Application of near-infrared spectroscopy for fast germplasm analysis and classification in multi-environment using intact-seed peanut(Arachis hypogaea L.)

Peanut is a worldwide oilseed crop and the need to assess germplasm in a non-destructive manner is important for seed nutritional breeding.In this study,Near Infrared Spectroscopy(NIRS)was applied to rapidly assess germplasm variability from whole seed of 699 samples,field-collected and assembled in four genetic and environmentbased sets:one set of 300 varieties of a core-collection and three sets of 133 genotypes of an interspecific population,evaluated in three environments in a large spatial scale of two countries,Mbalmayo and Bafia in Cameroon and Nioro in Senegal,under rainfed conditions.NIR elemental spectra were gathered on six subsets of seeds of each sample,after three rotation scans,with a spectral resolution of 16 cm-1over the spectral range of867 nm to 2530 nm.Spectra were then processed by principal component analysis(PCA)coupled with Partial least squares-discriminant analysis(PLS-DA).As results,a huge variability was found between varieties and genotypes for all NIR wavelength within and between environments.The magnitude of genetic variation was particularly observed at 11 relevant wavelengths such as 1723 nm,usually related to oil content and fatty acid composition.PCA yielded the most chemical attributes in three significant PCs(i.e.,eigenvalues>10),which together captured 93%of the total variation,revealing genetic and environment structure of varieties and genotypes into four clusters,corresponding to the four samples sets.The pattern of genetic variability of the interspecific population covers,remarkably half of spectrum of the core-collection,turning out to be the largest.Interestingly,a PLS-DA model was developed and a strong accuracy of 99.6%was achieved for the four sets,aiming to classify each seed sample according to environment origin.The confusion matrix achieved for the two sets of Bafia and Nioro showed 100%of instances classified correctly with 100%at both sensitivity and specificity,confirming that their seed quality was different from each other and all other samples.Overall,NIRS chemometrics is useful to assess and distinguish seeds from different environments and highlights the value of the interspecific population and core-collection,as a source of nutritional diversity,to support the breeding efforts.

Discrimination of Transgenic Rice Based on Near Infrared Reflectance Spectroscopy and Partial Least Squares Regression Discriminant Analysis

Near infrared reflectance spectroscopy （NIRS）, a non-destructive measurement technique, was combined with partial least squares regression discrimiant analysis （PLS-DA） to discriminate the transgenic （TCTP and mi166） and wild type （Zhonghua 11） rice. Furthermore, rice lines transformed with protein gene （OsTCTP） and regulation gene （Osmi166） were also discriminated by the NIRS method. The performances of PLS-DA in spectral ranges of 4 000-8 000 cm-1 and 4 000-10 000 cm-1 were compared to obtain the optimal spectral range. As a result, the transgenic and wild type rice were distinguished from each other in the range of 4 000-10 000 cm-1, and the correct classification rate was 100.0% in the validation test. The transgenic rice TCTP and mi166 were also distinguished from each other in the range of 4 000-10 000 cm-1, and the correct classification rate was also 100.0%. In conclusion, NIRS combined with PLS-DA can be used for the discrimination of transgenic rice.

Mathematic Models for Analysis of Quality Components in Sugarcane Juice with Fourier Transform Near Infrared Spectroscopy

With the technique of Fourier transform near infrared (FT-NIR) spectroscopy, the calibration models for quantitative analysis of sucrose and polarization in sugarcane juice were developed by using transmission mode and calibrating with partial least square (PLS) algorithm. The determination coefficients (R2) of the predicted models for sucrose and polarization in juice were 0. 9980 and 0. 9979 respectively; the root mean square errors of cross validation (RMSECV) were 0. 143 and 0. 155% for sucrose and polarization in juice respectively. The predictive errors measured by FT-NIR were close to those by routine laboratory methods. The results demonstrated that the FT-NIR methods had high accuracy and they were able to replace the routine laboratory analysis. It was also demonstrated that as a rapid and accurate measurement, the FT-NIR technique had potential applications in quality control of mill sugarcane, establishment of payment system based on sugarcane quality, and selection of clones in sugarcane breeding.

Visible and Near-Infrared Spectroscopic Discriminant Analysis Applied to Brand Identification of Wine

High-end wine brand is made through the use of high-quality grape variety and yeast strain, and through a unique process. Not only is it rich in nutrients, but also it has a unique taste and a fragrant scent. Brand identification of wine is difficult and complex because of high similarity. In this paper, visible and near-infrared (NIR) spectroscopy combined with partial least squares discriminant analysis (PLS-DA) was used to explore the feasibility of wine brand identification. Chilean Aoyo wine (2016 vintage) was selected as the identification brand (negative, 100 samples), and various other brands of wine were used as interference brands (positive, 373 samples). Samples of each type were randomly divided into the calibration, prediction and validation sets. For comparison, the PLS-DA models were established in three independent and two complex wavebands of visible (400 - 780 nm), short-NIR (780 - 1100 nm), long-NIR (1100 - 2498 nm), whole NIR (780 - 2498 nm) and whole scanning (400 - 2498 nm). In independent validation, the five models all achieved good discriminant effects. Among them, the visible region model achieved the best effect. The recognition-accuracy rates in validation of negative, positive and total samples achieved 100%, 95.6% and 97.5%, respectively. The results indicated the feasibility of wine brand identification with Vis-NIR spectroscopy.

Wavelet-based classification and influence matrix analysis method for the fast discrimination of Chinese herbal medicines according to the geographical origins with near infrared spectroscopy

A discriminant analysis technique using wavelet transformation(WT)and influence matrixanalysis(CAIMAN)method is proposed for the near infrared(NIR)spectroscopy classifi-cation.In the proposed methodology,NIR spectra are decomposed by WT for data com-pression and a forward feature selection is further employed to extract the relevant informationfrom the wavelet coefficients,reducing both classification errors and model complexity.Adiscriminant-CAIMAN(D-CAIMAN)method is utilized to build the classification model inwavelet domain on the basis of reduced wavelet coefficients of spectral variables.NIR spectradata set of 265 salviae miltiorrhizae radia samples from 9 different geographical origins is usedas an example to test the classification performance of the algorithm.For a comparison,k-nearest neighbor(KNN),linear discriminant analysis(LDA)and quadratic discriminant analysis(QDA)methods are also employed.D-CAIMAN with wavelet-based feature selection(WD-CAIMAN)method shows the best performance,achieving the total classification rate of ioo%in both cross-validation set and prediction set.It is worth noting that the WD-CAIMANclassifier also shows improved sensitivity,selectivity and model interpretability in thecla.ssifications.

Influence of signal-to-noise ratio on accuracy of spectral analysis by near infrared spectroscopy

As one of the important indicators of spectrometer,signal-to-noise ratio(SNR)reflects the ability of spectrometer to detect weak signals.To investigate the influence of SNR on the prediction accuracy of spectral analysis,we first introduce the major factors affecting the spectral SNR.Taking green tea as an example,the influence of spectral SNR on the prediction accuracy of the origin identification model is analyzed by experiments.At the same time,the relationship between the spectral SNR and prediction accuracy of spectral analysis model is fitted.Based on this,the common methods for improving the spectral SNR are discussed.The results show that the accuracy of the prediction set model first decreases slowly,then decreases linearly,and finally tends to be flat as the spectral SNR decreases.Through calculation,in order to achieve the prediction accuracy of prediction model reaching 90%and 85%,the spectral SNR is required to be higher than 23.42 dB and 21.16 dB,respectively.The overall results provide certain parameters support for the development of new online analytical spectroscopic instruments,especially for the technical indicators of SNR.

Near-Infrared Spectroscopy Combined with Partial Least Squares Discriminant Analysis Applied to Identification of Liquor Brands

The identification of liquor brands is very important for food safety. Most of the fake liquors are usually made into the products with the same flavor and alcohol content as regular brand, so the identification for the liquor brands with the same flavor and the same alcohol content is essential. However, it is also difficult because the components of such liquor samples are very similar. Near-infrared (NIR) spectroscopy combined with partial least squares discriminant analysis (PLS-DA) was applied to identification of liquor brands with the same flavor and alcohol content. A total of 160 samples of Luzhou Laojiao liquor and 200 samples of non-Luzhou Laojiao liquor with the same flavor and alcohol content were used for identification. Samples of each type were randomly divided into the modeling and validation sets. The modeling samples were further divided into calibration and prediction sets using the Kennard-Stone algorithm to achieve uniformity and representativeness. In the modeling and validation processes based on PLS-DA method, the recognition rates of samples achieved 99.1% and 98.7%, respectively. The results show high prediction performance for the identification of liquor brands, and were obviously better than those obtained from the principal component linear discriminant analysis method. NIR spectroscopy combined with the PLS-DA method provides a quick and effective means of the discriminant analysis of liquor brands, and is also a promising tool for large-scale inspection of liquor food safety.

Visible and Near-Infrared Spectroscopy with Multi-Parameters Optimization of Savitzky-Golay Smoothing Applied to Rapid Analysis of Soil Cr Content of Pearl River Delta

Using visible and near-infrared (Vis-NIR) spectroscopy combined with partial least squares (PLS) regression, the rapid reagent-free analysis model for chromium (Cr) content in tideland reclamation soil in the Pearl River Delta, China was established. Based on Savitzky-Golay (SG) smoothing and PLS regression, a multi-parameters optimization platform (SG-PLS) covering 264 modes was constructed to select the appropriately spectral preprocessing mode. The optimal SG-PLS model was determined according to the prediction effect. The selected optimal parameters d, p, m and LV were 2, 6, 23 and 8, respectively. Using the validation samples that were not involved in modeling, the root mean square error (SEPV), relative root mean square error (R-SEPV) and correlation coefficients (RP, V) of prediction were 11.66 mg·kg-1, 10.7% and 0.722, respectively. The results indicated that the feasibility of using Vis-NIR spectroscopy combined with SG-PLS method to analyze soil Cr content. The constructed multi-parameters optimization platform with SG-PLS is expected to be applied to a wider field of analysis. The rapid detection method has important application values to large-scale agricultural production.

Discriminant Analysis of Liquor Brands Based on Moving-Window Waveband Screening Using Near-Infrared Spectroscopy

Partial least squares discriminant analysis (PLS-DA) with integrated moving-window (MW) waveband screening was applied to the discriminant analysis of liquor brands with near-infrared (NIR) spectroscopy. Luzhou Laojiao, a popular liquor with strong fragrant flavor, was used as the identified liquor brand (160 samples, negative, 52 vol alcoholicity). Liquors of 10 other brands with strong fragrant flavor were used as the interferential brands (200 samples, positive, 52 vol alcoholicity). The Kennard-Stone algorithm was used for the division of modeling samples to achieve uniformity and representativeness. Based on the MW-PLS-DA, a simplified optimal model set with 157 wavebands was further proposed. This set contained five types of wavebands corresponding to the NIR absorption bands of water, ethanol, and other micronutrients (i.e., acids, aldehydes, phenols, and aromatic compounds) in liquor for practical choice. Using five selected simple models with 4775 - 4239, 7804 - 6569, 6264 - 5844, 9435 - 7896, and 12066 - 10373 cm-1, the validation recognition rates were obtained as 99.3% or higher. Results show good prediction performance and low model complexity, and also provided a valuable reference for designing small dedicated instruments. The proposed method is a promising tool for large-scale inspection of liquor food safety.

Visible and Near-Infrared Spectroscopic Discriminant Analysis Applied to Identification of Soy Sauce Adulteration

The identification of soy sauce adulteration can avoid fraud, and protect the rights and interests of producers and consumers. Based on two measurement models (1 mm, 10 mm), the visible and near-infrared (Vis-NIR) spectroscopy combined with standard normal variate-partial least squares-discriminant analysis (SNV-PLS-DA) was used to establish the discriminant analysis models for adulterated and brewed soy sauces. Chubang soy sauce was selected as an identification brand (negative, 70). The adulteration samples (positive, 72) were prepared by mixing Chubang soy sauce and blended soy sauce with different adulteration rates. Among them, the “blended soy sauce” sample was concocted of salt water (NaCl), monosodium glutamate (C5H10NNaO5) and caramel color (C6H8O3). The rigorous calibration-prediction-validation sample design was adopted. For the case of 1 mm, five waveband models (visible, short-NIR, long-NIR, whole NIR and whole scanning regions) were established respectively;in the case of 10 mm, three waveband models (visible, short-NIR and visible-short-NIR regions) for unsaturated absorption were also established respectively. In independent validation, the models of all wavebands in the cases of 1 mm and 10 mm have achieved good discrimination effects. For the case of 1 mm, the visible model achieved the optimal validation effect, the validation recognition-accuracy rate (RARV) was 99.6%;while in the case of 10 mm, both the visible and visible-short-NIR models achieved the optimal validation effect (RARV = 100%). The detection method does not require reagents and is fast and simple, which is easy to promote the application. The results can provide valuable reference for designing small dedicated spectrometers with different measurement modals and different spectral regions.

Classification of Barley according to Harvest Year and Species by Using Mid-infrared Spectroscopy and Multivariate Analysis

In order to monitor malt quality in the malting industry, despite yearly variations in the barley quality, 394 barley samples were analysed using conventional （moisture, protein and B-glucan content） and mid-infrared Fourier transform spectroscopy FT-IR. The experimental dataset included barley from three harvest years, two barley species, 77 barley varieties, and two-row and six-row barley, from 16 cultivation sites. For each sample, the malt quality indices were also assessed according to European Brewing Convention （EBC） standards. Principal component analysis （PCA） was carried out on mean-centred, normalized and derivative spectra using 200/cm width spectral bands. The most informative spectral bands were observed in the 800-1,000/cm and 1,000-1,200/cm ranges. PCA revealed that barley harvested in 2010 and in 2011 had bands that were very close together, while 2009 harvest clearly displayed a difference in its quality. PCA made it possible to distinguish two species and confirmed that two-row winter barley quality was closer to two-row spring barley quality than to six-row winter barley. Results indicate that mid-infrared spectrometry （MIR） could be a very useful and rapid analytical tool to assess barley qualitative quality.

Near-Infrared Spectroscopy Coupled with Kernel Partial Least Squares-Discriminant Analysis for Rapid Screening Water Containing Malathion

Near-infrared spectroscopy coupled with kernel partial least squares-discriminant analysis was used to rapidly screen water containing malathion. In the wavenumber of 4348 cm-1 to 9091 cm-1, the overall correct classification rate of kernel partial least squares-discriminant analysis was 100% for training set, and 100% for test set, with the lowest concentration detected malathion residues in water being 1 μg·ml-1. Kernel partial least squares-discriminant analysis was able to have a good performance in classifying data in nonlinear systems. It was inferred that Near-infrared spectroscopy coupled with the kernel partial least squares-discriminant analysis had a potential in rapid screening other pesticide residues in water.

Acupuncture enhances brain function in patients with mild cognitive impairment: evidence from a functional-near infrared spectroscopy study

Mild cognitive impairment(MCI)is a precursor to Alzheimer’s disease.It is imperative to develop a proper treatment for this neurological disease in the aging society.This observational study investigated the effects of acupuncture therapy on MCI patients.Eleven healthy individuals and eleven MCI patients were recruited for this study.Oxy-and deoxy-hemoglobin signals in the prefrontal cortex during working-memory tasks were monitored using functional near-infrared spectroscopy.Before acupuncture treatment,working-memory experiments were conducted for healthy control(HC)and MCI groups(MCI-0),followed by 24 sessions of acupuncture for the MCI group.The acupuncture sessions were initially carried out for 6 weeks(two sessions per week),after which experiments were performed again on the MCI group(MCI-1).This was followed by another set of acupuncture sessions that also lasted for 6 weeks,after which the experiments were repeated on the MCI group(MCI-2).Statistical analyses of the signals and classifications based on activation maps as well as temporal features were performed.The highest classification accuracies obtained using binary connectivity maps were 85.7%HC vs.MCI-0,69.5%HC vs.MCI-1,and 61.69%HC vs.MCI-2.The classification accuracies using the temporal features mean from 5 seconds to 28 seconds and maximum(i.e,max(5:28 seconds))values were 60.6%HC vs.MCI-0,56.9%HC vs.MCI-1,and 56.4%HC vs.MCI-2.The results reveal that there was a change in the temporal characteristics of the hemodynamic response of MCI patients due to acupuncture.This was reflected by a reduction in the classification accuracy after the therapy,indicating that the patients’brain responses improved and became comparable to those of healthy subjects.A similar trend was reflected in the classification using the image feature.These results indicate that acupuncture can be used for the treatment of MCI patients.

Rapid Detection of Accelerants in Fire Debris Using a Field Portable Mid-Infrared Quantum Cascade Laser Based Analyzer

Arson presents a challenging crime scene for fire investigators worldwide. Key to the investigation of suspected arson cases is the analysis of fire debris for the presence of accelerants or ignitable liquids. This study has investigated the application and method development of vapor phase mid-Infrared (mid-IR) spectroscopy using a field portable quantum cascade laser (QCL) based system for the detection and identification of accelerant residues such as gasoline, diesel, and ethanol in fire debris. A searchable spectral library of various ignitable fluids and fuel components measured in the vapor phase was constructed that allowed for real-time identification of accelerants present in samples using software developed in-house. Measurement of vapors collected from paper material that had been doused with an accelerant followed by controlled burning and then extinguished with water showed that positive identification could be achieved for gasoline, diesel, and ethanol. This vapor phase mid-IR QCL method is rapid, easy to use, and has the sensitivity and discrimination capability that make it well suited for non-destructive crime scene sample analysis. Sampling and measurement can be performed in minutes with this 7.5 kg instrument. This vibrational spectroscopic method required no time-consuming sample pretreatment or complicated solvent extraction procedure. The results of this initial feasibility study demonstrate that this portable fire debris analyzer would greatly benefit arson investigators performing analysis on-site.

Cluster Analysis for IR and NIR Spectroscopy: Current Practices to Future Perspectives

Supervised machine learning techniques have become well established in the study of spectroscopy data.However,the unsupervised learning technique of cluster analysis hasn’t reached the same level maturity in chemometric analysis.This paper surveys recent studies which apply cluster analysis to NIR and IR spectroscopy data.In addition,we summarize the current practices in cluster analysis of spectroscopy and contrast these with cluster analysis literature from the machine learning and pattern recognition domain.This includes practices in data pre-processing,feature extraction,clustering distance metrics,clustering algorithms and validation techniques.Special consideration is given to the specific characteristics of IR and NIR spectroscopy data which typically includes high dimensionality and relatively low sample size.The findings highlighted a lack of quantitative analysis and evaluation in current practices for cluster analysis of IR and NIR spectroscopy data.With this in mind,we propose an analysis model or workflow with techniques specifically suited for cluster analysis of IR and NIR spectroscopy data along with a pragmatic application strategy.

Determination of creatinine level in patient blood samples by Fourier NIR spectroscopy and multivariate analysis in comparison with biochemical assay

In this paper,in vivo spectra from 23 patients'blood samples with various Creatinine(Cr)concentration levels ranging from 0.96 to 12.5 mg/dL were measured using Fourier transform near-infrared spectrometer(FT-NIRS)and spectrum quantitative analysis method.Since Cr undergoes passive filtration,it serves as a key biomarker of kidneys function via the estimation of glomerular filtration rate.Thus,increased blood Cr concentration reflects impaired renal func-tion.After spectra pre processing and outlier exclusion,a spectral model was developed based on partial least squares regression(PLSR)method,wherein Cr concentrations correlated with filtered NIR spectra across several peaks,where Cr is know n to absorb NIR light.Several statistical metrics were applied to estimate the model efficiency during data analysis.Comparison of spectra-derived concentrations to reference Cr measurements by the current gold-standard Jaffe's method held in hospital lab revealed a Cr prediction accuracy of 1.64 mg/dL with good corre-lation of R=0.9.Bland-Altman plots were used to compare between our calculations and ref-erence lab values and reveal minimal bias between the two.The finding presented the potential of FT-NIRS coupled with PLSR technique for Cr determination.

Identification of Eight Carnation Cultivars by Fourier Transform Infrared(FTIR) Spectroscopy

In order to distinguish eight carnation cultivars, 40 samples were analyzed by Fourier transform infrared （FI＇IR） spectroscopy combined with principal component analysis （PCA） and hierarchical cluster analysis （HCA）. According to the results, infrared spectra of eight carnation cuhivars were similar, but signifi- cant differences were observed in wave numbers and absorption peak intensities in the range of 1 800 -700cm-1. The second order derivative spectra in the range of 1 800 -700 cm -l were selected to perform principal component analysis （PCA） and hierarchical cluster analysis （HCA）. The cumulative contribution rate of the first three principal components reached 96.2%. The classification accuracy rate of PCA and HCA was 95% and 100%, respectively. The results demonstrated that Fourier transform infrared （FTIR） spectroscopy combined with principal component analysis （PCA） and hierarchical cluster analysis （HCA） could be used for identification of different carnation cultivars.

Application of Grey-correlated Spectral Region Selection in Analysis of Near-infrared Spectra

The optimal selection method of spectral region based on the grey correlation analysis was applied in the analysis of near-infrared（NIR） spectra. In order to compute ＂characteristic＂ spectral region, 160 samples of tobacco were surveyed by NIR. Next, the whole spectral region was randomly divided into six regions, and the values of association coefficients and correlation orders of different regions were computed for total sugar, reducing sugar and nicotine. Moreover, two regions that owned the largest value of association coefficient were regarded as ＂characteristic＂ spectral region of a model. Finally, the quantitative analysis models of different components were established via the partial least squares method, and the common selection methods of spectral region were compared. The simulation results indicate that the models to choose the spectral region based on grey correlation analysis are more effective than the common selection methods of spectral region, the optimized time of algorithm is shorter, the prediction precision of the models is higher and generalization ability for quantitative analysis results is stronger. This research can provide the support for the quantitative analysis models of NIR spectra and new idea for commercial analysis software of NIR. So, it has a high application value in the analysis of NIR spectra.

Determination of Melamine by Infrared Spectroscopy Based on Nonlinear Modeling

[Objective] The aim was to develop a nonlinear model of quantitative analysis of melamine content by infrared spectroscopy and provide theoretical basis for the nondestructive detection of melamine. [Method] According to dynamics,mathematical modeling and optimization theory,linear and nonlinear models were respectively set up by taking an absorption peak of 1 550 cm-1 as characteristic absorption peak. [Result] The correlation coefficient of nonlinear model was 0.922 7 and the recovery was 96%,which showed that the nonlinear model was more accurate than linearity model with correlation coefficient of 0.904 9 and recovery of 557%. [Conclusion] It is feasible to determine melamine content by using the nonlinear model quantitatively.

Study on FTIR Spectra of Corn Germs and Endosperms of Three Different Colors Combining with Cluster Analysis

[Objective] This research aimed to study the FTIR spectra of corn germs and endosperms so as to provide a scientific way for identifying corn of different types. [Method] The corn germs and endosperms of three types were studied by using Fourier transform infrared spectroscopy（FTIR） technology, combined with cluster analysis. [Result] The overall characteristics of original FTIR spectra were basically similar within the range of 700-1 800 cm^-1. The FTIR spectra were mainly composed by the absorption peaks of polysaccharides, proteins and lipids. Within the wavelength range of 700-1 800 cm^-1, there were only tiny differences in original FTIR spectra among the corn germs and endosperms of three different types. The spectra were then processed by using first derivative and second derivative. The second derivative spectra were used for hierarchical cluster analysis（HCA）. The results showed that with the wavelength range of 700-1 800 cm^-1, the second derivative spectra of the 52 samples could be better clustered according to the tree types and corn germ and corn endosperm. The clustering correct rate reached 96.1%.[Conclusion] FTIR technology, combined with cluster analysis, can be used to identify different types of corn germs and endosperms, and it is characterized by convenience and rapidness.