A small-window moving average-based fully automated baseline estimation method for Raman spectra

A fully automated and model-free baseline-correction method for vibrational spectra is presented. It iteratively applies a small, but increasing, moving average window in conjunction with peak stripping to estimate spectral baselines. Peak stripping causes the area stripped from the spectrum to initially increase and then diminish as peak stripping proceeds to completion; a subsequent increase is generally indicative of the commencement of baseline stripping. Consequently, this local minimum is used as a stopping criterion. A backup is provided by a second stopping criterion based on the area under a third-order polynomial fitted to the first derivative of the current estimate of the baseline-free spectrum and also indicates whether baseline is being stripped. When the second stopping criterion is triggered instead of the first one, a proportionally scaled simulated Gaussian baseline is added to the current estimate of the baseline-free spectrum to act as an internal standard to facilitate subsequent processing and termination via the first stopping criterion. The method is conceptually simple, easy to implement, and fully automated. Good and consistent results were obtained on simulated and real Raman spectra, making it suitable for the fully automated baseline correction of large numbers of spectra.     

A simple background elimination method for Raman spectra

In this paper, we consider a new background elimination method for Raman spectra. The proposed method is based on peak detection, smoothing, and interpolation. Since the background is usually slowly varying with respect to wavelength, we could estimate the background by eliminating significant peaks. For this purpose, we seek the peaks by inspecting the smoothed derivative of a given spectrum. After clipping out the corresponding peak regions, we estimate the background by applying a modified linear interpolation. Then the background is eliminated from the measured Raman spectrum by simple subtraction. The experimental results showed that the proposed method gave satisfactory results for real Raman spectra as well as synthetic data. As the proposed method requires no prior knowledge of spectrum, we expect that the method could be applied to other spectral data as well.     

A fully automated radon exposure chamber

A fully automated radon exposure chamber is described. The chamber is made of stainless steel and has a volume of 1.46 m³. The chamber allows ²²²Rn, ²²⁰Rn or both to be injected from the bottom pipe-lines into the chamber in a 100% flow-through mode, 100% recirculate mode or flow-through/recirculate mode. Either atmospheric aerosol or monodisperse aerosol from aerosol generator can be injected into the chamber. The radon concentration; radon daughter concentration; unattached fraction of radon daughters; aerosol size distribution and activity size distribution of radon daughters in aerosols are continuously monitored by computers and feedback signals are used to maintain the specified condition. Though the chamber may be small when compared to walk-in type exposure room, it has the advantage of fast response to changes in the chamber condition and yet is large enough to preclude perturbations due to sampling or other activities.     

Automated method for subtraction of fluorescence from biological Raman spectra

One of the challenges of using Raman spectroscopy for biological applications is the inherent fluorescence generated by many biological molecules that underlies the measured spectra. This fluorescence can sometimes be several orders of magnitude more intense than the weak Raman scatter, and its presence must be minimized in order to resolve and analyze the Raman spectrum. Several techniques involving hardware and software have been devised for this purpose; these include the use of wavelength shifting, time gating, frequency-domain filtering, first- and second-order derivatives, and simple curve fitting of the broadband variation with a high-order polynomial. Of these, polynomial fitting has been found to be a simple but effective method. However, this technique typically requires user intervention and thus is time consuming and prone to variability. An automated method for fluorescence subtraction, based on a modification to least-squares polynomial curve fitting, is described. Results indicate that the presented automated method is proficient in fluorescence subtraction, repeatability, and in retention of Raman spectral lineshapes.     

A fully automated LC/MS method development and quantification protocol targeting 52 carbamates, thiocarbamates, and phenylureas

We have developed a fully automated LC/MS method development and quantification protocol targeting 52 carbamtes, thiocarbamates, and phenylureas. This is a simple LC/MS method with direct injection; no post-column derivatization was required. The method utilized the Waters Alliance HT Chromatography System and the Waters ZQ 2000 mass spectrometer. System control and data processing was by MassLynx 4.0 with QuanLynx Application Manager. Analyte separation was accomplished by Waters Symmetry reversed-phase C8 column. An ammonium acetate water/acetonitrile binary gradient was used for the separation. The MS multichannel ability minimized the LC method development time with less demand on chromatographic peak resolution. Quantification results were obtained for 46 analytes out of the 52 targets. The coefficients of determination ranged from 0.886 to 0.999. The automated LC/MS protocol has sufficient sensitivity to accommodate the current EPA requirements. The limits of detection (3 times the S/N) ranged from 0.091 to 19.3 ng/mL with 50-microL injection. The highly selective MS detector enabled the matrix effect to be minimized. This method was applied to local drinking water and wastewater samples. Each matrix was spiked with the 52 target analytes at 2 and 20 ng/mL. The recoveries were within the EPA acceptance range.     

Versatile, fully automated, microfluidic cell culture system

There is increasing demand for automated and quantitative cell culture technology, driven both by the intense activity in stem cell biology and by the emergence of systems biology. We built a fully automated cell culture screening system based on a microfluidic chip that creates arbitrary culture media formulations in 96 independent culture chambers and maintains cell viability for weeks. Individual culture conditions are customized in terms of cell seeding density, composition of culture medium, and feeding schedule, and each chamber is imaged with time-lapse microscopy. Using this device, we perform the first quantitative measurements of the influence of transient stimulation schedules on the proliferation, osteogenic differentiation, and motility of human primary mesenchymal stem cells.     

Orientation-insensitive spectra for Raman microspectroscopy

Separating effects due to molecular conformation from those due to orientation in the spectra of oriented samples obtained by Raman microspectroscopy is a complex issue. To solve this problem, we propose a procedure to calculate an orientation-insensitive spectrum (so-called isotropic spectrum) from polarized spectra obtained by Raman microspectroscopy that is valid for systems that exhibit a uniaxial symmetry. The method has first been tested on highly oriented samples of high-density polyethylene (HDPE). Polarized and isotropic spectra of a highly oriented HDPE cylindrical rod and an isotropic HDPE sample have been compared. The differences in the relative intensities, which occur in the polarized spectra and are due to orientation of the polyethylene chains, are nearly cancelled in the isotropic spectra, showing that the orientation-insensitive spectrum adequately represents the molecular conformation without contributions of orientation. Second, spectra of silk fibroins have been compared in the amide I region for Bombyx mori cocoon silk fibers and methanol-treated regenerated fibroin films. The similarity of the shape of the amide I band of the isotropic spectra indicates that the secondary structure of the fibroins is very close in both samples. These experimental results support the conclusion that the molecular conformation can be efficiently characterized from the intensity and the shape of Raman bands in the orientation-insensitive spectrum.     

Shift-excitation Raman difference spectroscopy-difference deconvolution method for the luminescence background rejection from Raman spectra of solid samples

The feasibility of the shift-excitation Raman difference spectroscopy-difference deconvolution (SERDS-DDM) method for fluorescence suppression from Raman spectra of solid samples is discussed. For SERDS measurements a tunable diode laser source with an emission band centered at 684 nm is coupled to a conventional micro-Raman apparatus and a monochromator device is used for checking the excitation frequency stability. The shifted Raman spectra are then mathematically treated and a deconvolution procedure is used to reconstruct the Raman spectrum devoid of fluorescence. Two different cases are presented. In the first one, fluorescence is intrinsic to the sample and the Raman spectrum of cinnabar pigment is finally reconstructed. In the second, the presence of an external luminescence background in the spectrum of a pure sulfur crystal is considered. The SERDS-DDM reconstructed spectra are compared with spectra obtained via multi-point baseline subtraction and a significant improvement in the detection of weak bands is demonstrated. Practical insights for the application of this method are presented as well.     

New method for the microscopic, nondestructive acquisition of ultraviolet resonance Raman spectra from plant cell walls

Raman spectroscopy has long been used for the chemical analysis of organic matter, including natural products, using excitation wavelengths in the visible, infrared, or ultraviolet portions of the spectrum. The use of ultraviolet resonance Raman spectroscopy (UVRR) to study bulk samples of plant tissue has typically been carried out by rotating homogeneous macro-samples beneath the laser beam in order to minimize the amount of UV radiation impinging on any one spot, thereby avoiding its potentially damaging effects on the organic matter analyzed. This paper extends the use of UVRR to the study on a microscopic scale of individual plant cell walls by use of the controlled micro-displacement of a sample.     

FTIR and Raman spectra of bioceramics obtained by an innovative method

Bioceramic coatings with defined chemical composition and structure are often needed to satisfy specific biocompatibility properties in the prosthetic field. An example is hydroxyapatite (HA) for coatings, which, according to the Standard Specifications of the ASTM, must be crystalline and have a stoichiometric molar ratio Ca/P=1.67 with a 95% minimum amount of HA. Since the methods (plasma flame spray, ion beam sputtering, etc.) to obtain bioceramic coatings, in particular those for HA, induce changes in the chemical composition, structure and physical state of the coating, an alternative and innovative method (the so-called polymeric route) which provides bioceramic coatings under less severe conditions with controlled chemical composition and structure, was used in this work. The method was applied to the preparation not only of HA, but also, for the first time, of high-temperature-melting calcium phosphate bioactive glasses with a molar ratio CaO/P₂O₅=1 (calcium metaphosphate) and in the range 1–1.5 (calcium oligophosphates). The different phases of the process were characterized by vibrational FTIR spectra. The structure of the final glasses were also studied by Raman spectroscopy and compared with the spectra of the same products obtained by the traditional melting method.     

A fully implicit splitting method for accurate tidal computations

Often industrial codes for the numerical integration of the 2D shallow water equations are based on an Alternating Direction Implicit method. However, for large time steps these codes suffer from inaccuracies when dealing with a complex geometry or bathymetry. This reduces the performance considerably. In this paper a new method is presented in which these inaccuracies are absent, even for large time steps. The method is a fully implicit time integration method. In order to obtain linear systems that can be solved efficiently, we introduce a time splitting method. The resulting linear systems are solved iteratively by using the preconditioned Conjugate Gradients Squared method.     

A general computational method for converting normal spectra into derivative spectra

The mathematical problem of converting a normal spectrum into the corresponding first- and second-derivative spectra is formulated as an integral equation of the first kind. Tikhonov regularization is then applied to solve the spectral conversion problem. The end result is a set of linear algebraic equations that takes in as input the original spectrum and produces as output the second-derivative spectrum, which is then integrated to yield the first-derivative spectrum. Noise amplification is kept under control by adjusting the regularization parameter (guided by generalized cross-validation) in the algebraic equations. The performance of this procedure is demonstrated by applying it to different types of spectral data taken from the literature.     

An integrated software system for processing, analyzing, and classifying Raman spectra

Raman spectroscopy is a powerful technique for analyzing various substances, but a significant amount of processing is required to extract useful information from raw spectra. Many research groups develop custom software systems to process spectra, which leads to standard algorithms being repeatedly implemented and novel techniques being difficult to share. This paper presents an integrated software system that processes, analyzes, and classifies Raman spectra. The system is freely available (http://cares.wayne.edu/rp/), open, cross-platform, and extensible, enabling interested parties to utilize and contribute to a common implementation of Raman processing algorithms.A wide variety of useful features are included, such as noise filtering, automated background fluorescence subtraction, principal component analysis, linear discriminant analysis, artificial neural network classification, and support vector machine classification. The system supports customizable groupings of related spectra and is able to retrieve spectra using a searchable database. Everything is executed through a simple graphical user interface.The developed system was used to process two data sets containing different types of spectra. The results demonstrate that the system is capable of fast, accurate processing of Raman spectra. The open system will become even more powerful if other developers are willing to add new and improved features. In addition, it is intended that the freely available system will make Raman spectroscopy more accessible to all researchers and promote progress in the field.     

A simple method for linearizing nonlinear spectra for calibration

The development and acceptance of spectral calibration methods has been an important success story for the field of chemometrics. This paper contains a new study of a very old calibration method (K-matrix calibration, parallel calibration, or generalized inverse prediction) and partial least squares (PLS), the mainstay of modern chemometrics. We show that with some modest amount of modification, the old method of calibration is comparable, in terms of prediction, to PLS for spectroscopy involving nonlinear spectral responses.     

Wavelet based Raman spectra comparison

In this paper a novel blind peak detector for Raman spectra based on the continuous wavelet transform is proposed. The peak detector is shown to correctly identify peaks of different widths and intensities, and is well suited for subsequent peak-to-peak matching for the process of identifying unknown Raman spectra with the help of a library of reference spectra. No background reduction or initial noise filtering is necessary. The described methods were verified by successfully identifying 73 paint pigments by a spectral search through a Raman library for 638 pigments. In all except 7 cases, the Schmincke-Kremer pairings from the truth reference were found to be amongst the two top pairings with the largest matching cost function. These 7 cases were again inspected by the paintings conservator and doubts were raised regarding the truthfulness of the initial pairing. The proposed methods are equally applicable to other spectral methods.     

Orientation-independent spectra for biaxial systems in polarized Raman microspectrometry

From an extension of the scattering intensity expressions in polarized Raman macrospectrometry to the case of micro-Raman backscattering experiments, we have established theoretical expressions to calculate orientation-independent intensity sums. This approach makes use of the K2 Raman invariant and of correction coefficients due to integration of the Raman scattering over the cone of collection of the objective lens, and it may be applied to uniaxial as well as to biaxial symmetry systems. The intensity sums thus obtained are expected to be orientation insensitive and allow one to compare conformational changes in various biaxially oriented polymer samples, either amorphous and/or semicrystalline thin films. As application examples we have compared the polarized Raman results obtained for various biaxially oriented amorphous and semicrystalline polystyrene (PS), poly(ethylene terenaphthalate) (PEN), and poly(ethylene terephthalate) (PET) thin film samples with their respective "isotropic spectrum" and have considered the different main conformational changes in related polymer systems. The method is thus tested on these macromolecular systems and appears quite successful in providing evidence for the molecular conformational changes without interferences from spectral contributions due to orientation.     

CIFTER: automated charge-state determination for peptide tandem mass spectra

Tandem mass spectrometry (MS/MS) has become a common and useful tool for analyzing complex protein mixtures. Database search programs are the most popular means for peptide identification from MS/MS spectra. However, estimations of charge states of peptide MS/MS spectra obtained from low-resolution mass spectrometers have not been reliable. They require repetitive database searches and additional analyses of the search results. We propose here an algorithm designed to reliably differentiate doubly charged spectra from triply charged ones. We conducted a rigorous analysis of various spectral features and their effects. We employed the distinguishing features found in our analysis and developed a classifier for multiply charged spectra using a machine learning approach. The test on various data sets showed that our method could be successfully applied independent of experimental setup and mass instrument. This algorithm can be used to prefilter spectra so that only reasonably good spectra are submitted to database search programs, thereby saving considerable time. The software for MS/MS charge-state determination, which we named "CIFTER", is available at a website http://prix.uos.ac.kr/sifter/cifter.     

Measurement of texture and formability parameters with a fully automated,ultrasonic instrument

A fully automatic, ultrasonic instrument to measure texture and formability parameters on metal sheet is described. Arrays of EMAT transducers are used to transmit and receiveS _o Lamb waves propagating at 0°, 45°, and 90° with respect to the rolling direction. By analyzing the frequency dependence of the phase of the received signals, the long wavelength limit of the velocities is obtained. Included is a discussion of this algorithm, and subsequent processing steps to predict the ODC'sW ₄₀₀,W ₄₂₀, andW ₄₄₀. On steel, the prediction of drawability parametersr and r based on a correlation developed previously by Mould and Johnson is also discussed. Results of blind field trials at facilities of three suppliers/users of steel sheet for automotive applications and one supplier of aluminum sheet for beverage can production are reported. The former confirmed the Mould-Johnson correlation for lowr material but indicated that refinements are needed for modern steels with highr. The aluminum data suggest a correlation between W₄₄₀ and the degree of four-fold earing.     

Fe@洋葱状富勒烯的拉曼特征

采用化学气相沉积方法制备了Fe@洋葱状富勒烯并采用高分辨透射电镜（HRTEM）、拉曼（Raman）分析对其进行了表征。结果表明：产物粒径稳定在50nm左右，拉曼特征峰相对于HOPG发生了软化，这是由于其特殊的弯曲层状结构造成。