent and resolution-of-identity approximated Becke'05 density functional model of nondynamic electron correlation

In a recent letter [E. Proynov, Y. Shao, and J. Kong, Chem. Phys. Lett. 493, 381 (2010)], Becke's B05 model of nondynamic electron correlation in density functional theory was implemented self-consistently with computational efficiency (the "SCF-RI-B05" scheme). Important modifications of the algorithm were done in order to make the self-consistency feasible. In the present work, we give a complete account of the SCF-RI-B05 algorithm, including all the formulae for the analytical representation of the B05 functional and for its self-consistent field (SCF) potential. The average performance of the SCF-RI-B05 method reported in the above letter was somewhat less accurate, compared to the original B05 implementation, mainly because the parameters of the original B05 model were optimized with post-local-spin-density calculations. In this work, we report improved atomization energies with SCF-RI-B05, based on a SCF re-optimization of its four linear parameters. The re-optimized SCF-RI-B05 scheme is validated also on reaction barriers, and on the subtle energetics of NO dimer, an exemplary system of strong nondynamic correlation. It yields both the binding energy and the singlet-triplet splitting of the NO dimer correctly, and close to the benchmarks reported in the literature.     

Continuous development of schemes for parallel computing of the electrostatics in biological systems: Implementation in DelPhi

Due to the enormous importance of electrostatics in molecular biology, calculating the electrostatic potential and corresponding energies has become a standard computational approach for the study of biomolecules and nano‐objects immersed in water and salt phase or other media. However, the electrostatics of large macromolecules and macromolecular complexes, including nano‐objects, may not be obtainable via explicit methods and even the standard continuum electrostatics methods may not be applicable due to high computational time and memory requirements. Here, we report further development of the parallelization scheme reported in our previous work (Li, et al., J. Comput. Chem. 2012, 33, 1960) to include parallelization of the molecular surface and energy calculations components of the algorithm. The parallelization scheme utilizes different approaches such as space domain parallelization, algorithmic parallelization, multithreading, and task scheduling, depending on the quantity being calculated. This allows for efficient use of the computing resources of the corresponding computer cluster. The parallelization scheme is implemented in the popular software DelPhi and results in speedup of several folds. As a demonstration of the efficiency and capability of this methodology, the electrostatic potential, and electric field distributions are calculated for the bovine mitochondrial supercomplex illustrating their complex topology, which cannot be obtained by modeling the supercomplex components alone. © 2013 Wiley Periodicals, Inc.     

Phenol adsorption on closed carbon nanotubes

We present the results of systematic studies of phenol adsorption on closed commercially available, unmodified carbon nanotubes. Phenol adsorption is determined by the value of tube-specific surface area, the presence of small amount of surface groups influence adsorption only in very small amount. Phenol can be applied as a probe molecule for comparative analysis of tube surface areas. Tube curvature influences adsorption from solution, i.e., we observe increasing adsorption energy (and slower desorption process) with the decrease in tube curvature. This is in full accordance with molecular simulation results.     

BF3-mediated additions of organolithiums to ketimines: X-ray crystal structures of BF3-ketimine complexes

[reaction: see text] Additions of lithium acetylides and n-BuLi to N-alkyl ketimines mediated by BF(3)-Et(2)O in THF afford hindered tert-alkylamines in moderate to good yields. Stereochemical results and crystal structures of three BF(3)-imine complexes suggest that allylic strain strongly influences conformation and may be an important determinant of reactivity and selectivity.     

A further study of the cytotoxic constituents of a milnamide-producing sponge

A reinvestigation of Auletta sp. yielded the novel compound milnamide C (3) plus the known compounds milnamide A (1), milnamide B (hemiasterlin) (2), jasplakinolide (5), and geodiamolides A (6), D (7), E (8), and G (9). The isolation work was guided by cytoskeletal bioactivity data. Compounds 2 and 3 were shown to cause microtubule depolymerization, and 6-9 were shown to cause microfilament disruption. This biological activity and the structural elucidation of 3, including X-ray analysis, are reported here. [structure: see text]     

Highly efficient and exact method for parallelization of grid‐based algorithms and its implementation in DelPhi

The Gauss–Seidel (GS) method is a standard iterative numerical method widely used to solve a system of equations and, in general, is more efficient comparing to other iterative methods, such as the Jacobi method. However, standard implementation of the GS method restricts its utilization in parallel computing due to its requirement of using updated neighboring values (i.e., in current iteration) as soon as they are available. Here, we report an efficient and exact (not requiring assumptions) method to parallelize iterations and to reduce the computational time as a linear/nearly linear function of the number of processes or computing units. In contrast to other existing solutions, our method does not require any assumptions and is equally applicable for solving linear and nonlinear equations. This approach is implemented in the DelPhi program, which is a finite difference Poisson–Boltzmann equation solver to model electrostatics in molecular biology. This development makes the iterative procedure on obtaining the electrostatic potential distribution in the parallelized DelPhi several folds faster than that in the serial code. Further, we demonstrate the advantages of the new parallelized DelPhi by computing the electrostatic potential and the corresponding energies of large supramolecular structures. © 2012 Wiley Periodicals, Inc.     

A Three-Dimensional Two-Phase Model for Thermal Plasma Chemical Vapor Deposition with Liquid Feedstock Injection

In this paper, a comprehensive model for thermal plasma chemical vapor deposition (TPCVD) with liquid feedstock injection is documented. The gas flow is assumed to be steady, of a single temperature. Radiation and charged species contributions are excluded, but extensive homogeneous and heterogeneous chemistry is included. The liquid phase is traced by considering individual droplets. Discussion on the model's application to diamond production from acetone in a hydrogen–argon plasma is included. The major conclusions are: (1) Liquid injection possesses a capability to deliver the hydrocarbon precursor directly onto the deposition target. (2) For the case of complete evaporation of the droplet before reaching the substrate, the deposition rate is similar to that obtained with gaseous precursors. (3) The computational results compare well with experimental data. The modeling results can be used to optimize the injection parameters with regard to the deposition rate.