bluuebunny/crossref_metadata_2025 huggingface dataset:
Prism-Based Infrared Spectrographs Using Modern-Day Detectors
Authors: Keltner Zachary , Kayima Katherine , Lanzarotta Adam , Lavalle Luis , Canepa Marina , Dowrey Anthony E. , Story Gloria M. , Marcott Curtis , Sommer André J.
Published: October 2009

A comparison of prism-based spectrographs to grating-based spectrographs is made when each of the systems is coupled to a modern-day liquid-nitrogen-cooled photovoltaic array detector. A comparison of the systems is also made using a room-temperature microbolometer array detector. Finally, infrared microspectroscopy of samples whose size is ∼10 micrometers will be demonstrated using a prism spectrograph outfitted with both types of detectors. The results of the study show that prism-based spectrographs offer an economical alternative to grating-based systems when spectral coverage is more critical than spectral resolution. The results also demonstrate that spectra with good signal-to-noise ratios can be collected on any of the systems with a total integration time of 10 seconds or less.
Combining Self-Modeling Curve Resolution Methods and Partial Least Squares to Develop a Quantitative Reaction Monitoring Method with Minimal Reference Data
Authors: Pedge Nicholas I. , Walmsley Anthony D.
Published: October 2009

An example of combining self-modeling curve resolution (SMCR) methods and partial least squares (PLS) to construct a quantitative model using minimal reference data is presented. The objective was to construct a quantitative calibration model to allow real-time in situ ultraviolet–attenuated total reflection (UV/ATR) measurements to determine the end-point during a chlorination reaction. Time restrictions for development combined with difficult reaction sampling conditions required the method to be developed using only a few key reference measurements. Utilizing evolving factor analysis (EFA) and the orthogonal projection approach (OPA), initial estimates of the concentration and spectral profiles for the intermediate and product were obtained. Further optimization by multivariate curve resolution–alternating least squares (MCR-ALS) led to refined estimates of the concentration profiles. A PLS2 model was then constructed using the calculated concentration profiles and the preprocessed UV spectra. Using a standard PLS model compatible with the spectrometer's standard process software facilitated real-time predictions for new batches. This method was applied to five 45 liter batches in a large-scale laboratory facility. The method successfully predicted the product concentration of batch 1 but exhibited larger prediction error for subsequent batches. The largest prediction error was attained during batch 3, for which a final concentration of 0.22 mole·L−1 was predicted, while the true measured value was 0.271 mole·L−1 (an error of 18.8%). However, the qualitative real-time profiles proved to be extremely useful as they allowed the end-point to be determined without sampling or performing off-line analysis. Furthermore, the concentration profile of the intermediate species, which could not be observed by the off-line method, could also be observed in real-time and gave further confidence that the process was approaching the end-point. Another benefit of real-time reaction profiles was encountered during the manufacture when the formation of product in batch 3 appeared to be progressing slower than was observed in previous batches. This prompted a check of the batch temperature and it was found to be 10 °C lower than the required set-point. The temperature was corrected and the batch successfully reached completion in the expected time.
Concentration Dependence in the Spectra of Polycyclic Aromatic Hydrocarbon Mixtures by Front-Surface Fluorescence Analysis
Authors: Sinski Joseph F. , Exner Jeffrey
Published: October 2009

Polycyclic aromatic hydrocarbons (PAHs) are a challenge for fluorescence analysis. Inner-filter quenching effects and energy transfers of PAHs in petroleum differ with concentration, leading to characteristically different fluorescence. At high concentrations of single PAH molecules and petroleum mixtures the classic rectangular quartz cell presents a particular challenge due to inner filter effects from right-angle illumination. While quite a few instrumental and mathematical corrections for these effects are reported throughout the literature, for researchers with standard instrumental sample compartments a triangular fluorometer cell can be used to emulate front-surface fluorescence analysis. This work presents concentration study results from the single PAH molecules fluoranthene and azulene dissolved in spectral-grade cyclohexane and also seeks to correct an aspect of our past work on the fluorescence of petroleum mixtures.
Characterization of Raman Spectra Measured in Vivo for the Detection of Cervical Dysplasia
Authors: Robichaux-Viehoever Amy , Kanter Elizabeth , Shappell Heidi , Billheimer Dean , Jones Howard , Mahadevan-Jansen Anita
Published: October 2009

Raman spectroscopy has been shown to have the potential for providing differential diagnosis in the cervix with high sensitivity and specificity in previous studies. The research presented here further evaluates the potential of near-infrared Raman spectroscopy to detect cervical dysplasia in a clinical setting. Using a portable system, Raman spectra were collected from the cervix of 79 patients using clinically feasible integration times (5 seconds on most patients). Multiple Raman measurements were taken from colposcopically normal and abnormal areas prior to the excision of tissue. Data were processed to extract Raman spectra from measured signal, which includes fluorescence and noise. The resulting spectra were correlated with the corresponding histopathologic diagnosis to determine empirical differences between different diagnostic categories. Using histology as the gold standard, logistic regression discrimination algorithms were developed to distinguish between normal ectocervix, squamous metaplasia, and high-grade dysplasia using independent training and validation sets of data. An unbiased estimate of the accuracy of the model indicates that Raman spectroscopy can distinguish between high-grade dysplasia and benign tissue with sensitivity of 89% and specificity of 81%, while colposcopy in expert hands was able to discriminate with a sensitivity and specificity of 87% and 72%.
Silver Nanorod Arrays as a Surface-Enhanced Raman Scattering Substrate for Foodborne Pathogenic Bacteria Detection
Authors: Chu Hsiaoyun , Huang Yaowen , Zhao Yiping
Published: October 2009

Surface-enhanced Raman scattering (SERS) using novel silver nanorod array substrates has been used for the detection of pathogenic bacteria. The substrate consists of a base layer of 500 nm silver film on a glass slide and a layer of silver nanorod array with a length of ∼1 μm produced by the oblique angle deposition method at a vapor incident angle of 86°. Spectra from whole cell bacteria, Generic Escherichia coli, E. coli O157:H7, E. coli DH 5α, Staphylococcus aureus, S. epidermidis, and Salmonella typhimurium, and bacteria mixtures have been obtained. This SERS active substrate can detect spectral differences between Gram types, different species, their mixture, and strains. Principal component analysis (PCA) has been applied to classify the spectra. Viable and nonviable cells have also been examined, and significantly reduced SERS responses were observed for nonviable cells. SERS detection of bacteria at the single cell level, excited at low incident laser power (12 μW) and short collection time (10 s), has also been demonstrated. These results indicate that the SERS-active silver nanorod array substrate is a potential analytical sensor for rapid identification of microorganisms with a minimum of sample preparation.
Attenuated Total Reflection Infrared Spectroscopy: An Efficient Technique to Quantitatively Determine the Orientation and Conformation of Proteins in Single Silk Fibers
Authors: Boulet-Audet Maxime , Lefèvre Thierry , Buffeteau Thierry , Pézolet Michel
Published: October 2009

Polarized attenuated total reflection (ATR) infrared spectroscopy is an efficient technique to determine the orientation and conformation of a large variety of samples, but it is more difficult to apply to very small specimens such as silk fibers. The Golden Gate single-reflection ATR accessory that uses diamond as an ATR element and a focalized beam turns out to be highly efficient to study quantitatively the orientation and conformation of a single silk fibroin filament of the silkworm Bombyx mori that is about 10 μm in diameter. For orientation measurements, rotating the sample instead of the electric field greatly simplifies the theoretical analysis and keeps the penetration depth of the infrared radiation constant. A sample holder that can be fitted on the ATR accessory has thus been developed to allow accurate rotation of the sample and to obtain spectra with a low, non-damaging, and reproducible pressure on the fiber. To validate the method, spectra have been recorded as a function of the angle θ between the fiber axis and the polarization of the incident radiation. The data have been fitted following the cosine square dependency of the absorbance with respect to the angle θ. The procedure has been applied to the spectral components of the amide I bands, as determined from spectral decomposition. Multiple angle measurements turn out to be quite useful to correct systematic angle errors and validate the accuracy of the curve-fitting parameters of the band decomposition. By using the calculated dichroic ratio, a parameter 〈 P2〉 of —0.46 ± 0.01 has been calculated for the antiparallel β-sheets and −0.04 ± 0.02 for the remaining structures. From the orientation-insensitive spectrum A0, the amount of β-sheets has been estimated to 49 ± 3%. The results obtained from only two measurements with the electric field of the incident radiation parallel and perpendicular to the fiber axis has demonstrated that ATR spectroscopy can be used routinely in quantitative studies of the molecular orientation and conformation of macromolecules.
Attenuated Total Reflection—Fourier Transform Infrared Imaging of Large Areas Using Inverted Prism Crystals and Combining Imaging and Mapping
Authors: Chan K. L. Andrew , Kazarian Sergei G.
Published: October 2009

Attenuated total reflection–Fourier transform infrared (ATR-FT-IR) imaging is a very useful tool for capturing chemical images of various materials due to the simple sample preparation and the ability to measure wet samples or samples in an aqueous environment. However, the size of the array detector used for image acquisition is often limited and there is usually a trade off between spatial resolution and the field of view (FOV). The combination of mapping and imaging can be used to acquire images with a larger FOV without sacrificing spatial resolution. Previous attempts have demonstrated this using an infrared microscope and a Germanium hemispherical ATR crystal to achieve images of up to 2.5 mm × 2.5 mm but with varying spatial resolution and depth of penetration across the imaged area. In this paper, we demonstrate a combination of mapping and imaging with a different approach using an external optics housing for large ATR accessories and inverted ATR prisms to achieve ATR-FT-IR images with a large FOV and reasonable spatial resolution. The results have shown that a FOV of 10 mm × 14 mm can be obtained with a spatial resolution of approximately 40–60 μm when using an accessory that gives no magnification. A FOV of 1.3 mm × 1.3 mm can be obtained with spatial resolution of approximately 15–20 μm when using a diamond ATR imaging accessory with 4× magnification. No significant change in image quality such as spatial resolution or depth of penetration has been observed across the whole FOV with this method and the measurement time was approximately 15 minutes for an image consisting of 16 image tiles.
Loopy MSC: A Simple Way to Improve Multiplicative Scatter Correction
Authors: Windig Willem , Shaver Jeremy , Bro Rasmus
Published: October 2009

Multiplicative scatter correction (MSC) is a widely used normalization technique. It aims to correct spectra in such a way that they are as close as possible to a reference spectrum, generally the mean of the data set, by changing the scale and the offset of the spectra. When there are other differences in the spectra than just a scale and an offset, the mean spectrum changes after MSC. As a result, another MSC, with the new mean spectrum as the reference, will result in an additional correction. This paper studies the effect of multiple applications of MSC.
Polarized Raman Microspectroscopy Can Reveal Structural Changes of Peritumoral Dermis in Basal Cell Carcinoma
Authors: Piot Elodie Ly Olivier , Durlach Anne , Bernard Philippe , Manfait Michel
Published: October 2009

Polarized Raman microspectroscopy can provide precious information regarding the orientation and ordering of the molecules in a sample without staining or particular preparation. This technique is used for the first time on a human skin section to probe the molecular modifications of the surrounding dermis in superficial basal cell carcinoma. Spectra using polarized and conventional Raman microspectroscopies were recorded on dermis bordering either the tumor or healthy epidermis. Band areas and spectral decomposition on selected vibrations were computed. Significant differences in dermal collagen vibration bands are detected using both polarized and conventional micro-spectroscopies, but the spectral changes between tumor and healthy tissues are enhanced using polarized Raman microspectroscopy. The analysis of these spectral differences highlights structural modifications of the triple helix of collagen. We see polarized Raman microspectroscopy as a potential tool that could be implemented for clinical analyses to guide clinicians and surgeons in the treatment of aggressive skin cancers. The information obtainable could also help better elucidate the molecular mechanisms induced in basal cell carcinoma development.
Determining the Lifetime of Detectable Amounts of Gunshot Residue on the Hands of a Shooter Using Laser-Induced Breakdown Spectroscopy
Authors: Rosenberg Matthew B. , Dockery Christopher R.
Published: October 2009

Laser-induced breakdown spectroscopy (LIBS) has been used to determine the period of time that a shooter will test positive for gunshot residue (GSR) after firing a revolver. Multiple rounds of primer were fired and samples collected at multiple hour intervals using an adhesive tape pressed against the skin. Samples were analyzed directly using a commercially available laser-induced breakdown spectrometer where barium emission (originating from barium nitrate in the primer) was observed. Population statistics were used to compare suspected GSR to a library of blank samples from which a threshold value was established. Statistically significant results, positive for GSR, are obtained 5.27 days after a firearm discharge using these techniques.
Man-Portable Laser-Induced Breakdown Spectroscopy System for in Situ Characterization of Karstic Formations
Authors: Cuñat J. , Fortes F. J. , Cabalín L. M. , Carrasco F. , Simón M. D. , Laserna J. J.
Published: October 2009

This paper reports the development and field testing of a man-portable instrument based on laser-induced breakdown spectrometry (LIBS) for inspection and analysis of speleothems. The 50 mJ of a Q-switched Nd:YAG laser operating at 1064 nm was used to generate a plasma on the sample. Plasma emission was then guided using a fiber-optic cable to a 1/10 m spectrometer equipped with a charge-coupled device (CCD) array detector. Plasma light was automatically processed in order to obtain surface and in-depth information from the speleothems. A field campaign in the interior of Nerja Cave (a large karstic formation in the South of Spain) has been carried out, aimed at evaluating the analytical performance of the instrument when operating in an unfriendly environment. Identification analysis of the speleothems' alteration layers and depth profiles of Sr and Ca is carried out and reported.
Reflectance Microspectroscopy of Natural Rock Samples in the Visible and near Infrared
Authors: Mouroulis Pantazis , Van Gorp Byron , Blaney Diana , Green Robert O.
Published: October 2009

We have collected reflectance spectra of various unprocessed rock samples in the 450–1650 nm wavelength range with a spatial resolution of 60 and 120 μm (diameter) and using three illumination modes. Spectra taken in diffuse reflectance (dark field) mode are comparable to those obtained from macroscopic measurements and can provide the basis for mineral detection at that spatial scale. The spectral discrimination of the dark field mode is demonstrated to be consistent with the spatial resolution of the microscope for the samples examined. These results support the conclusion that reflectance microspectroscopy in the visible and near-infrared regions can be a valuable tool for understanding mineral formation at the spatial scale of tens of micrometers.
The Tendon-to-Bone Transition of the Rotator Cuff: A Preliminary Raman Spectroscopic Study Documenting the Gradual Mineralization across the Insertion in Rat Tissue Samples
Authors: Wopenka Brigitte , Kent Alistair , Pasteris Jill D. , Yoon Young , Thomopoulos Stavros
Published: October 2009

We applied Raman spectroscopy to monitor the distribution of mineral and the degree of mineralization across the tendon-bone insertion site in the shoulders of five rats. We acquired Raman spectra from 100 to 4000 Δcm−1 on individual 1 μm points across the 120 μm wide transition zone of each tissue sample and identified all the peaks detected in pure tendon and in pure bone, as well as in the transition zone. The intensity of the 960 Δcm−1 P–O stretch for apatite (normalized to either the 2940 Δcm−1 C–H stretch or the 1003 Δcm−1 C–C stretch for collagen) was used as an indicator of the abundance of mineral. We relate the observed histological morphology in the tissue thin section with the observed Raman peaks for both the organic component (mostly collagen) and the inorganic component (a carbonated form of the mineral apatite) and discuss spectroscopic issues related to peak deconvolution and quantification of overlapping Raman peaks. We show that the mineral-to-collagen ratio at the insertion site increases linearly ( R2 = 0.8 for five samples) over the distance of 120 μm from tendon to bone, rather than abruptly, as previously inferred from histological observations. In addition, narrowing of the 960 Δcm−1 band across the traverse indicates that the crystalline ordering within the apatite increases concomitantly with the degree of mineralization. This finding of mineral gradation has important clinical implications and may explain why the uninjured tendon-to-bone connection of the rotator cuff can sustain very high loads without failure. Our finding is also consistent with recent mechanical models and calculations developed to better understand the materials properties of this unusually strong interface.
Multiple Peak Reference Method for Polarized Fourier Transform Infrared—Attenuated Total Reflection Spectroscopy to Determine the Three-Dimensional Orientation of a Uniaxially Drawn Poly(Trimethylene 2,6-Naphthalate) Film
Authors: Liang Yongri , Choi Ki Woon , Lee Han Sup
Published: October 2009

The polarized Fourier transform infrared-attenuated total reflection (FT-IR-ATR) technique is a very useful infrared spectroscopic method for characterizing the three-dimensional orientation of thick samples, to which the conventional transmission FT-IR method cannot easily be applied. To quantitatively analyze polarized FT-IR-ATR spectra, the dependence of the optical contact between the sample and the ATR crystal during the clamping and reclamping processes must be controlled. In this work, a new multiple peak reference (MPR) method is proposed and used to carry out a three-dimensional analysis of a poly(trimethylene 2,6-naphthalate) (PTN) polymer sample. The conventional single peak reference (SPR) analysis technique cannot be applied to such a sample due to the lack of an established reference peak. A new artificial reference band was generated by the MPR method using two different infrared bands, at 1602 cm−1 and 917 cm−1, in identical spectra with a combination constant of 0.95. The new artificial reference band was successfully used to calculate the three-dimensional orientation of various infrared bands of a uniaxially drawn PTN film, which has not previously been studied by three-dimensional orientation analyses using the polarized FT-IR-ATR method.
Molecular Hydraulic Properties of Montmorillonite: A Polarized Fourier Transform Infrared Spectroscopic Study
Authors: Amarasinghe Priyanthi M. , Katti Kalpana S. , Katti Dinesh R.
Published: October 2009

Understanding the rates at which fluid flows into clay interlayers at the molecular level is fundamental to designing an effective clay barrier system. In this work, molecular interactions at the Na-montmorillonite (MMT)–water interface, emphasizing the flow properties of the clay interlayer, have been studied at the molecular and nanoscale level using polarized Fourier transform infrared (FT-IR) spectroscopic and X-ray diffraction (XRD) techniques. Clay-water slurries were smeared on inert gold-coated metal substrates for FT-IR experiments and slurries were smeared on quartz plates for XRD experiments. By analyzing the O–H stretching and H–O–H bending vibrations in clay slurries, it was concluded that the molecular behavior of interlayer water is significantly different from the molecular behavior of bulk water. With increasing clay-water interaction time, it was also seen that the Si–O stretching bands of clay are being significantly altered by the water molecules in the interlayer. Using these spectroscopic techniques we have estimated the time required for water to flow into the clay interlayer. Further, by analyzing the particle size of the clay using atomic force microscopy (AFM) imaging, we were able to estimate the flow velocity of the water in the clay interlayer. This velocity is found to be 3.23 × 10−9 cm/s. This flow velocity was found to be of the same order of magnitude as the hydraulic conductivity of smectite-type clay reported elsewhere. Also described in this work is the correct positioning of the Si–O out-of-plane vibration band of MMT at the two-layer saturation level in the interlayer. This band was only observed in p-polarized spectra at 1211 cm−1. Thus, we attribute this band to the Si–O out-of-plane vibration band.
Finite Element Analysis Modeling of Pulse-Laser Excited Photothermal Deflection (Mirage Effect) from Aerosols
Authors: Dada Oluwatosin O. , Bialkowski Stephen E.
Published: October 2009

A finite element analysis method for numerical modeling of the photothermal deflection spectroscopy of aerosols is presented. The models simulate pulse-laser excited photothermal deflection from aerosols collected on a plane surface substrate in air medium. The influence of the aerosol and substrate properties on the transient photothermal deflection signal is examined. We have previously obtained experimental results for photothermal deflection spectrometry of aerosols deposited onto a plate from an impactor system (O. O. Dada and S. E. Bialkowski, Appl. Spectrosc. 62, 1336 (2008)). This paper supports the validity of the experimental results presented in that paper and helps in answering some of the questions raised. The modeling results presented here demonstrate that the (peak) normalized transient temperature change profile and (peak) normalized transient photothermal deflection profile are a good approximation and invariant with number of particles, inter-particle distance, and particulate shape, which suggests that the photothermal deflection signal amplitude may be calibrated linearly with total mass of aerosols and the method could be applied to analysis of complex aerosols.
Use of Dendrograms of Slice Spectra as a New Graphical Tool for the Interpretation of Two-Dimensional Correlation Spectra
Authors: De Gussem Kris , Vandenabeele Peter , Verbeken Annemieke , Moens Luc
Published: October 2009

In this paper a procedure is established to identify spectral bands that show similar behavior in two-dimensional correlation spectra. Slice spectra of bands that are affected in a single spectral event are highly similar. It is shown that this can be used to simplify the interpretation of two-dimensional (2D) correlation diagrams. One functional group frequently gives rise to multiple spectral bands in a Raman spectrum. In such occasions, the sequential order rules assign a sequential order, which is invalid, to the changes in these bands. We therefore apply cluster analysis to the slice spectra of bands with intensity changes during the experiment. Results indicate that cluster analysis of selected slice spectra can help in the interpretation of 2D correlation spectra in an intuitive and graphical way. The procedure should be used together with the widely used sequential order rules to determine the order of spectral events. The procedure enabled us to reveal the reaction steps in two simulated datasets and a dataset that comprises Raman spectra of oxidating latex of Lactarius fluens (Basidiomycota, Fungi).
Perchlorate Detection at Nanomolar Concentrations by Surface-Enhanced Raman Scattering
Authors: Gu Baohua , Ruan Chuanmin , Wang Wei
Published: October 2009

Perchlorate (ClO4−) has emerged as a widespread environmental contaminant and has been detected in various food products and even in human breast milk and urine. This research developed a sensing technique based on surface-enhanced Raman scattering (SERS) for rapid screening and monitoring of this contaminant in groundwater and surface water. The technique was found to be capable of detecting ClO4− at concentrations as low as 10−9 M (or ∼0.1 μg/L) by using 2-dimethylaminoethanethiol (DMAE) modified gold nanoparticles as a SERS substrate. Quantitative analysis of ClO4− was validated with good reproducibility by using both simulated and contaminated groundwater samples. When coupled with a portable Raman spectrometer, this technique has the potential to be used as an in situ, rapid screening tool for perchlorate in the environment.
Methods for Kinetic Modeling of Temporally Resolved Hyperspectral Confocal Fluorescence Images
Authors: Cutler Patrick J. , Haaland David M. , Erikries David M. , Gemperline Paul J.
Published: October 2009

Elucidating kinetic information (rate constants) from temporally resolved hyperspectral confocal fluorescence images offers some very important opportunities for the interpretation of spatially resolved hyperspectral confocal fluorescence images but also presents significant challenges, these being (1) the massive amount of data contained in a series of time-resolved spectral images (one time course of spectral data for each pixel) and (2) unknown concentrations of the reactants and products at time = 0, a necessary precondition normally required by traditional kinetic fitting approaches. This paper describes two methods for solving these problems: direct nonlinear (DNL) estimation of all parameters and separable least squares (SLS). The DNL method can be applied to reactions of any rate law, while the SLS method is restricted to first-order reactions. In SLS, the inherently linear and nonlinear parameters of first-order reactions are solved in separate linear and nonlinear steps, respectively. The new methods are demonstrated using simulated data sets and an experimental data set involving photobleaching of several fluorophores. This work demonstrates that both DNL and SLS hard-modeling methods applied to the kinetic modeling of temporally resolved hyperspectral images can outperform traditional soft-modeling and hard/soft-modeling methods which use multivariate curve resolution–alternating least squares (MCR-ALS) methods. In addition, the SLS method is much faster and is able to analyze much larger data sets than the DNL method.
Assessment of a Novel Flow Visualization Technique Using Photodissociation Spectroscopy
Authors: Zhao Yan , Tong Chenning , Ma Lin
Published: October 2009

The study of complicated flows continuously calls for new nonintrusive flow diagnostics. A novel flow visualization technique based on photodissociation spectroscopy (PDS) is described, demonstrated, and assessed in this paper. This technique is centered around the creative use of photodissociation (PD). A PD precursor is seeded in the flow of interest, either passive or reactive. A laser pulse is then generated to completely and rapidly photodissociate both the precursor and the products formed from the precursor (if it reacts) into photofragments. A target photofragment is then imaged to obtain multidimensional information about the flow. An analytical methodology was developed to assess the feasibility of the PDS-based technique. This analytical method was applied to the case where molecular iodine was used as an example PD precursor, and the results were validated by experimental data. Both the analytical and experimental findings provided a promising outlook for this new technique as a practical flow visualization technique. With a properly chosen PD precursor, the PDS-based technique provides an attractive alternative for imaging several critical flow properties, including the mixture fraction and temperature field. This technique shares some key advantages with established techniques, e.g., a high spatial and temporal resolution comparable to the planar laser-induced fluorescence (PLIF) technique. Meanwhile, this technique offers several unique advantages to overcome the limitations of existing techniques, including enhancing the signal level and simplifying the interpretation of the signal.
Stress Perturbation Method for the Assessment of Cathodoluminescence Probe Response Functions
Authors: Zhu Wenliang , Munisso Maria Chiara , Matsutani Atsuo , Ge Wanyin , Pezzotti Giuseppe
Published: October 2009

A method to determine the in-plane cathodoluminescence (CL) probe response function (PRF) (i.e., the function characterizing the in-plane luminescence intensity distribution within the electron probe volume) is proposed, which is based on “perturbing” the spectral position of a selected luminescence band using a highly graded stress field. The method is applied to the stress field developed ahead of the tip of an equilibrium crack in three different cases of CL bands, which arise from different structural phenomena: (i) the F+ (oxygen excess) defect band in a nominally stoichiometric sapphire (α-Al2O3) single crystal; (ii) the chromophoric R-line in ruby lattice (α-Al2–xCrxO3); and (iii) the near band-gap line in n-type GaN semiconductor crystal. A computer-aided data restoration procedure was applied to rationalize data retrieved from crack-tip line scans performed at different acceleration voltages. For the excitonic band-gap in GaN and for F+ emission in sapphire the CL probe in the electron focal plane was found to be comparable, but not necessarily coincident, in size to the electron probe. On the other hand, the occurrence of self-absorption in the case of R-line photons in ruby resulted in a significantly broadened CL probe with respect to the average scattering length of electrons.
Reducing Inter-Replicate Variation in Fourier Transform Infrared Spectroscopy by Extended Multiplicative Signal Correction
Authors: Kohler A. , Böcker U. , Warringer J. , Blomberg A. , Omholt S. W. , Stark E. , Martens H.
Published: October 2009

Fourier transform infrared (FT-IR) spectroscopy is a powerful tool for characterizing biological tissues and organisms, but it is plagued by replicate variation of various sources. Here, a method for estimating and correcting unwanted replicate variation in multivariate measurement signals, based on extended multiplicative signal correction (EMSC), is presented. Systematic patterns of unwanted methodological variations are estimated from replicate spectra, modeled by a linear subspace model, and implemented into EMSC. The method is applied to FT-IR spectra of two different sets of microorganisms (different double gene knockout strains of Saccharomyces cerevisiae and different species of Listeria) and compared to other preprocessing methods used in FT-IR absorption spectroscopy of microorganisms. The EMSC replicate correction turns out to perform best among the compared methods.
Application of Time-of-Flight Near-Infrared Spectroscopy to Fruits: Analysis of Absorption and Scattering Conditions of Near-Infrared Radiation Using Cross-Correlation of the Time-Resolved Profile
Authors: Kurata Yohei , Tsuchikawa Satoru
Published: October 2009

The absorption and scattering conditions of near-infrared radiation in a grapefruit, a popular thick-peeled fruit, were investigated by time-offlight near-infrared spectroscopy (TOF-NIRS). The cross-correlation function was introduced to obtain fine spectroscopic information from the time-resolved profile. Variation of the optical parameters in both the time-resolved profile and the cross-correlation function showed that the NIR radiation was largely absorbed in the peel and considerably scattered in the flesh of the fruit. It also reflected the straightness of the input pulsed laser. The substantial optical path length of the grapefruit estimated from the cross-correlation function was approximately 4 to 5 times as long as the nominal optical path length (NOPL). The cross-correlation function was an effective tool to analyze the absorption/scattering conditions of NIR radiation in a sample where an unstable light source such as a Nd:YAG laser with high output energy was employed.
Near-Infrared Spectroscopy for the Prediction of Disease Ratings for Fiji Leaf Gall in Sugarcane Clones
Authors: Purcell Deborah E. , O'Shea Michael G. , Johnson Robert A. , Kokot Serge
Published: October 2009

This paper demonstrates how inferential measurements or indirect methods using near-infrared (NIR) methodology and chemometrics can be used to predict sugarcane clonal performance. Fiji leaf gall resistance is used in this study as an example. Fiji leaf gall is one of Australia's most serious sugarcane diseases, representing a significant problem in almost half of the total area under production. Traditional rating of sugarcane clones for resistance/susceptibility is difficult and expensive because of the nature of field-based methods and variable infection levels of the trials. Thus, the aim of this work was to investigate the potential of NIR spectroscopy as an alternative means to rate clones from direct measurement of sugarcane leaf spectra and to examine its ability to successfully predict traditional resistance ratings using a calibration model based on a chemometrics method such as partial least squares (PLS). A scanning electron microscopy (SEM) study of the leaf substrate was undertaken to elucidate the nature of the NIR sample site. In addition, an NIR study of freeze-dried sugarcane leaf samples resolved the heavily overlapping O–H bands present in the NIR spectrum due to water/cellulose interaction. A significant decrease in the spectral intensity between 5205 and 5393 cm−1 was observed and a similar decrease was noted in the OH stretching overtone (7114 cm−1) with an accompanying shift to lower wavenumbers. PLS modeling based on traditional ratings as the dependent variable and the corresponding NIR spectra showed satisfactory results with standard error of validation (SEV) and standard error of prediction (SEP) values being 0.98 ( R2 = 0.97) and 1.20 ( R2 = 0.88), respectively. This methodology has now been recommended for more extensive field trials.
Some Advances in Fourier Transform Infrared Transflection Analysis and Potential Applications in Forensic Chemistry
Authors: Koçak A. , Lucania J. P. , Berets S. L.
Published: October 2009

The transflection technique offers significant potential for both qualitative and quantitative analysis in the mid-infrared region. The higher sensitivity for bands in the mid-infrared provides a distinct advantage over the lower absorbance values typically encountered in the near-infrared region. Other advantages, such as small sample size and little sample preparation, make this technique a good candidate for the analysis of forensic substances. Small amounts of illegal drugs such as cocaine can be reliably and nondestructively identified with little or no sample preparation. With the approach to transflection described in this paper, single grains can be quickly identified by simply placing the sample on a specially designed substrate and recording the Fourier transform infrared (FT-IR) spectrum. Transflection was applied to the qualitative analysis of aqueous solutions and solid particles using relatively simple equipment in conjunction with a commercially available diffuse reflection accessory. Improvements in both equipment and technique are discussed. Extensions of the equipment into two new forms, with potential uses in proteomics and forensics, are introduced.
Fourier Transform Spectrometry with a Near-Infrared Supercontinuum Source
Authors: Michaels Chris A. , Masiello Tony , Chu Pamela M.
Published: October 2009

Optical fiber based supercontinuum light sources combine the brightness of lasers with the broad bandwidth of incandescent lamps and thus are promising candidates for sources in spectroscopic applications requiring high brightness and broad bandwidth. Herein, near-infrared (IR) Fourier transform (FT) spectrometry with a supercontinuum (SC) light source is investigated. The efficient, collimated propagation of broad bandwidth SC light through an 18 m path length multipass cell is demonstrated. A normalized spectral difference is calculated for the SC spectrum on consecutive FT mirror scans and is found to vary by less than 0.5%, indicating excellent spectral stability. The rms noise on zero absorbance lines is obtained as a function of the number of mirror scans at 0.125, 2, and 16 cm−1 resolution for both the SC and conventional tungsten lamp source. The SC source has approximately a factor of ten times more noise than the lamp under comparable conditions for each resolution and data acquisition time. This clearly indicates that spectral acquisition with the SC source is not detector noise limited. NIR-FT spectra of methane and methyl salicylate, acquired with both the SC and lamp source, are reported. These spectra illustrate the advantage the SC source has over the incandescent source in that it can efficiently traverse long path lengths, thus providing a sensitivity advantage. The spectra also demonstrate the disadvantage of the SC source with respect to the lamp in the increased level of amplitude noise. Prospects for the future use of SC sources in absorption spectroscopy, including possible noise mitigation strategies, are briefly discussed.
Digital Dewaxing of Raman Signals: Discrimination between Nevi and Melanoma Spectra Obtained from Paraffin-Embedded Skin Biopsies
Authors: Tfayli Ali , Gobinet Cyril , Vrabie Valeriu , Huez Regis , Manfait Michel , Piot Olivier
Published: October 2009

Malignant melanoma (MM) is the most severe tumor affecting the skin and accounts for three quarters of all skin cancer deaths. Raman spectroscopy is a promising nondestructive tool that has been increasingly used for characterization of the molecular features of cancerous tissues. Different multivariate statistical analysis techniques are used in order to extract relevant information that can be considered as functional spectroscopic descriptors of a particular pathology. Paraffin embedding (waxing) is a highly efficient process used to conserve biopsies in tumor banks for several years. However, the use of non-dewaxed formalin-fixed paraffin-embedded tissues for Raman spectroscopic investigations remains very restricted, limiting the development of the technique as a routine analytical tool for biomedical purposes. This is due to the highly intense signal of paraffin, which masks important vibrations of the biological tissues. In addition to being time consuming and chemical intensive, chemical dewaxing methods are not efficient and they leave traces of the paraffin in tissues, which affects the Raman signal. In the present study, we use independent component analysis (ICA) on Raman spectral images collected on melanoma and nevus samples. The sources obtained from these images are then used to eliminate, using non-negativity constrained least squares (NCLS), the paraffin contribution from each individual spectrum of the spectral images of nevi and melanomas. Corrected spectra of both types of lesion are then compared and classified into dendrograms using hierarchical cluster analysis (HCA).
A Laboratory Technique for Thermal Emission Measurement of Hydrated Minerals
Authors: Baldridge A. M. , Christensen P. R.
Published: October 2009

Laboratory emission spectra are measured at Arizona State University's Mars Space Flight Facility for comparison to remotely sensed data from Earth and Mars. Such emission spectroscopy using an interferometric spectrometer measures the energy of the sample, including reflected and emitted background sources. The detector is uncooled at ambient temperature, which produces a very low signal when measuring the energy from a sample that has a temperature close to its own. In order to increase the energy difference between the sample and the detector, thereby increasing the signal received by the detector, samples are typically heated to between 60 and 80 °C for several hours prior to measurement. While this method is acceptable for most rock and mineral samples, some hydrous minerals dehydrate quickly at low relative humidity and temperatures above room temperature. This change is evident in both the physical appearance of the mineral and in the position and shape of its spectral absorptions. One solution to this problem is to heat samples to lower temperatures (e.g., 40 °C) for only a short time period. However, this approach results in a low signal from the sample and does not always avoid dehydration. For this reason, we have developed a technique for measuring and calibrating emission spectra of hydrated minerals that involves cooling samples to well below the temperature of the detector, which avoids dehydration, while creating a large delta temperature and a strong signal from the sample. Our method allows for accurate library spectra, with discrete, pronounced spectral features (high spectral contrast), of hydrated minerals that can be used for comparison to planetary surfaces.
A Rapid Technique for Classifying Phytoplankton Fluorescence Spectra Based on Self-Organizing Maps
Authors: Aymerich Ismael F. , Piera Jaume , Soria-Frisch Aureli , Cros Lluïsa
Published: October 2009

Fluorescence spectroscopy has been demonstrated to be a powerful tool for characterizing phytoplankton communities in marine environments. Using different fluorescence spectra techniques, it is now possible to discriminate the major phytoplankton groups. However, most of the current techniques are based on fluorescence excitation measurements, which require stimulation at different wavelengths and thus considerable time to obtain the complete spectral profile. This requirement may be an important constraint for several mobile oceanographic platforms, such as vertical profilers or autonomous underwater vehicles, which require rapid-acquisition instruments. This paper presents a novel technique for classifying fluorescence spectra based on self-organizing maps (SOMs), one of the most popular artificial neural network (ANN) methods. The method is able to achieve phytoplankton discrimination using only fluorescence emission spectra (single wavelength excitation), thus reducing the acquisition time. The discrimination capabilities of SOM using excitation and emission spectra are compared. The analysis shows that the SOM has a good performance using excitation spectra, whereas data preprocessing is required in order to obtain similar discrimination capabilities using emission spectra. The final results obtained using emission spectra indicate that the discrimination is properly achieved even between algal groups, such as diatoms and dinoflagellates, which cannot be discriminated with previous methods. We finally point out that although techniques based on excitation spectra can achieve a better taxonomic accuracy, there are some applications that require faster acquisition processes. Acquiring emission spectra is almost instantaneous, and techniques such as SOM can achieve good classification performance using appropriately preprocessed data.
Does the Spectral Format Matter in Diffuse Reflection Spectroscopy?
Authors: Reeves James B.
Published: October 2009

Near-infrared, and more recently, mid-infrared diffuse reflection spectroscopy (more commonly and erroneously called reflectance spectroscopy) have come to be extensively used to determine the composition of products ranging from forages and drugs to soils. In these methods, spectra are generally collected as reflectance or R and transformed to log (1/reflectance). However, some near-infrared researchers do not transform the data, but use the data directly as reflectance. As it is generally held that procedures such as partial least squares regression do not work well with nonlinear data and the log (1/reflectance) transformation is held to be a best effort at linearization for near-infrared diffuse reflection spectral data, the question arises as to why then does not everyone transform the data? The objective of this work was to investigate this question using near-infrared and mid-infrared spectra in various formats. Calibrations were developed using spectral data from forages in several formats: reflectance, log (1/reflectance), non-background corrected single beam spectra, interferograms, and Kubelka–Munk transformed data. Calibrations were developed using both non-pretreated spectra and using data pretreatments such as derivatives. Results showed that calibrations using partial least squares regression did not require any specific data format. Accurate calibrations were developed for fiber, digestibility, and protein measures in forages using any of the aforementioned spectral formats including non-background-corrected single beam spectra and even interferograms. While calibrations could be developed using any of the formats, results indicated that those using Kubelka–Munk and especially interferograms did not perform as well as the others, although they were still quite good. In conclusion, results using forage spectra indicated that accurate and equivalent calibrations can be developed using diffuse reflectance data, with (reflectance) or without background correction (single beam spectra), or log (1/reflectance) at least when using partial least squares regression for calibration development.
Raman Microspectroscopy as a Valuable Additional Method to X-Ray Diffraction and Electron Microscope/Microprobe Analysis in the Study of Iron Arsenates in Environmental Samples
Authors: Filippi Michal , Machovič Vladimír , Drahota Petr , Böhmová Vlasta
Published: October 2009

In this paper, we demonstrate that combined application of X-ray diffraction (XRD), electron microscope/microprobe analysis (EMPA), and Raman microspectroscopy is an available and powerful approach for identification and characterization of iron arsenate minerals in complex environmental samples. Arsenic-rich material from the medieval mining dump close to the Giftkies mine in the Jáchymov ore district (Czech Republic) has been studied. Scorodite, kaňkite, amorphous iron arsenate (pitticite), and, to a lesser extent, native sulfur were determined in the studied samples as products of low-temperature arsenopyrite weathering. Scorodite and kaňkite form mixed nodules and crusts, which are locally coated by hardened gel-like amorphous pitticite. Pitticite also borders fractures in the mineralized rock fragments in the dump. Native sulfur, in microscopic crystals and grainy aggregates, originates directly in places with dissolved arsenopyrite and forms pseudomorphs. The Raman spectra presented in the paper can serve as comparative data for phase identification in other contaminated areas. New Raman data for the hydroxyl stretching region of scorodite (important bands: 3514, 3427, and 3600 cm−1) and the whole Raman spectrum for pitticite (important bands: 472, 831, 884, 2935, 3091, 3213, 3400, and 3533 cm−1) are a valuable output of this paper.