Correcting attenuated total reflection-Fourier transform infrared spectra for water vapor and carbon dioxide

Comparison of binding sites and affinity of flavonol-Cu(II) complexes with the same parent nucleus: Synthesis, DFT prediction, and coordination pattern

This study explores the coordination dynamics between dietary polyphenols, specifically kaempferol, quercetin, and myricetin, and Cu ions in aqueous environments. A novel synthesis method for flavonol-Cu(II) coordination compounds is introduced, effectively reducing interference from free metal ions. Our results reveal consistent binding patterns of Cu ions with flavonols (2:1 ratio of flavonol to Cu(II)), predominantly at the 4,5 sites. Various analytical techniques are used to validate these coordination ratios and sites. The binding affinity of the flavonols for Cu ions follows a descending sequence: myricetin > quercetin > kaempferol. Notably, coordination with Cu ions enhances the free-radical scavenging activities of these flavonols. These findings hold substantial importance for food chemistry, biology, and medicine, providing crucial insights into the way dietary flavonols form stable structures in environments similar to human body fluids and their interactions with metal ions, opening new possibilities for their application and understanding in diverse scientific domains.

Preparation and Preliminary Analysis of Several Nanoformulations Based on Plant Extracts and Biodegradable Polymers as a Possible Application for Chronic Venous Disease Therapy

Nanotechnology is one of the newest directions for plant-based therapies. Chronic venous disease often predisposes to long-term and invasive treatment. This research focused on the inclusion of vegetal extracts from Sophorae flos (SE), Calendulae flos (CE), and Ginkgo bilobae folium (GE) in formulations with PHB and PLGA polymers and their physicochemical characterization as a preliminary stage for possible use in the development of a complex therapeutic product. The samples were prepared by an oil-water emulsification and solvent evaporation technique, resulting in suspensions with high spreadability and a pH of 5.5. ATR-FTIR analysis revealed bands for stretching vibrations (O-H, C=O, and C-H in symmetric and asymmetric methyl and methylene) in the same regions as the base components, but switched to high or low wavenumbers and absorbance, highlighting the formation of adducts/complexes between the extracts and polymers. The obtained formulations were in the amorphous phase, as confirmed by XRD analysis. AFM analysis emphasized the morphological peculiarities of the extract-polymer nanoformulations. It could be noticed that, in the case of SE-based formulations, the dominant characteristics for SE-PHB and SE-PLGA composition were the formation of random large (SE-PHB) and smaller uniform (SE-PLGA) particles; further on, these particles tended to aggregate in the case of SE-PHB-PLGA. For the CE- and GE-based formulations, the dominant surface morphology was their porosity, generally with small pores, but larger cavities were observed in some cases (CE- and GE-PHB). The highest roughness values at the (8 µm × 8 μm) scale were found for the following samples and succession: CE-PHB < SE-PLGA < SE-PHB-PLGA. In addition, by thermogravimetric analysis, impregnation in the matrix of compression stockings was evaluated, which varied in the following order: CE-polymer > SE-polymer > GE-polymer. In conclusion, nine vegetal extract-polymer nanoformulations were prepared and preliminarily characterized (by advanced physicochemical methods) as a starting point for further optimization, stability studies, and possible use in complex pharmaceutical products.

Biomolecular alterations detected in multiple sclerosis skin fibroblasts using Fourier transform infrared spectroscopy

Multiple sclerosis (MS) is the leading cause of non-traumatic disability in young adults. New avenues are needed to help predict individuals at risk for developing MS and aid in diagnosis, prognosis, and outcome of therapeutic treatments. Previously, we showed that skin fibroblasts derived from patients with MS have altered signatures of cell stress and bioenergetics, which likely reflects changes in their protein, lipid, and biochemical profiles. Here, we used Fourier transform infrared (FTIR) spectroscopy to determine if the biochemical landscape of MS skin fibroblasts were altered when compared to age- and sex-matched controls (CTRL). More so, we sought to determine if FTIR spectroscopic signatures detected in MS skin fibroblasts are disease specific by comparing them to amyotrophic lateral sclerosis (ALS) skin fibroblasts. Spectral profiling of skin fibroblasts from MS individuals suggests significant alterations in lipid and protein organization and homeostasis, which may be affecting metabolic processes, cellular organization, and oxidation status. Sparse partial least squares-discriminant analysis of spectral profiles show that CTRL skin fibroblasts segregate well from diseased cells and that changes in MS and ALS may be unique. Differential changes in the spectral profile of CTRL, MS, and ALS cells support the development of FTIR spectroscopy to detect biomolecular modifications in patient-derived skin fibroblasts, which may eventually help establish novel peripheral biomarkers.

A Brief Review of FT-IR Spectroscopy Studies of Sphingolipids in Human Cells

In recent years, sphingolipids have attracted significant attention due to their pivotal role in cellular functions and physiological diseases. A valuable tool for investigating the characteristics of sphingolipids can be represented via FT-IR spectroscopy, generally recognized as a very powerful technique that provides detailed biochemical information on the examined sample with the unique properties of sensitivity and accuracy. In the present paper, some fundamental aspects of sphingolipid components of human cells are summarized, and the most relevant articles devoted to the FT-IR spectroscopic studies of sphingolipids are revised. A short description of different FT-IR experimental approaches adopted for investigating sphingolipids is also given, with details about the most commonly used data analysis procedures. The present overview of FT-IR investigations, although not exhaustive, attests to the relevant role this vibrational technique has played in giving significant insight into many aspects of this fascinating class of lipids.

Discrimination and Prediction of Lonicerae japonicae Flos and Lonicerae Flos and Their Related Prescriptions by Attenuated Total Reflectance Fourier Transform Infrared Spectroscopy Combined with Multivariate Statistical Analysis

LJF and LF are commonly used in Chinese patent drugs. In the Chinese Pharmacopoeia, LJF and LF once belonged to the same source. However, since 2005, the two species have been listed separately. Therefore, they are often misused, and medicinal materials are indiscriminately put in their related prescriptions in China. In this work, firstly, we established a model for discriminating LJF and LF using ATR-FTIR combined with multivariate statistical analysis. The spectra data were further preprocessed and combined with spectral filter transformations and normalization methods. These pretreated data were used to establish pattern recognition models with PLS-DA, RF, and SVM. Results demonstrated that the RF model was the optimal model, and the overall classification accuracy for LJF and LF samples reached 98.86%. Then, the established model was applied in the discrimination of their related prescriptions. Interestingly, the results show good accuracy and applicability. The RF model for discriminating the related prescriptions containing LJF or LF had an accuracy of 100%. Our results suggest that this method is a rapid and effective tool for the successful discrimination of LJF and LF and their related prescriptions.

Infrared Spectroscopy in Aqueous Solutions: Capabilities and Challenges

Fourier-transform infrared (FTIR) spectroscopy provides rapid, reliable, quantitative, and qualitative analysis of samples in different aggregation states, i.e., gases, thin films, solids, liquids, etc. However, when analyzing aqueous solutions, particular issues associated with the rather pronounced IR absorption characteristics of water appear to interfere with the solute determination. In this review, Fourier-transform infrared spectroscopic techniques and their analytical capabilities for analyzing aqueous solutions are reviewed, and highlight examples are discussed.

Attenuated Total Reflection (ATR) Micro-Fourier Transform Infrared (Micro-FT-IR) Spectroscopy to Enhance Repeatability and Reproducibility of Spectra Derived from Single Specimen Organic-Walled Dinoflagellate Cysts

The chemical composition of recent and fossil organic-walled dinoflagellate cyst walls and its diversity is poorly understood and analyses on single microscopic specimens are rare. A series of infrared spectroscopic experiments resulted in the proposition of a standardized attenuated total reflection micro-Fourier transform infrared-based method that allows the collection of robust data sets consisting of spectra from individual dinocysts. These data sets are largely devoid of nonchemical artifacts inherent to other infrared spectrochemical methods, which have typically been used to study similar specimens in the past. The influence of sample preparation, specimen morphology and size and spectral data processing steps is also assessed within this methodological framework. As a result, several guidelines are proposed which facilitate the collection and qualitative interpretation of highly reproducible and repeatable spectrochemical data. These, in turn, pave the way for a systematic exploration of dinocyst chemistry and its assessment as a chemotaxonomical tool or proxy.

Low-energy Ar+ and N+ ion beam induced chemical vapor deposition using hexamethyldisilazane for the formation of nitrogen containing SiC and carbon containing SiN films

We proposed an experimental methodology for producing films on substrates with an ion beam induced chemical vapor deposition (IBICVD) method using hexamethyldisilazane (HMDS) as a source material. In this study, both HMDS and ion beam were simultaneously injected onto a Si substrate. We selected Ar⁺ and N⁺ as the ion beam. The energy of the ion beam was 101 eV. Temperature of the Si substrate was set at 540 °C. After the experiments, films were found to be deposited on the substrates. The films were then analyzed by Fourier transform infrared (FTIR) spectroscopy, stylus profilometer, X-ray diffraction, atomic force microscopy, and X-ray photoelectron spectroscopy (XPS). The FTIR and XPS results showed that silicon carbide films containing small amount of nitrogen were formed when Ar⁺ ions were injected in conjunction with HMDS. On the other hand, in the cases of N⁺ ion beam irradiation, silicon nitride films involving small amount of carbon were formed. It was noted that no film deposition was observed when HMDS alone was supplied to the substrates without any ion beam injections.

Attenuated Total Reflection Fourier Transform Infrared (ATR FT-IR) Spectroscopy for the Quantitative Analysis of Deuterium in Plasma: Application to Total Body Water Determination in Humans and Other Animals

Conventional methods for measuring the concentration of deuterium in body fluids are by either isotope ratio mass spectrometry or Fourier transform infrared transmission (FT-IR) spectroscopy. The latter method is often preferred as it is less expensive and time consuming; however, having a lower sensitivity means a larger sample volume is required. This study investigated an alternative FT-IR spectroscopic method, attenuated total reflection Fourier transform infrared spectroscopy (ATR FT-IR), which has the potential to provide shorter analysis times while requiring smaller sample volumes. Deuterium was assayed using ATR FT-IR in plasma in the concentration range 0.5 to 2.5 mg mL^-1, typical of those observed in tracer dilution measurements of total body water. Minimal sample preparation was required and analysis time was substantially decreased compared to transmission FT-IR. Samples were analyzed with high precision (coefficient of variation (CV) < 0.5%). Precision of assay was maintained when assaying plasma volumes of only 10 µL. The application of the method to the determination of total body water in humans and animals (horses) was demonstrated. A rapid and simple method for the measurement of deuterium in plasma is described that only requires very small sample volumes, rendering the method suitable for use in pediatrics where blood sampling is required to be kept to a minimum.

Evaluating biochemical differences in thyroglobulin from normal and goiter tissues by infrared spectral imaging

Thyroglobulin is a glycoiodoprotein that is produced by thyroid follicular cells; it is stored in follicles in structures known as colloids. The main function of this protein is to stock the hormones triiodothyronine (T3) and thyroxine (T4) until the body requires them. This study aims to demonstrate that infrared spectral imaging with appropriate multivariate analysis can reveal biochemical changes in this glycoprotein. The results achieved herein point out biochemical differences in the colloid samples obtained from normal and goiter patients including glycosylation and changes in the secondary conformational structure. We have presented the first spectral histopathology-based method to detect biochemical differences in thyroid colloids, such as TG iodination, glycosylation, and changes in the secondary structure in normal and goiter patients. The observed changes in the colloids were mainly due to the alterations in amide I and amide II (secondary conformation of proteins) and there is a correlation with different glycosylation between normal and goiter tissues.

Spectral Analysis and Deconvolution of the Amide I Band of Proteins Presenting with High-Frequency Noise and Baseline Shifts

The challenge of deriving quantitative information from the infrared spectra of proteins arises from the large number of secondary structures and amino acid side-chain functional groups that all contribute to the spectral intensity, such as within the amide I band (1600-1700 cm^-1). The band is invariably heavily convoluted from overlapping spectral features, thereby making interpretation difficult such that deconvolution is usually required. This work critically examines the methods available to deconvolute the spectra and assesses the commonly used methods and algorithms applied to vibrational spectra for smoothing and peak identification. We show that unless their spectra have very high signal-to-noise ratios, quantitative analysis to decipher protein constituents is not feasible. The advantages and disadvantages of spectral smoothing using adjacent averaging, the Savitzky-Golay filter and the fast Fourier transform filter are examined in detail. The use of derivative spectra to identify peaks is described with particular reference to the influence and reduction of interfering water bands in the amide I region. The reliability of band narrowing techniques such as second-derivative analysis or Fourier deconvolution that lead to the identification of the contributing protein peaks is investigated. Both methods are shown to be limited in their capacity to resolve features with very similar frequencies. Additionally, the presence of narrow bands arising from high-frequency noise whether from atmospheric water vapor, acoustic vibrations, or electrical interference results in both methods becoming increasingly unusable as narrow bands are preferentially enhanced at the expense of broad ones such as the amide I bands. An optimal strategy is critically developed to allow accurate determination and quantification of protein constituents and their conformations. Additionally, quantitative methods are proposed to account for baseline shifts, which would otherwise introduce significant errors in similarity indices.

OCTAVVS: A Graphical Toolbox for High-Throughput Preprocessing and Analysis of Vibrational Spectroscopy Imaging Data

Modern vibrational spectroscopy techniques enable the rapid collection of thousands of spectra in a single hyperspectral image, allowing researchers to study spatially heterogeneous samples at micrometer resolution. A number of algorithms have been developed to correct for effects such as atmospheric absorption, light scattering by cellular structures and varying baseline levels. After preprocessing, spectra are commonly decomposed and clustered to reveal informative patterns and subtle spectral changes. Several of these steps are slow, labor-intensive and require programming skills to make use of published algorithms and code. We here present a free and platform-independent graphical toolbox that allows rapid preprocessing of large sets of spectroscopic images, including atmospheric correction and a new algorithm for resonant Mie scattering with improved speed. The software also includes modules for decomposition into constituent spectra using the popular Multivariate Curve Resolution-Alternating Least Squares (MCR-ALS) algorithm, augmented by region-of-interest selection, as well as clustering and cluster annotation.

Micro ATR-FTIR spectroscopic imaging of colon biopsies with a large area Ge crystal

A new large-area germanium ATR crystal is utilised with an FTIR microscope to improve the acquired images of de-paraffinized colon biopsy sections, without recourse to a synchrotron source. The large crystal (⌀ = 28 mm) offers significant improvements compared to slide-on small germanium crystal (⌀ = 3.5 mm); for example, it facilitates more uniform distribution of higher signal intensity within the field of view and more rapid acquisition time. Mapping of a larger sample area up to ca. 350 × 350 μm² with this new set-up, coupled with imaging using an FPA detector, is demonstrated for the first time on biological specimens. The performance of k-means clustering algorithm applied to classify the different anatomical structures of the colon biopsies is greatly improved with mapping. Comparison of H&E stained adjacent tissue sections with false-colour k-means images strongly support differentiation of five distinct regions within tissues. The efficiency of the methodology to categorise colon tissues at various stages of malignancy is analysed via multivariate chemometrics. The second derivative spectra extracted from the crypt region of the colon were subjected to Partial Least Squares classification. Good separation between data in clusters occurs when projecting spectra on a PLS score plot on a plane made by the first 3 principal components. Important spectral biomarkers for colon malignancy classification were identified to exist mostly in the fingerprint region of the FTIR spectrum based on the chemometrics analysis.

Graphene Oxide Decorated with Titanium Nanoparticles to Reinforce the Anti-Corrosion Performance of Epoxy Coating

Graphene oxide–titanium (GO-Ti) composite materials were fabricated using GO as a precursor and then anchoring nano titanium (Nano-Ti) particles on GO sheets with the help of a silane coupling agent. Then, the coating samples were prepared by dispersing GO, Nano-Ti particles, and GO-Ti in an epoxy resin at a low weight fraction of 1 wt %. The GO-Ti composites were investigated by X-ray photoelectron spectroscopy (XPS), X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM), and transmission electron microscopy (TEM). The dispersibility and anti-corrosion mechanism of the coatings were studied by sedimentation experiments, electrochemical impedance spectroscopy (EIS), SEM, and salt spray tests. The mechanical properties of the coatings were analyzed by friction and wear tests. The results showed that the Nano-Ti particles were successfully loaded on the GO surface by chemical bonds, which made GO-Ti composites exhibit better dispersibility in the epoxy than GO. Compared with Nano-Ti particles and GO, the GO-Ti composite exhibited significant advantages in improving the corrosion resistance of epoxy coatings at the same contents, which was attributed to the excellent dispersibility, inherent corrosion resistance, and sheet structure. Among the different proportions of composite materials, the GO-Ti (2:1) material exhibited the best dispersibility and corrosion resistance. In addition, the composite material also greatly improved the wear resistance of the coating.

Vapor correction of FTIR spectra - A simple automatic least squares approach

FTIR spectroscopy is one of the best techniques to study intermolecular interactions. However, such an application requires high quality spectra with as little noise as possible, which are often difficult to obtain. One of the main sources of unwanted interference is water vapor. Here a robust method is proposed for automatic, fast and reliable vapor correction of FTIR spectra. The presented least squares approach of vapor subtraction using many vapor spectra and a special residual function provides a much better correction. It does not rely on the researcher's experience, no coefficients are arbitrarily chosen or tweaked, thus such results are more trustworthy and accurate.

Spectral histopathology of the lung: A review of two large studies

This paper summarizes results from two large lung cancer studies comprising over 700 samples that demonstrate the ability of spectral histopathology (SHP) to distinguish cancerous tissue regions from normal tissue, to differentiate benign lesions from normal tissue and cancerous lesions, and to classify lung cancer types. Furthermore, malignancy-associated changes can be identified in cancer-adjacent normal tissue. The ability to differentiate a multitude of normal cells and tissue types allow SHP to identify tumor margins and immune cell infiltration. Finally, SHP easily distinguishes small cell lung cancer (SCLC) from non-SCLC (NSCLC) and provides a further differentiation of NSCLC into adenocarcinomas and squamous cell carcinomas with an accuracy comparable of classical histopathology combined with immunohistochemistry. Case studies are presented that demonstrates that SHP can resolve interobserver discrepancies in standard histopathology.

Fourier transform infrared spectroscopic imaging of colon tissues: evaluating the significance of amide I and C-H stretching bands in diagnostic applications with machine learning

Fourier transform infrared (FTIR) spectroscopic imaging of colon biopsy tissues in transmission combined with machine learning for the classification of different stages of colon malignancy was carried out in this study. Two different approaches, an optical and a computational one, were applied for the elimination of the scattering background during the measurements and compared with the results of the machine learning model without correction for the scattering. Several different data processing pathways were implemented in order to obtain a high accuracy of the prediction model. This study demonstrates, for the first time, that C-H stretching and amide I bands are of little to no significance in the classification of the colon malignancy, based on the Gini importance values by random forest (RF). The best prediction outcome is found when supervised RF classification was carried out in the fingerprint region of the spectral data between 1500 and 1000 cm^-1 (excluding the contribution of amide I and II bands). An overall prediction accuracy higher than 90% is achieved through the RF. The results also show that dysplastic and hyperplastic tissues are well distinguished. This leads to the insight that the important differences between hyperplastic and dysplastic colon tissues lie within the fingerprint region of FTIR spectra. In this study, computational correction performed better than optical correction, but the findings show that the disease states of colon biopsies can be distinguished effectively without elimination of Mie scattering effect. Graphical abstract.

Second Generation of Multiple-Angle Incidence Resolution Spectrometry

Infrared surface spectroscopic techniques commonly have long-term issues that (1) the multiple reflections of light in the substrate yield optical interference fringes in the absorption spectrum and (2) the double modulation of light at the interferometer in a Fourier transform infrared spectrometer makes the water-vapor subtraction impossible. These measurement troubles often disturb the quantitative analysis of chemical bands of the analyte thin film. Multiple-angle incidence resolution spectrometry (MAIRS) is not an exception in this matter, either. In the present study, the long-term common issues have first been resolved by fixing the angle of incidence at a large angle, whereas the polarization angle is changed. With this simple conceptual change of MAIRS, as a result, we are ready for concentrating on spectral analysis only without concerning about the measurement troubles.

Comments on recent reports on infrared spectral detection of disease markers in blood components

The search for disease markers in whole blood, or easily accessible blood components by spectral methods is a highly important aspect in the field of biophotonic research for disease diagnostics and screening, since it promises a minimally invasive approach to assess an individual's state of health. Fourier transform infrared spectroscopy, in particular, promises to be a fast, inexpensive method to search for markers of disease, since it detects variation in the proteome, lipidome and metabolome of biofluids, or activation of immune cells. However, the analysis of any materials by spectral methods is confounded by external factors such as those related to sample deposition and data acquisition, and by inherent variations in blood plasma concentration of small molecules (lactate, carbonate, phosphate, glucose) that varies between individual subjects and even for a given individual, as a function of time. Furthermore, observed differences in spectral patterns between patient samples and the control group may be due to the body's immune response (in particular, to the albumin to globulin ratio) and therefore, may not be specific to disease. These factors need to be accounted for in any effort to reliably detect much smaller variations in the concentration of disease-specific markers.

Discrimination and prediction of the origin of Chinese and Korean soybeans using Fourier transform infrared spectrometry (FT-IR) with multivariate statistical analysis

The ability to determine the origin of soybeans is an important issue following the inclusion of this information in the labeling of agricultural food products becoming mandatory in South Korea in 2017. This study was carried out to construct a prediction model for discriminating Chinese and Korean soybeans using Fourier-transform infrared (FT-IR) spectroscopy and multivariate statistical analysis. The optimal prediction models for discriminating soybean samples were obtained by selecting appropriate scaling methods, normalization methods, variable influence on projection (VIP) cutoff values, and wave-number regions. The factors for constructing the optimal partial-least-squares regression (PLSR) prediction model were using second derivatives, vector normalization, unit variance scaling, and the 4000-400 cm-1 region (excluding water vapor and carbon dioxide). The PLSR model for discriminating Chinese and Korean soybean samples had the best predictability when a VIP cutoff value was not applied. When Chinese soybean samples were identified, a PLSR model that has the lowest root-mean-square error of the prediction value was obtained using a VIP cutoff value of 1.5. The optimal PLSR prediction model for discriminating Korean soybean samples was also obtained using a VIP cutoff value of 1.5. This is the first study that has combined FT-IR spectroscopy with normalization methods, VIP cutoff values, and selected wave-number regions for discriminating Chinese and Korean soybeans.

Infrared micro-spectroscopy of human tissue: principles and future promises

This article summarizes the methods employed, and the progress achieved over the past two decades in applying vibrational (Raman and IR) micro-spectroscopy to problems of medical diagnostics and cellular biology. During this time, several research groups have verified the enormous information contained in vibrational spectra; in fact, information on protein, lipid and metabolic composition of cells and tissues can be deduced by decoding the observed vibrational spectra. This decoding process is aided by the availability of computer workstations and advanced algorithms for data analysis. Furthermore, commercial instrumentation for the fast collection of both Raman and infrared micro-spectral data has enabled the collection of images of cells and tissues based solely on vibrational spectroscopic data. The progress in the field has been manifested by a steady increase in the number and quality of publications submitted by established and new research groups in vibrational spectroscopy in the biological and biomedical arenas.

No stone unturned: The presence of kidney stones in a skeleton from 19th century Peoria, Illinois

During the excavation of the 19th century Peoria City Cemetery (Peoria, Illinois), a skeleton of a female, aged 20-30 years old, was found with large, bilateral calcified masses in the abdominal region. The masses were analyzed by Fourier transform infrared (FTIR) spectroscopy, and the results compared to published clinical data in an effort to determine the etiology of the stones. The calcified masses were determined to be staghorn struvite uroliths, which commonly result from chronic urinary tract infection and likely impacted the overall health of this individual.

Discrimination and prediction of cultivation age and parts of Panax ginseng by Fourier-transform infrared spectroscopy combined with multivariate statistical analysis

Panax ginseng C.A. Meyer is a herb used for medicinal purposes, and its discrimination according to cultivation age has been an important and practical issue. This study employed Fourier-transform infrared (FT-IR) spectroscopy with multivariate statistical analysis to obtain a prediction model for discriminating cultivation ages (5 and 6 years) and three different parts (rhizome, tap root, and lateral root) of P. ginseng. The optimal partial-least-squares regression (PLSR) models for discriminating ginseng samples were determined by selecting normalization methods, number of partial-least-squares (PLS) components, and variable influence on projection (VIP) cutoff values. The best prediction model for discriminating 5- and 6-year-old ginseng was developed using tap root, vector normalization applied after the second differentiation, one PLS component, and a VIP cutoff of 1.0 (based on the lowest root-mean-square error of prediction value). In addition, for discriminating among the three parts of P. ginseng, optimized PLSR models were established using data sets obtained from vector normalization, two PLS components, and VIP cutoff values of 1.5 (for 5-year-old ginseng) and 1.3 (for 6-year-old ginseng). To our knowledge, this is the first study to provide a novel strategy for rapidly discriminating the cultivation ages and parts of P. ginseng using FT-IR by selected normalization methods, number of PLS components, and VIP cutoff values.

Fundamental developments in infrared spectroscopic imaging for biomedical applications

Infrared chemical imaging is a rapidly emerging field with new advances in instrumentation, data acquisition and data analysis. These developments have had significant impact in biomedical applications and numerous studies have now shown that this technology offers great promise for the improved diagnosis of the diseased state. Relying on purely biochemical signatures rather than contrast from exogenous dyes and stains, infrared chemical imaging has the potential to revolutionise histopathology for improved disease diagnosis. In this review we discuss the recent advances in infrared spectroscopic imaging specifically related to spectral histopathology (SHP) and consider the current state of the field. Finally we consider the practical application of SHP for disease diagnosis and consider potential barriers to clinical translation highlighting current directions and the future outlook.

A method for the comparison of multi-platform spectral histopathology (SHP) data sets

Results of a study comparing infrared imaging data sets collected on different instruments or instrument platforms are reported, along with detailed methods developed to permit such comparisons. It was found that different instrument platforms, although employing different detector technologies and pixel sizes, produce highly similar and reproducible spectral results. However, differences in the absolute intensity values of the reflectance data sets were observed that were caused by heterogeneity of the sample substrate in terms of reflectivity and planarity.

FTIR spectral signature of anticancer drugs. Can drug mode of action be identified?

Infrared spectroscopy has brought invaluable information about proteins and about the mechanism of action of enzymes. These achievements are difficult to transpose to living organisms as all biological molecules absorb in the mid infrared, with usually a high degree of overlap. Deciphering the contribution of each enzyme is therefore almost impossible. On the other hand, small changes in the infrared spectra of cells induced by environmental conditions or drugs may provide an accurate signature of the metabolic shift experienced by the cell as a response to a change in the growth medium. The present paper aims at reviewing the contribution of infrared spectroscopy to the description of small chemical changes that occur in cells when they are exposed to a drug. In particular, this review will focus on cancer cells and anti-cancer drugs. Results accumulated so far tend to demonstrate that infrared spectroscopy could be a very accurate descriptor of the mode of action of anticancer drugs. If confirmed, such a segmentation of potential drugs according to their "mode of action" will be invaluable for the discovery of new therapeutic molecules. This article is part of a Special Issue entitled: Physiological Enzymology and Protein Functions.

Using Fourier transform IR spectroscopy to analyze biological materials

IR spectroscopy is an excellent method for biological analyses. It enables the nonperturbative, label-free extraction of biochemical information and images toward diagnosis and the assessment of cell functionality. Although not strictly microscopy in the conventional sense, it allows the construction of images of tissue or cell architecture by the passing of spectral data through a variety of computational algorithms. Because such images are constructed from fingerprint spectra, the notion is that they can be an objective reflection of the underlying health status of the analyzed sample. One of the major difficulties in the field has been determining a consensus on spectral pre-processing and data analysis. This manuscript brings together as coauthors some of the leaders in this field to allow the standardization of methods and procedures for adapting a multistage approach to a methodology that can be applied to a variety of cell biological questions or used within a clinical setting for disease screening or diagnosis. We describe a protocol for collecting IR spectra and images from biological samples (e.g., fixed cytology and tissue sections, live cells or biofluids) that assesses the instrumental options available, appropriate sample preparation, different sampling modes as well as important advances in spectral data acquisition. After acquisition, data processing consists of a sequence of steps including quality control, spectral pre-processing, feature extraction and classification of the supervised or unsupervised type. A typical experiment can be completed and analyzed within hours. Example results are presented on the use of IR spectra combined with multivariate data processing.

Fourier-transformed infrared spectroscopy: a tool to identify gross chemical changes from healthy to yellow band disease tissues

Yellow band disease (YBD) is a common and wide-spread Caribbean syndrome that affects the genus Orbicella, a group of species that constitute the framework of Caribbean coral reefs. Previous studies have shown that the structure and function of bacterial assemblages vary between healthy tissues and YBD lesions; however, how the molecular composition of tissues varies as tissues transition from healthy to YBD has not been determined before. The present study provides the first survey of macromolecules found from healthy (H), apparently healthy (AH), transition (TR) and YBD tissues of Orbicella faveolata. For this, we used Fourier-transformed mid-infrared spectroscopy (FTIR) to compare absorption profiles as a proxy for the gross molecular composition of decalcified H, AH and YBD tissues. We found a significantly higher level of infrared absorption for bands assigned to lipids in H tissues compared to YBD tissues, suggesting that lipid compounds are more abundant in compromised tissues in relation to other macromolecules. We also found a lower level of intensity of bands assigned to carbohydrates and proteins in YBD tissues, compared to H and AH tissues. A similar pattern was observed for phospholipidic compounds in relation to fatty acids. This study is the first to show that healthy and YBD-compromised tissues have different infrared absorption profiles, suggesting that alterations in the biochemical composition occur during pathogenesis. Future studies should focus on determining the actual concentration of these compounds in H, AH, TR and YBD tissues and on testing the role of translocation of photoassimilates from H tissues and/or from endolithic algae to YBD tissues.

Atmospheric compensation in Fourier transform infrared (FT-IR) spectra of clinical samples

A new method is proposed for the elimination of the spectral contribution of two atmospheric gases (CO2 and H2O) in Fourier transform infrared (FT-IR) spectra of clinical samples. The algorithm is based on the measurement of reference spectra of H2O followed by an automatic calculation of the spectral contribution of the above-mentioned gases to the sample spectra. Then this contribution is compensated by spectral subtraction. Attenuated total reflectance FT-IR spectra of serum and urine samples in the presence of atmospheric gases were corrected and compared with spectra obtained with an N2 purge. Visual inspection of the spectra as well as calculated noise levels confirmed that the method compensated for the contribution of CO2 and H2O to serum and urine spectra to a great extent. As compared with the correction performed by a commercial software package, the proposed method clearly improved the correction of CO2 and provided similar results for H2O compensation. Correlation values between corrected spectra and those obtained under N2-purged conditions in the fingerprint region were higher than 0.995, and noise values in regions where samples did not absorb confirmed the suitability of the correction. The proposed method is fast, easy, and extensible to other gaseous interferences, devices, and acquisition conditions.

Cluster analysis of infrared spectra can differentiate intact and repaired articular cartilage

OBJECTIVE

Successful repair of articular cartilage (AC) defects would be a major advantage due to the low ability of AC to heal spontaneously. Sensitive methods to determine changes in AC composition and structure are required to monitor the success of repair. This study evaluates the ability of unsupervised cluster analysis applied to Fourier transform infrared (FTIR) microspectroscopy to discriminate between healthy and repaired AC.

METHODS

Osteochondral lesions (3 mm in depth) were surgically created in patellar grooves of rabbit femurs and were either left to heal spontaneously (n = 6) or surgically repaired with autologous chondrocytes in type II collagen gel (n = 6). After 6 months, tissues were harvested, FTIR microspectroscopy was conducted and Fuzzy c-means (FCM) cluster analysis applied to spectra of pairs of intact and repaired AC samples from each rabbit. Two spectral regions [amide I and carbohydrate (CHO)] were analyzed and the results from the two types of repair were compared.

RESULTS

Two separate regions of repair were detected with FCM. The estimated proteoglycan content (from CHO region) in the repaired AC was significantly lower than that in intact AC. The spontaneously repaired AC was better distinguished from the intact AC than the collagen II gel repaired AC. The most distinct clustering was observed for spontaneously repaired samples using CHO region.

CONCLUSIONS

This study revealed that unsupervised cluster analysis applied to FTIR microspectroscopy can detect subtle differences in infrared spectra between normal and repaired AC. The method may help in evaluation and optimization of future AC repair strategies.

Evaluating different fixation protocols for spectral cytopathology, part 2: cultured cells

Spectral cytopathology (SCP) is a robust and reproducible diagnostic technique that employs infrared spectroscopy and multivariate statistical methods, such as principal component analysis to interrogate unstained cellular samples and discriminate changes on the biochemical level. In the past decade, SCP has taken considerable strides in its application for disease diagnosis. Cultured cell lines have proven to be useful model systems to provide detailed biological information to this field; however, the effects of sample fixation and storage of cultured cells are still not entirely understood in SCP. Conventional cytopathology utilizes fixation and staining methods that have been established and widely accepted for nearly a century and are focused on maintaining the morphology of a cell. Conversely, SCP practices must implement fixation protocols that preserve the sample's biochemical composition and maintain its spectral integrity so not to introduce spectral changes that may mask variance significant to disease. It is not only necessary to evaluate the effects on fixed exfoliated cells but also fixed cultured cells because although they are similar systems, they exhibit distinct differences. We report efforts to study the effects of fixation methodologies commonly used in traditional cytopathology and SCP including both fixed and unfixed routines applied to cultured HeLa cells, an adherent cervical cancer cell line. Data suggest parallel results to findings in Part 1 of this series for exfoliated cells, where the exposure time in fixative and duration of sample storage via desiccation contribute to minor spectral changes only. The results presented here reinforce observations from Part 1 indicating that changes induced by disease are much greater than changes observed as a result of alternate fixation methodologies. Principal component analysis of HeLa cells fixed via the same conditions and protocols as exfoliated cells (Part 1) yield nearly identical results. More importantly, the overall conclusion is that it is necessary that all samples subjected to comparative analysis should be prepared identically because although changes are minute, they are present.

Characterization of Xenorhabdus and Photorhabdus bacteria by Fourier transform mid-infrared spectroscopy with attenuated total reflection (FT-IR/ATR)

The use of Fourier transform mid-infrared spectroscopy with attenuated total reflection for characterizing entomopathogenic bacteria from genera Xenorhabdus and Photorhabdus is evaluated for the first time. The resulting spectra of Xenorhabdus poinarii and Photorhabdus luminiscens were compared with the spectrum of Escherichia coli samples. The absorption spectra generated by the bacteria samples, were very different at the region below 1400cm(-1) which represents the stretching vibrations of phosphate and carbohydrates. Star diagrams of the fingerprint section of nematodes spectra (between 1,350 and 1,650 cm(-1)) for separation between spectra was used and showed to be a useful tool for classification purposes.

Formation of smooth, conformal molecular layers on ZnO surfaces via photochemical grafting

We have investigated the photochemical grafting of organic alkenes to atomically flat ZnO(10 ̅10) single crystals and ZnO nanorods as a way to produce functional molecule-semiconductor interfaces. Atomic force microscopy shows that photochemical grafting produces highly conformal, smooth molecular layers with no detectable changes in the underlying structure of the ZnO terraces or steps. X-ray photoelectron spectroscopy measurements show that grafting of a methyl ester-terminated alkene terminates near one monolayer, while alkenes bearing a trifluoroacetamide-protected amine form very smooth multilayers. Even with multilayers, it is possible to deprotect the amines and to link a second molecule to the surface with excellent efficiency and without significant loss of molecules from the surface. This demonstrates that the use of photochemical grafting, even in the case of multilayer formation, enables multistep chemical processes to be conducted on the ZnO surface. Photoresponse measurements demonstrate that functionalization of the surface does not affect the ability to induce field effects in the underlying ZnO, thereby suggesting that this approach to functionalization may be useful for applications in sensing and in hybrid organic-inorganic transistors and related devices.

Protein secondary structure content in solution, films and tissues: redundancy and complementarity of the information content in circular dichroism, transmission and ATR FTIR spectra

The paper presents a simple and robust method to determine protein secondary structure from circular dichroism, transmission and attenuated total reflection (ATR) Fourier transform infrared spectra. It is found that the different spectroscopic methods bring valuable but roughly identical information on the secondary structure of proteins. ATR and transmission FTIR spectra display distinct differences, yet the secondary structure can be predicted from their spectra with roughly the same success. It is also found that one wavenumber or wavelength includes the large majority of the information correlated with secondary structure content and no more than 3 significant independent wavenumbers/wavelengths could be found for any of the spectroscopic data. This finding indicates that more complex linear combinations of the absorbance or ellipticities will not further improve secondary structure predictions. Furthermore, the information content in CD, transmission and ATR FTIR spectra is largely redundant. If combining CD and FTIR results in some improvement of structure prediction quality, the improvement is too modest to prompt spectroscopists to collect different spectroscopic data for structure prediction purposes. On the other hand, the data collected show that the quality of the FTIR spectrometers is such that biosensors or imaging methods sampling from 10(-9) to 10(-15) g yield spectra of sufficient quality to analyze protein secondary structure. These new techniques open the way to a new area of research, both in protein conformational response to ligand and imaging at sub-cellular scales.

Estimating and correcting mie scattering in synchrotron-based microscopic fourier transform infrared spectra by extended multiplicative signal correction

We present an approach for estimating and correcting Mie scattering occurring in infrared spectra of single cells, at diffraction limited probe size, as in synchrotron based microscopy. The Mie scattering is modeled by extended multiplicative signal correction (EMSC) and subtracted from the vibrational absorption. Because the Mie scattering depends non-linearly on alpha, the product of the radius and the refractive index of the medium/sphere causing it, a new method was developed for estimating the Mie scattering by EMSC for unknown radius and refractive index of the Mie scatterer. The theoretically expected Mie contributions for a range of different alpha values were computed according to the formulae developed by Van de Hulst (1957). The many simulated spectra were then summarized by a six-dimensional subspace model by principal component analysis (PCA). This subspace model was used in EMSC to estimate and correct for Mie scattering, as well as other additive and multiplicative interference effects. The approach was applied to a set of Fourier transform infrared (FT-IR) absorbance spectra measured for individual lung cancer cells in order to remove unwanted interferences and to estimate ranges of important alpha values for each spectrum. The results indicate that several cell components may contribute to the Mie scattering.