Sample handling for mass spectrometric proteomic investigations of human sera

Proteomic investigations of sera are potentially of value for diagnosis, prognosis, choice of therapy, and disease activity assessment by virtue of discovering new biomarkers and biomarker patterns. Much debate focuses on the biological relevance and the need for identification of such biomarkers while less effort has been invested in devising standard procedures for sample preparation and storage in relation to model building based on complex sets of mass spectrometric (MS) data. Thus, development of standardized methods for collection and storage of patient samples together with standards for transportation and handling of samples are needed. This requires knowledge about how sample processing affects MS-based proteome analyses and thereby how nonbiological biased classification errors are avoided. In this study, we characterize the effects of sample handling, including clotting conditions, storage temperature, storage time, and freeze/thaw cycles, on MS-based proteomics of human serum by using principal components analysis, support vector machine learning, and clustering methods based on genetic algorithms as class modeling and prediction methods. Using spiking to artificially create differentiable sample groups, this integrated approach yields data that--even when working with sample groups that differ more than may be expected in biological studies--clearly demonstrate the need for comparable sampling conditions for samples used for modeling and for the samples that are going into the test set group. Also, the study emphasizes the difference between class prediction and class comparison studies as well as the advantages and disadvantages of different modeling methods.     

Theoretical analysis of a new, efficient microfluidic magnetic bead separator based on magnetic structures on multiple length scales

We present a theoretical analysis of a new design for microfluidic magnetic bead separation. It combines an external array of mm-sized permanent magnets with magnetization directions alternating between up and down with μm-sized soft magnetic structures integrated in the bottom of the separation channel. The concept is studied analytically for simple representative geometries and by numerical simulation of an experimentally realistic system geometry. The array of permanent magnets provides long-range magnetic forces that attract the beads to the channel bottom, while the soft magnetic elements provide strong local retaining forces that prevent captured beads from being torn loose by the fluid drag. The addition of the soft magnetic elements increases the maximum retaining force by two orders of magnitude. The design is scalable and provides an efficient and simple solution to the capture of large amounts of magnetic beads on a microsystem platform.     

Cross-categorization of legal concepts across boundaries of legal systems: in consideration of inferential links

This work contrasts Giovanni Sartor’s view of inferential semantics of legal concepts (Sartor in Artif Intell Law 17:217–251, 2009) with a probabilistic model of theory formation (Kemp et al. in Cognition 114:165–196, 2010). The work further explores possibilities of implementing Kemp’s probabilistic model of theory formation in the context of mapping legal concepts between two individual legal systems. For implementing the legal concept mapping, we propose a cross-categorization approach that combines three mathematical models: the Bayesian Model of Generalization (BMG; Tenenbaum and Griffiths in Behav Brain Sci 4:629–640, 2001), the probabilistic model of theory formation, i.e., the Infinite Relational Model (IRM) first introduced by Kemp et al. (The twenty-first national conference on artificial intelligence, 2006, Cognition 114:165–196, 2010) and its extended model, i.e., the normal-IRM (n-IRM) proposed by Herlau et al. (IEEE International Workshop on Machine Learning for Signal Processing, 2012). We apply our cross-categorization approach to datasets where legal concepts related to educational systems are respectively defined by the Japanese- and the Danish authorities according to the International Standard Classification of Education. The main contribution of this work is the proposal of a conceptual framework of the cross-categorization approach that, inspired by Sartor (Artif Intell Law 17:217–251, 2009), attempts to explain reasoner’s inferential mechanisms.     

Lipochitin Oligosaccharides Immobilized through Oximes in Glycan Microarrays Bind LysM Proteins

Glycan microarrays have emerged as novel tools to study carbohydrate–protein interactions. Here we describe the preparation of a covalent microarray with lipochitin oligosaccharides and its use in studying proteins containing LysM domains. The glycan microarray was assembled from glycoconjugates that were synthesized by using recently developed bifunctional chemoselective aminooxy reagents without the need for transient carbohydrate protecting groups. We describe for the first time the preparation of a covalent microarray with lipochitin oligosaccharides and its use for studying proteins containing LysM domains. Lipochitin oligosaccharides (also referred to as Nod factors) were isolated from bacterial strains or chemoenzymatically synthesized. The glycan microarray also included peptidoglycan‐related compounds, as well as chitin oligosaccharides of different lengths. In total, 30 ligands were treated with the aminooxy linker molecule. The identity of the glycoconjugates was verified by mass spectrometry, and they were then immobilized on the array. The presence of the glycoconjugates on the array surface was confirmed by use of lectins and human sera (IgG binding). The functionality of our array was tested with a bacterial LysM domain‐containing protein, autolysin p60, which is known to act on the bacterial cell wall peptidoglycan. P60 showed specific binding to Nod factors and to chitin oligosaccharides. Increasing affinity was observed with increasing chitin oligomer length.     

Topological model of alkali germanate glasses and exploration of the germanate anomaly

Germanate glasses are of particular interest for their excellent optical properties as well as their abnormal structural changes that appear with the addition of modifiers, giving rise to the so-called germanate anomaly. This anomaly refers to the nonmonotonic compositional scaling of properties exhibited by alkali germanate glasses and has been studied with various spectroscopy techniques. However, it has been difficult to understand its atomic scale origin, especially since the germanium nucleus is not easily observed by nuclear magnetic resonance. To gain insights into the mechanisms of the germanate anomaly, we have constructed a structural model using statistical mechanics and topological constraint theory to provide an accurate prediction of alkali germanate glass properties. The temperature onsets for the rigid bond constraints are deduced from in situ Brillouin light scattering, and the number of constraints is shown to be accurately calculable using statistical methods. The alkali germanate model accurately captures the effect of the germanate anomaly on glass transition temperature, liquid fragility, and Young's modulus. We also reveal that compositional variations in the glass transition temperature and Young's modulus are governed by the O–Ge–O angular constraints, whereas the variations in fragility are governed by the Ge–O radial constraints.     

Synthesis of small molar mass perdeuterated polyethylpropylene (d-PEP) as an auxiliary for neutron studies

Summary An inert non-crystalline cryoprotectant oil was needed as a non-incoherent scattering matrix for neutron studies of solvent containing crystalline materials. This led us to prepare perdeuterated polyethylpropylene (PEP) with a molar mass around 1100 g/mol. On route to this material an improved method for the preparation of isoprene-d₈ starting from calcium carbide and acetone-d₆ was devised. Subsequent anionic polymerization using t-butyl lithium as initiator resulted in an oligomeric perdeuterated polyisoprene (PI) with an average chain length of approx. 15 monomer units and Mw/Mn: 1.1. This polymer was deuterated with D₂ and Pd/C (10%) in cyclohexane to yield the desired perdeutero polymer (PEP-d). The polymer fulfill the important properties that it does not crystallize at low temperature and has a low neutron scattering efficiency. Received: 15 September 1999/Revised version: 3 November 1999/Accepted: 3 November 1999     

A MATLAB program for estimation of unsaturated hydraulic soil parameters using an infiltrometer technique

We combined an inverse routine for assessing the hydraulic soil parameters of the Campbell/Mualem model with the power series solution developed by Philip for describing one-dimensional vertical infiltration into a homogenous soil. We based the estimation routine on a proposed measurement procedure especially suitable for early-time infiltrometer experiments where the flow can be considered as one-dimensional. The routine requires input of the initial soil water content and cumulative infiltration in two experiments with different pressures at the upper boundary and/or initial conditions. An independent measurement of the soil water content at saturation may reduce the uncertainty of estimated parameters. Response surfaces of the objective function were analysed. Scenarios for various soils and conditions, using numerically generated synthetic cumulative infiltration data with normally distributed errors, show promising results for finding the true values of the optimized parameters. We also investigated the effects of measurement frequency for the cumulative infiltration and errors in water content determinations.     

Tea classification and quality assessment using laser-induced fluorescence and chemometric evaluation

Laser-induced fluorescence was used to evaluate the classification and quality of Chinese oolong teas and jasmine teas. The fluorescence of four different types of Chinese oolong teas-Guangdong oolong, North Fujian oolong, South Fujian oolong, and Taiwan oolong was recorded and singular value decomposition was used to describe the autofluoresence of the tea samples. Linear discriminant analysis was used to train a predictive chemometric model and a leave-one-out methodology was used to classify the types and evaluate the quality of the tea samples. The predicted classification of the oolong teas and the grade of the jasmine teas were estimated using this method. The agreement between the grades evaluated by the tea experts and by the chemometric model shows the potential of this technique to be used for practical assessment of tea grades.     

Fused thiophene/quinoxaline low band gap polymers for photovoltaic's with increased photochemical stability

We investigate a family of low band-gap polymers based on the common acceptor moiety 2,3-bis-(3-octyloxyphenyl)quinoxaline (Q) combined with thiophene (T) or the fused thiophene systems: benzo[2,1-b:3,4-b′]-dithiophene (BDT) or dithieno[3,2-b,2′,3′-d]-thiophene (DTT). The photochemical stability of the three polymers was examined and compared to P3HT. They were found to be substantially more robust than P3HT with a ranking of DTTQ>BDTQ>TQ1?P3HT, indicating that the fused ring systems of DTT and BDT impart a large degree of photochemical stability than thiophene. Furthermore devices with normal and inverted geometry were prepared and tested in air. The normal geometry devices showed the highest efficiencies compared to the inverted, in particular owing to a higher V_oc, with TQ1 being the most efficient with a power conversion efficiency (PCE) of 1.5% (1000 W m⁻², AM1.5 G). For the inverted devices TQ1 and DTTQ showed the best PCEs of 0.9%.