Browse
Submit Data
Databases
API
Help

Dataset Information

17 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Infrared attenuated total reflectance spectroscopy: an innovative strategy for analyzing mineral components in energy relevant systems.

ABSTRACT: The direct qualitative and quantitative determination of mineral components in shale rocks is a problem that has not been satisfactorily resolved to date. Infrared spectroscopy (IR) is a non-destructive method frequently used in mineral identification, yet challenging due to the similarity of spectral features resulting from quartz, clay, and feldspar minerals. This study reports on a significant improvement of this methodology by combining infrared attenuated total reflection spectroscopy (IR-ATR) with partial least squares (PLS) regression techniques for classifying and quantifying various mineral components present in a number of different shale rocks. The developed multivariate classification model was calibrated using pure component mixtures of the most common shale minerals (i.e., kaolinite, illite, montmorillonite, calcite, and quartz). Using this model, the IR spectra of 11 real-world shale samples were analyzed and evaluated. Finally, the performance of the developed IR-ATR method was compared with results obtained via X-ray diffraction (XRD) analysis.

SUBMITTER: Muller CM

PROVIDER: S-EPMC4215304 | biostudies-other | 2014

REPOSITORIES: biostudies-other

ACCESS DATA

Json Xml

Similar Datasets

Use of attenuated total reflectance Fourier transform infrared spectroscopy to identify microbial metabolic products on carbonate mineral surfaces.

Project description:This paper demonstrates the use of attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy to detect microbial metabolic products on carbonate mineral surfaces. By creating an ATR-FTIR spectral database for specific organic acids using ATR-FTIR spectroscopy we were able to distinguish metabolic acids on calcite surfaces following Escherichia coli growth. The production of these acids by E. coli was verified using high-performance liquid chromatography with refractive index detection. The development of this technique has allowed us to identify microbial metabolic products on carbonate surfaces in nutrient-limited cave environments.

| S-EPMC2493160 | biostudies-literature

Undistorted structural analysis of soluble proteins by attenuated total reflectance infrared spectroscopy.

Project description:Water from the solvent very strongly absorbs light in the frequency range of interest for studying protein structure by infrared (IR) spectroscopy. This renders handling of the observation cells painstaking and time consuming, and limits the reproducibility of the measurements when IR spectroscopy is applied to proteins in aqueous solutions. These difficulties are circumvented by the use of an Attenuated Total Reflectance (ATR) accessory. However, when protein solutions are studied, ATR spectroscopy suffers from several drawbacks, the most severe being nonproportionality of the observed absorbance with the protein concentration and spectral distortions that vary from protein to protein and from sample to sample. In this study, we show (1) that the nonproportionality is due to adsorption of the protein on the ATR crystal surface; (2) that the contribution of the crystal-adsorbed protein can easily be taken into account, rendering the corrected absorbance proportional to the protein concentration; (3) that the observed variable base line distortions, likely due to changes in the penetration depth of the light beam in solutions with the refractive index that depends on the protein concentration, can be easily eliminated; and (4) that ATR IR spectra thus corrected for protein adsorption and light penetration can be used to properly analyze the secondary structure of proteins in solution.

| S-EPMC2253228 | biostudies-literature

Reagent-Free Identification of Clinical Yeasts by Use of Attenuated Total Reflectance Fourier Transform Infrared Spectroscopy.

Project description:Invasive fungal infections by opportunistic yeasts have increased concomitantly with the growth of an immunocompromised patient population. Misidentification of yeasts can lead to inappropriate antifungal treatment and complications. Attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy is a promising method for rapid and accurate identification of microorganisms. ATR-FTIR spectroscopy is a standalone, inexpensive, reagent-free technique that provides results within minutes after initial culture. In this study, a comprehensive spectral reference database of 65 clinically relevant yeast species was constructed and tested prospectively on spectra recorded (from colonies taken from culture plates) for 318 routine yeasts isolated from various body fluids and specimens received from 38 microbiology laboratories over a 4-month period in our clinical laboratory. ATR-FTIR spectroscopy attained comparable identification performance with matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). In a preliminary validation of the ATR-FTIR method, correct identification rates of 100% and 95.6% at the genus and species levels, respectively, were achieved, with 3.5% unidentified and 0.9% misidentified. By expanding the number of spectra in the spectral reference database for species for which isolates could not be identified or had been misidentified, we were able to improve identification at the species level to 99.7%. Thus, ATR-FTIR spectroscopy provides a new standalone method that can rival MALDI-TOF MS for the accurate identification of a broad range of medically important yeasts. The simplicity of the ATR-FTIR spectroscopy workflow favors its use in clinical laboratories for timely and low-cost identification of life-threatening yeast strains for appropriate treatment.

| S-EPMC6498014 | biostudies-literature

In Situ Time-Resolved Attenuated Total Reflectance Infrared Spectroscopy for Probing Metal-Organic Framework Thin Film Growth.

Project description:In situ chemical measurements of solution/surface reactions during metal-organic framework (MOF) thin film growth can provide valuable information about the mechanistic and kinetic aspects of key reaction steps, and allow control over crystal quality and material properties. Here, we report a new approach to study the growth of MOF thin films in a flow cell using attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR). Real-time spectra recorded during continuous flow synthesis were used to investigate the mechanism and kinetics that govern the formation of (Zn, Cu) hydroxy double salts (HDSs) from ZnO thin films and the subsequent conversion of HDS to HKUST-1. We found that both reactions follow pseudo-first order kinetics. Real-time measurements also revealed that the limited mass transport of reactants may lead to partial conversion of ZnO to HDS and therefore leaves an interfacial ZnO layer beneath the HDS film providing strong adhesion of the HKUST-1 coating to the substrate. This in situ flow-cell ATR-FTIR method is generalizable for studying the dynamic processes of MOF thin film growth, and could be used for other solid/liquid reaction systems involving thin films.

| S-EPMC5846636 | biostudies-literature

Fourier transform infrared with attenuated total reflectance applied to the discrimination of freshwater planktonic coccoid green microalgae.

Project description:Despite the recent advances on fine taxonomic discrimination in microorganisms, namely using molecular biology tools, some groups remain particularly problematic. Fine taxonomy of green algae, a widely distributed group in freshwater ecosystems, remains a challenge, especially for coccoid forms. In this paper, we propose the use of the Fourier Transform Infrared (FTIR) spectroscopy as part of a polyphasic approach to identify and classify coccoid green microalgae (mainly order Sphaeropleales), using triplicated axenic cultures. The attenuated total reflectance (ATR) technique was tested to reproducibility of IR spectra of the biological material, a primary requirement to achieve good discrimination of microalgal strains. Spectral window selection was also tested, in conjunction with the first derivative treatment of spectra, to determine which regions of the spectrum provided better separation and clustering of strains. The non-metric multidimensional scaling (NMDS), analysis of similarities (ANOSIM) and hierarchical clusters (HCA), demonstrated a correct discrimination and classification of closely related strains of chlorophycean coccoid microalgae, with respect to currently accepted classifications. FTIR-ATR was highly reproducible, and provided an excellent discrimination at the strain level. The best separation was achieved by analyzing the spectral windows of 1500-1200 cm(-1) and 900-675 cm(-1), which differs from those used in previously studies for the discrimination of broad algal groups, and excluding spectral regions related to storage compounds, which were found to give poor discrimination. Furthermore, hierarchical cluster analyses have positioned the strains tested into clades correctly, reproducing their taxonomic orders and families. This study demonstrates that FTIR-ATR has great potential to complement classical approaches for fine taxonomy of coccoid green microalgae, though a careful spectrum region selection is needed.

| S-EPMC4277285 | biostudies-literature

Monitoring Molecular Weight Changes during Technical Lignin Depolymerization by Operando Attenuated Total Reflectance Infrared Spectroscopy and Chemometrics.

Project description:Technical lignins are increasingly available at industrial scale, offering opportunities for valorization, such as by (partial) depolymerization. Any downstream lignin application requires careful tailoring of structural properties, such as molecular weight or functional group density, properties that are difficult to control or predict given the structure variability and recalcitrance of technical lignins. Online insight into changes in molecular weight (Mw ), to gauge the extent of lignin depolymerization and repolymerization, would be highly desired to improve such control, but cannot be readily provided by the standard ex-situ techniques, such as size exclusion chromatography (SEC). Herein, operando attenuated total reflectance infrared (ATR-IR) spectroscopy combined with chemometrics provided temporal changes in Mw during lignin depolymerization with high resolution. More specifically, ex-situ SEC-derived Mw and polydispersity data of kraft lignin subjected to aqueous phase reforming conditions could be well correlated with ATR-IR spectra of the reaction mixture as a function of time. The developed method showed excellent regression results and relative error, comparable to the standard SEC method. The method developed has the potential to be translated to other lignin depolymerization processes.

| S-EPMC9299174 | biostudies-literature

Comparison of Attenuated Total Reflectance Mid-Infrared, Near Infrared, and 1H-Nuclear Magnetic Resonance Spectroscopies for the Determination of Coffee's Geographical Origin.

Project description:The sensorial properties of Colombian coffee are renowned worldwide, which is reflected in its market value. This raises the threat of fraud by adulteration using coffee grains from other countries, thus creating a demand for robust and cost-effective methods for the determination of geographical origin of coffee samples. Spectroscopic techniques such as Nuclear Magnetic Resonance (NMR), near infrared (NIR), and mid-infrared (mIR) have arisen as strong candidates for the task. Although a body of work exists that reports on their individual performances, a faithful comparison has not been established yet. We evaluated the performance of 1H-NMR, Attenuated Total Reflectance mIR (ATR-mIR), and NIR applied to fraud detection in Colombian coffee. For each technique, we built classification models for discrimination by species (C. arabica versus C. canephora (or robusta)) and by origin (Colombia versus other C. arabica) using a common set of coffee samples. All techniques successfully discriminated samples by species, as expected. Regarding origin determination, ATR-mIR and 1H-NMR showed comparable capacity to discriminate Colombian coffee samples, while NIR fell short by comparison. In conclusion, ATR-mIR, a less common technique in the field of coffee adulteration and fraud detection, emerges as a strong candidate, faster and with lower cost compared to 1H-NMR and more discriminating compared to NIR.

| S-EPMC5672123 | biostudies-literature

Attenuated Total Reflectance Fourier Transform Infrared Spectroscopy: An analytical technique to understand therapeutic responses at the molecular level.

Project description:Rapid monitoring of the response to treatment in cancer patients is essential to predict the outcome of the therapeutic regimen early in the course of the treatment. The conventional methods are laborious, time-consuming, subjective and lack the ability to study different biomolecules and their interactions, simultaneously. Since; mechanisms of cancer and its response to therapy is dependent on molecular interactions and not on single biomolecules, an assay capable of studying molecular interactions as a whole, is preferred. Fourier Transform Infrared (FTIR) spectroscopy has become a popular technique in the field of cancer therapy with an ability to elucidate molecular interactions. The aim of this study, was to explore the utility of the FTIR technique along with multivariate analysis to understand whether the method has the resolution to identify the differences in the mechanism of therapeutic response. Towards achieving the aim, we utilized the mouse xenograft model of retinoblastoma and nanoparticle mediated targeted therapy. The results indicate that the mechanism underlying the response differed between the treated and untreated group which can be elucidated by unique spectral signatures generated by each group. The study establishes the efficiency of non-invasive, label-free and rapid FTIR method in assessing the interactions of nanoparticles with cellular macromolecules towards monitoring the response to cancer therapeutics.

| S-EPMC4645174 | biostudies-literature

In Situ Determination of Nitrate in Water Using Fourier Transform Mid-Infrared Attenuated Total Reflectance Spectroscopy Coupled with Deconvolution Algorithm.

Project description:Fourier transform infrared attenuated total reflectance (FTIR-ATR) spectroscopy has been used to determine the nitrate content in aqueous solutions. However, the conventional water deduction algorithm indicated considerable limits in the analysis of samples with low nitrate concentration. In this study, FTIR-ATR spectra of nitrate solution samples with high and low concentrations were obtained, and the spectra were then pre-processed with deconvolution curve-fitting (without water deduction) combined with partial least squares regression (PLSR) to predict the nitrate content. The results show that the typical absorption of nitrate (1200-1500 cm-1) did not clearly align with the conventional algorithm of water deduction, while this absorption was obviously observed through the deconvolution algorithm. The first principal component of the spectra, which explained more than 95% variance, was linearly related to the nitrate content; the correlation coefficient (R2) of the PLSR model for the high-concentration group was 0.9578, and the ratio of the standard deviation of the prediction set to that of the calibration set (RPD) was 4.22, indicating excellent prediction performance. For the low-concentration group model, R2 and RPD were 0.9865 and 3.15, respectively, which also demonstrated significantly improved prediction capability. Therefore, FTIR-ATR spectroscopy combined with deconvolution curve-fitting can be conducted to determine the nitrate content in aqueous solutions, thus facilitating rapid determination of nitrate in water bodies with varied concentrations.

| S-EPMC7764078 | biostudies-literature

Detection and quantification of early-stage malaria parasites in laboratory infected erythrocytes by attenuated total reflectance infrared spectroscopy and multivariate analysis.

Project description:New diagnostic modalities for malaria must have high sensitivity and be affordable to the developing world. We report on a method to rapidly detect and quantify different stages of malaria parasites, including ring and gametocyte forms, using attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FT-IR) and partial least-squares regression (PLS). The absolute detection limit was found to be 0.00001% parasitemia (<1 parasite/?L of blood; p < 0.008) for cultured early ring stage parasites in a suspension of normal erythrocytes. Future development of universal and robust calibration models can significantly improve malaria diagnoses, leading to earlier detection and treatment of this devastating disease.

| S-EPMC4014274 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data