Non‐rotational Tucker3 core simplification

A simple and efficient approach is reported to estimate the sparsest Tucker3 model for a considered linear dependent multiway data array using PARAFAC profiles. Employing the least possible number of non‐zero core elements equal to the pseudo array rank of data, a better and easier interpretation of the data array is possible. The approach does not require any prior information. The type of rank deficiency, that is rank overlap or closure in different modes, and the Tucker3 core size can be determined from a congruency factor while running the algorithm. The replacement method (RM) of optimization is applied to determine the pattern (positions and values) of non‐zero elements in the sparsest core of the Tucker3 model. Full rank and rank deficient simulated data sets in different conditions as well as an experimental 3D fluorescence data set from gold nanoparticle (AuNP) interaction with HIV genome are successfully used for evaluating the performance of the algorithm. Copyright © 2016 John Wiley & Sons, Ltd.     

Three-way principal component analysis of chemical data from Lake Como watershed

A large data set obtained by a one-year monthly determination of ions (F⁻, Cl⁻, Br⁻, NO₃⁻, NO₂⁻, PO₄³⁻, SO₄²⁻, Na⁺, K⁺, Ca²⁺, Mg²⁺, NH₄⁺) and trace metals of environmental concern (Ni, Co, Mn, Fe) from the tributaries of Lake Como (Lombardy, Northern Italy) was treated by three-way Principal Component Analysis. The results showed that the chemical features of the investigated rivers are mainly related to the lithology of the watershed. Some cases of contamination were evidenced and rationalized on the basis of anthropic pollution or on the basis of the geochemical features of the territory. The method here proposed allows an easy and quick interpretation of the chemical data by means of graphical devices. The information extracted by the three-way models would be very useful to regional agencies in developing a strategy to manage water resources in the whole basin of Lake Como.     

Solving the sign indeterminacy for multiway models

Bilinear and multilinear models such as principal component analysis and PARAFAC have intrinsic sign indeterminacies. For example, any loading vector can be multiplied by −1 if another vector of that particular component is also multiplied by −1 without affecting the loss function values. This sometimes causes problems, for example, with respect to interpretation. In this paper, a method is developed to fix the sign indeterminacy for the PARAFAC, Tucker3 and PARAFAC2 models. Copyright © 2013 John Wiley & Sons, Ltd.     

A Tucker model based approach for analysis of complex oil biodegradation data

A novel method based on gas chromatography–mass spectrometry in selected ion monitoring mode (GC–MS/SIM) and Tucker models is developed to evaluate the effects of oil type, microbial treatments and incubation time on the biodegradation of petroleum hydrocarbons. The data set consists of sections of the m/z 180, 192 and 198 GC–MS/SIM chromatograms of oil extracts from a biodegradation experiment where four oil types were exposed to four microbial treatments over a period of one year. The chosen sections, which are specific to methylfluorenes, phenanthrenes and dibenzothiophenes, were combined in a 4-way array (incubation time × oil type × treatment × combined chromatographic retention times) that was analyzed using both principal component analysis and the Tucker model. Several conclusions could be reached: the light fuel oil was the least degradable of those tested, 2- and 3-methyl isomers were more easily degraded compared to the 4-methyl isomers, the mixture of surfactant producers and PAC degraders provided the most effective degradation and the largest part of the degradation occurred between 54 and 132 days.     

Thermodynamic consistency of data banks

Data sets originated from different sources are typically used simultaneously either in data banks or in data bases of flowsheeting programs. If these data sets concern different kinds of data, they ought to be in accordance with the laws of thermodynamics. This is not assured, however, and in many cases it is not even checked. Methods used for data compilation rely on approximate models, which may bias the residuals.

Two model-free methods are proposed, where the residuals of the thermodynamic differential equations are investigated.

The first method is a χ² test based on a quadratic form of the f residuals, involving variances of the elementary measurements, if they are available.

The second method is a rather sensitive trend/shift analysis of residuals, which does not require the knowledge of error variances.

The examples are the Clausius-Clapeyron equation, a binary vapor-liquid equilibrium data set and a simultaneous treatment of PVT and caloric data.     

Principal component and Tucker3 analyses of high performance liquid chromatography with diode-array detection fingerprints of crude extracts of Erythrina speciosa Andrews leaves

Mixtures of ethanol, dichloromethane, hexane and acetone obtained according to a statistical design have been used to extract substances from Erythrina speciosa Andrew leaves for chromatographic fingerprinting. The plant extracts from each mixture were analyzed by HPLC-DAD providing UV–vis spectra for each chromatographic peak. These chromatograms and spectra for the design mixtures were then treated with principal component (PCA), Tucker3 and PARAFAC analyses. PCA indicated the existence of five different chromatographic fingerprints for the leave extracts depending on the solvent mixture composition. Different chromatographic peak areas were strongly correlated with the mixture proportions of acetone, dichloromethane and ethanol. Tucker3 and PARAFAC analyses were very useful for identifying simultaneous correlations between chromatographic peak areas, spectral band absorbances and solvent proportions. The acetone proportion was highly correlated with the area of the 3.69 min retention time peak and the spectral absorbances between 250 and 260 nm, consistent with the presence of natural polyphenols. The dichloromethane mixture proportion was strongly correlated with the 12.19 min chromatographic peak area and a single spectral absorbance at 201 nm. This spectral absorption is characteristic of the electronic structures of terpenes and alkaloids.     

Preparation and mechanism of Fe_3O_4/Au core/shell super-paramagnetic microspheres

In the presence of Fe3O4 nano-particles, a new type of super-paramagnetic Fe3O4/Au microspheres with core/shell structures was prepared by reduction of Au3+ with hydroxylamine. The formation mechanism of the core/shell microspheres was studied in some detail. It was shown that the formation of the complex microspheres can be divided into two periods, that is, surface reaction-controlled process and diffusion-controlled process. The relative time lasted by either process depends upon the amount of Fe3O4 added and the initial concentration of Au3+. XPS analysis revealed that along with increasing in coating amount, the strength of the characteristic peaks of Au increased, and the Auger peaks of Fe weakened and even disappeared. Size distribution analysis showed that the core/shell microspheres are of an average diameter of 180 nm, a little bit larger than those before coating.     

Microporous hypercrosslinked polystyrene Styrosorb as a restricted access packing in sample clean-up for high performance liquid chromatography. Part I: Evaluation of restricted access properties

Summary Styrosorb is a beaded microporous polystyrene with particle sizes between 2 and 4 m. In spite of hypercrosslinkage the material was seen to swell in organic solvents. The native material is functionalized with Tris-groups at the outer surface of the particles. The average pore diameter was determined as 1.45±0.3 nm from size exclusion data using polystyrene and polyethylene standards in THF. The reversed phase behavior of the restricted access phase Styrosorb was investigated by injection of two test mixtures. Mixture I contained five aromatic amines, mixture II consisted of Amperozide^R and four related compounds. The optimum range of mobile phase composition was assessed so that analytes were separated whilst any proteins present were eluted unretained. Due to the small particle size short columns of 29×4 mm can be used for both sample clean-up and analytical separation of Amperozide^R and its metabolite.     

A novel method for quality consistency evaluation of Glycyrrhiza formula granules based on a spectrum-effect study

Quality consistency of Glycyrrhiza formula granules is essential for guaranteeing clinical efficacy. However, a suitable method to accurately and conveniently evaluate the consistency of the clinical efficacy of Glycyrrhiza formula granules is currently not available. This study established a method for the simultaneous determination of 12 active components in Glycyrrhiza formula granules using ultra-high-performance liquid chromatography coupled with quadrupole-time-of-flight tandem mass spectrometry. The rate of inhibition of cyclooxygenase-2 by different batches of Glycyrrhiza formula granules was determined. Near-infrared spectra were collected for different batches of Glycyrrhiza formula granules to detect their biological activity in the inhibition of cyclooxygenase-2. The quality consistency of the 11 batches of Glycyrrhiza formula granules was evaluated using principal component and correlation analyses. The results showed significant differences in the formula granules of Glycyrrhiza uralensis produced by the different manufacturers. Some differences were also observed among batches of formula granules produced by the same manufacturer. Correlation analysis of the chemical components and cyclooxygenase-2 activity showed that glycyrrhizic acid, liquiritin, and isoliquiritin were the main active components of Glycyrrhiza. Correlation analysis of the near-infrared spectra and cyclooxygenase-2 inhibition activity showed a high correlation between the active components and three characteristic bands: 3383–3995, 4227–4651, and 5315–5878 cm⁻¹. In this study, the main active anti-inflammatory components of Glycyrrhiza granules were screened. Thus, the near-infrared spectrum and characteristic active band of multi-index active components can be used to quickly detect the quality consistency of Glycyrrhiza formula granules, thereby improving the ability to control the quality and consistency of these granules.     

Two-dimensional linear discriminant analysis for classification of three-way chemical data

The two-dimensional linear discriminant analysis (2D-LDA) algorithm was originally proposed in the context of face image processing for the extraction of features with maximal discriminant power. However, despite its promising performance in image processing tasks, the 2D-LDA algorithm has not yet been used in applications involving chemical data. The present paper bridges this gap by investigating the use of 2D-LDA in classification problems involving three-way spectral data. The investigation was concerned with simulated data, as well as real-life data sets involving the classification of dry-cured Parma ham according to ageing by surface autofluorescence spectrometry and the classification of edible vegetable oils according to feedstock using total synchronous fluorescence spectrometry. The results were compared with those obtained by using the spectral data with no feature extraction, U-PLS-DA (Partial Least Squares Discriminant Analysis applied to the unfolded data), and LDA employing TUCKER-3 or PARAFAC scores. In the simulated data set, all methods yielded a correct classification rate of 100%. However, in the Parma ham and vegetable oil data sets, better classification rates were obtained by using 2D-LDA (86% and 100%), compared with no feature extraction (76% and 77%), U-PLS-DA (81% and 92%), PARAFAC-LDA (76% and 86%) and TUCKER3-LDA (86% and 93%).     

Combining restricted access material (RAM) and turbulent flow for the rapid on-line extraction of the cyclooxygenase-2 inhibitor rofecoxib in plasma samples

Restricted access material (RAM) has been used in the packing of a solid-phase extraction (SPE) column for on-line extractions under turbulent flow conditions. The bio-compatible RAM material works by the principle of size exclusion in addition to conventional reversed-phase chromatography, thereby allowing the extraction and preconcentration of small analyte molecules from biological samples such as plasma. Using small column dimensions (0.76 mm x 50 mm) and a consequently high linear velocity, turbulent flow was achieved during online sample extractions. The improved mass-transfer rate characteristic of turbulent flow allows fast sample cleanup without decreased extraction efficiency. The novel use of the RAM column, connected upstream to a C18 monolithic column, allowed the direct injection, extraction, separation, and MS/MS detection of plasma samples spiked with rofecoxib in a span of 5 min. Calibration curves obtained using this RAM turbulent flow coupled column method showed good linearity (R2 > 0.99) and reproducibility (%RSD < or = 7%). The lower limit of quantitation of rofecoxib in plasma samples was found to be 40 ng/ml. The extraction method showed good recovery of rofecoxib from a plasma matrix with minimal signal loss and robustness after more than 200 plasma injections.     

Top‐down characterization of mouse core histones

Histone post‐translational modifications (PTMs) play various roles in chromatin‐related cellular processes, and comprehensive analysis of these combinatorial PTMs at the intact protein level by top‐down proteomics is the method of choice to reveal their crosstalk and biological functions. Here, we report our top‐down characterization of the core histones from mouse fibroblasts cells NIH/3T3, which is a classic model used in many kinds of research. With nanoRPLC‐MS/MS analysis and ProteinGoggle database search, 547 protein species were identified with spectrum‐level FDR ≤ 1%, where PTMs in 51 protein species were unambiguously localized with PTM scores ≥1. High‐resolution MS/MS data also allowed the unambiguous identification of acetylation instead of trimethylation. This study presents a general picture of combinatorial PTMs of mouse core histones, which serves as a basic reference for all future related biological studies.     

The crystallographic structure of the natural air-hydrate in Greenland dye-3 deep ice core

We have carried out X-ray diffraction studies on single crystals of natural air-hydrate in deep ice cores recovered at Dye-3 Greenland. Integrated intensities for 470 diffracting planes were measured by an automated four-circle diffractometer. The space group determined is cubicFd3m and the lattice constant is 17.21(3) Å. These results indicate that the crystallographic structure is the Stackelberg's structure II, in contrast to the previously anticipated structure. This finding agrees with the recent results on the synthetic air-hydrate by Davidsonet al. It was also found by difference Fourier synthesis for guest molecules that electron density in a 16-hedral cage has multiple maxima displaced from the center of the cage while that in the 12-hedron was approximately spherical.Dedicated to Dr D. W. Davidson in honor of his great contributions to the sciences of inclusion phenomena.     

Rank annihilation correction for the amendment of instrumental inconsistencies

The globalisation of the analysis of a series of individual measurements often results in more robust and reliable outcomes. However, instrumental drifts that can occur between individual measurements destroy the ideal data structure and thus the advantages. A method based on rank annihilation factor analysis (RAFA) is introduced for the correction of several types of instrumental inconsistencies. It can be applied to many series of bilinear datasets. Experimental examples discussed in this paper comprise the successful correction of non-uniform retention time drifts in chromatography due to temperature or pressure changes, wavelength shifts in IR spectroscopy in an industrial control situation, and background absorption shifts in UV-VIS spectroscopy applied to equilibrium investigations.     

一种含1,3,5-三嗪环的六臂引发核的合成与表征

三聚氯氰由于分子中的均三嗪环热、氧稳定性良好,并且具有光活性和生物活性[1-2],分子中的三个氯原子具有类似酰氯的反应活性,并且可以通过控制温度达到分步取代:第一个氯原子取代温度在0～10℃,第二个氯原子在25～35℃开始反应,第三个在80～90℃开始反应[3].     

Engineered 3D tissue models for cell-laden microfluidic channels

Delivery of nutrients and oxygen within three-dimensional (3D) tissue constructs is important to maintain cell viability. We built 3D cell-laden hydrogels to validate a new tissue perfusion model that takes into account nutrition consumption. The model system was analyzed by simulating theoretical nutrient diffusion into cell-laden hydrogels. We carried out a parametric study considering different microchannel sizes and inter-channel separation in the hydrogel. We hypothesized that nutrient consumption needs to be taken into account when optimizing the perfusion channel size and separation. We validated the hypothesis by experiments. We fabricated circular microchannels (r = 400 μm) in 3D cell-laden hydrogel constructs (R = 7.5 mm, volume = 5 ml). These channels were positioned either individually or in parallel within hydrogels to increase nutrient and oxygen transport as a way to improve cell viability. We quantified the spatial distribution of viable cells within 3D hydrogel scaffolds without channels and with single- and dual-perfusion microfluidic channels. We investigated quantitatively the cell viability as a function of radial distance from the channels using experimental data and mathematical modeling of diffusion profiles. Our simulations show that a large-channel radius as well as a large channel to channel distance diffuse nutrients farther through a 3D hydrogel. This is important since our results reveal that there is a close correlation between nutrient profiles and cell viability across the hydrogel. Young Seok Song and Richard L. Lin have contributed equally to this contribution     

Evaluation of thermodynamic consistency of isobaric and isothermal binary vapor–liquid equilibrium data using the PAI test II,alcohol + n-alkane, +aromatic, +cycloalkane systems

The thermodynamic consistency of binary vapor–liquid equilibrium data has been examined for 46 binary alcohol + hydrocarbon systems with 310 data sets in total (145 isobaric and 165 isothermal sets) using the PAI test proposed in our previous study. The PAI test permits an overall check of the data by combining three tests: a point test, an area test, and an infinite dilution test. In this work, the PAI test was incorporated with the NRTL equation for fitting data. The results of the PAI test for the vapor–liquid equilibrium data showed that the PAI test was able to strictly select reliable data.     

An augmented effective core potential basis set for the calculation of molecular polarizabilities

Calculations of molecular polarizabilities require basis sets capable of accurately describing the responses of the electrons to an external perturbation. Unfortunately, basis sets that yield suitable quantitative results have traditionally been all-electron sets with large numbers of primitives, making their use computationally intractable even for moderately sized systems. We present a systematic augmentation of the effective core potential basis set of Stevens et al. [J Chem Phys 81, 12 (1984), Can J Chem 70, 612 (1992)] for 39 main group elements based on the procedure used to construct diffuse and polarization functions in the well-known Sadlej basis sets [Collec Czech Chem Comm 53, 1995 (1988)]. Representative calculations have been performed and we have shown that results to within 1% of all-electron calculations using the Sadlej basis set can be obtained for <1-35% of the computational cost using this new basis set.     

PuO3和PuO+3的分子结构与分子光谱

用相对论有效原子实势RECP和密度泛函(B3LYP, BHANDHLYP)、HF方法对PuO3的分子结构与分子光谱进行了研究.计算比较了C2v, D3h, C3v等构型以及计算方法等对PuO3分子能量和平衡结构的影响,结果表明中性的PuO3能够稳定存在,基态结构为C2v,状态为7B1 (B3LYP R1＝0.19143 nm, R2(＝R3)＝0.22057 nm, ∠OPuO＝102.2108°),比较而言PuO3分子还可能存在D3h结构的亚稳态7A2″,不存在稳定的C3v结构的PuO3分子.计算还同时首次给出了不同多重性的PuO3分子及其一价正离子PuO+3完整的能量、平衡几何结构、光谱数据、电荷布居、自旋密度、极化率与电偶极矩等系列数据.     

Fe2O3@Au core/shell nanoparticle-based electrochemical DNA biosensor for Escherichia coli detection

A Fe₂O₃@Au core/shell nanoparticle-based electrochemical DNA biosensor was developed for the amperometric detection of Escherichia coli (E. coli). Magnetic Fe₂O₃@Au nanoparticles were prepared by reducing HAuCl₄ on the surfaces of Fe₂O₃ nanoparticles. This DNA biosensor is based on a sandwich detection strategy, which involves capture probe immobilized on magnetic nanoparticles (MNPs), target and reporter probe labeled with horseradish peroxidase (HRP). Once magnetic field was added, these sandwich complexes were magnetically separated and HRP confined at the surfaces of MNPs could catalyze the enzyme substrate and generate electrochemical signals. The biosensor could detect the concentrations upper than 0.01 pM DNA target and upper than 500 cfu/mL of E. coli without any nucleic acid amplification steps. The detection limit could be lowered to 5 cfu/mL of E. coli after 4.0 h of incubation.