Partial Least Squares Discriminant Analysis Model Research Articles

Tuning multispectral fluorescence quantum dot–based identification of short-length amyloid β peptides by applying Cu(II) ions

Currently available methods for detecting amyloid β (Aβ) derivatives are mainly dedicated to determining the long forms Aβ1-42 and Aβ1-40. At the same time, the number of physiologically occurring Aβ analogs is much higher, including those truncated at the N- and C-termini. Their identification using standard methods is challenging due to the structural similarity of various Aβ analogs, but could highly benefit from both biomarkers discovery and pathophysiological studies of Alzheimer’s disease. Therefore a “chemical tongue” sensing strategy was employed for the detection of seven Aβ peptide derivatives: Aβ1-16, Aβ4-16, Aβ4-9, Aβ5-16, Aβ5-12, Aβ5-9, Aβ12-16. The proposed sensing system is based on competitive interactions between quantum dots, Cu(II) ions, and Aβ peptides, providing unique fluorescence fingerprints useful for the identification of analytes. After carefully evaluating the Aβ sample preparation protocol, perfect determination of all studied Aβ peptides was achieved using partial least square–discriminant analysis (PLS-DA). The developed PLS-DA models are characterized by excellent accuracy, sensitivity, precision, and specificity of analyte determination, emphasizing the potential of the proposed sensing strategy.Graphical abstract

Early Metabolomic Profiling as a Predictor of Renal Function Six Months After Kidney Transplantation

Background: Kidney transplantation is the therapy of choice for patients with advanced chronic kidney disease; however, predicting graft outcomes remains a significant challenge. Early identification of reliable biomarkers could enhance post-transplant management and improve long-term outcomes. This study aimed to identify metabolomic biomarkers within the first week after kidney transplantation that predict renal function at six months. Methods: We conducted a prospective study involving 50 adult patients who received deceased donor kidney transplants. Plasma samples collected one week after transplant were analyzed using liquid chromatography–mass spectrometry in a semi-targeted metabolomic approach. A Partial Least Squares-Discriminant Analysis (PLS-DA) model identified metabolites associated with serum creatinine > 1.5 mg/dL at six months. Metabolites were selected based on a Variable Importance in Projection (VIP) score > 1.5, which was used to optimize model performance. Results: The PLS-DA model demonstrated strong predictive performance with an area under the curve (AUC) of 0.958. The metabolites negatively associated with serum creatinine > 1.5 mg/dL were 3-methylindole, guaiacol, histidine, 3-indolepropionic acid, and α-lipoic acid. Conversely, the metabolites positively associated with worse kidney graft outcomes included homocarnosine, 5-methylcytosine, xanthosine, choline, phenylalanine, kynurenic acid, and L-kynurenine. Conclusions: Early metabolomic profiling after transplantation shows promise in predicting renal function. Identifying metabolites with antioxidant and anti-inflammatory properties, as well as those that are harmful and could be targeted therapeutically, underscores their potential clinical significance. The link between several metabolites and the tryptophan pathway suggests that further specific evaluation of this pathway is warranted. These biomarkers can enhance patient management and graft survival.

Unrevealing the Halyomorpha halys Damage Fingerprint on Hazelnut Metabolome by Multiomic Platforms and AI-Aided Strategies.

The brown marmorated stink bug (Halyomorpha halys) poses a significant threat to hazelnut crops by affecting kernel development and causing quality defects, reducing the market value. While previous studies have identified bitter-tasting compounds in affected kernels, the impact of stink bug feeding on the hazelnut metabolome, particularly concerning aroma precursors, remains underexplored. This study aims to map the nonvolatile metabolome and volatilome of hazelnut samples obtained by caging H. halys on different cultivars in two locations to identify markers for diagnosing stink bug damage. Using a multiomic approach involving headspace solid-phase microextraction (HS-SPME), comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry (GC × GC-TOF MS), and liquid chromatography-high-resolution mass spectrometry (LC-HRMS), both raw and roasted hazelnuts are analyzed, with artificial intelligence (AI) and machine learning tools employed to explore data correlations. The study finds that the hazelnut metabolome and volatilome exhibit high chemical complexity with significant classes of compounds such as aldehydes, ketones, alcohols, and terpenes identified in both raw and roasted hazelnuts. Multivariate analysis indicates that the orchard location significantly impacts the metabolome, followed by damage type, with cultivar differences being less pronounced. Partial least-squares discriminant analysis (PLS-DA) models achieve high predictive accuracy for orchard location (99%) and damage type (≈80%), with the roasted volatilome showing the highest predictive accuracy. Correlation matrices reveal significant relationships between raw hazelnut metabolites and aroma compounds in roasted samples, suggesting potential markers for stink bug damage that could guide the quality assessment and mitigation strategies. Data fusion techniques further enhance classification performance, particularly in predicting damage type, underscoring the potential of integrating multiple data sets for comprehensive quality assessment.

Detection of serum alterations in polysubstance use patients by FT-Raman spectroscopy

Substance use disorders pose significant health risks and treatment challenges due to the diverse interactions between substances and their impact on physical and mental health. The chemical effects of multiple substance use on bodily fluids are not yet fully understood. Therefore, this study aimed to investigate the chemical changes induced by a combination of substances compared to a control group. Analysis of FT-Raman spectra revealed structural alterations in the amide III, I, and C = O functional groups of lipids in subjects treated with opioids, alcohol and cannabis (polysubstance group). These changes were evident in the form of peak shifts compared to the control group. Additionally, an imbalance in the amide-lipid ratio was observed, indicating perturbations in serum protein and lipid levels. Furthermore, a 2D plot of two-track two-dimensional correlation spectra (2T2D-COS) demonstrated a shift towards dominance of lipid vibrations in the polysubstance use groups, contrasting with the predominance of the amide fraction in the control group. This observation suggests distinct molecular changes induced by multiple substance use, potentially contributing to the pathophysiology of substance use disorders. Principal Component Analysis (PCA) was utilized to visualize the data structure and identify outliers. Subsequently, Partial Least Squares Discriminant Analysis (PLS-DA) was employed to classify the polysubstance use and control groups. The PLS-DA model demonstrated high classification accuracy, achieving 100.00 % in the training dataset and 94.74 % in the test dataset. Furthermore, receiver operating characteristic (ROC) analysis yielded perfect AUC values of 1.00 for both the training and test sets, underscoring the robustness of the classification model.This study highlights the quantitative and qualitative changes in serum protein and lipid levels induced by polysubstance use groups, as evidenced by FT-Raman spectroscopy. The findings underscore the importance of understanding the chemical effects of polysubstance use on bodily fluids for improved diagnosis and treatment of substance use disorders. Moreover, the successful classification of spectral data using machine learning techniques emphasizes the potential of these approaches in clinical applications for substance abuse monitoring and management.

Classification of Kudoa thyrsites infected and uninfected fish using a handheld near-infrared spectrophotometer, SIMCA and PLS-DA.

Kudoa thyrsites infection of marine fish typically results in myoliquefaction, which is only apparent 24 to 56 h post-mortem. The traditional methods for the detection of K. thyrsites infected fish are time-consuming and destructive, reducing its marketability. This poses a challenge for the fish industry to remove infected fish before it reaches the market or further processing activities. This study investigated the use of near-infrared (NIR) spectroscopy, in combination with soft independent modelling of class analogy (SIMCA) and partial least square discriminant analysis (PLS-DA), for discriminating K. thyrsites infected fish from uninfected fish. Performance of the classification models was evaluated by calculating the sensitivity, specificity and precision. A total of 334 fish samples (200 sardine, 64 hake and 70 kingklip) were used for this study. Infection of K. thyrsites was determined with the use of qPCR assays. Ninety per cent (90%) of the sardine samples, 78% of the hake samples and 37% of the kingklip samples were infected. Class groups of infected and uninfected fish samples were created for the purpose of generating SIMCA and PLS-DA classification models for each species of fish, as well as for a species independent data set. Principal component analysis (PCA) of NIR spectra did not show any clustering for infected and uninfected samples. Calibration and test sample sets were generated for the purpose of building and testing the SIMCA and PLD-DA classification models. SIMCA and PLS-DA were unable to classify test samples correctly into the two classes. The number of misclassifications (NMC) was higher for the SIMCA models than for the PLS-DA models, with more than 60% incorrectly classified. SIMCA classified most of the test samples into both classes. The precision for PLS-DA were 89% for sardine, 81% for hake, 0% for kingklip and 87% for species independent models, however, most samples were classified at infected. The use of NIR spectroscopy and classification models such as SIMCA and PLS-DA showed limited use as a method to distinguish between K. thyrsites infected and uninfected fish samples. Textural and chemical changes during extended frozen storage of the fish samples may have masked the effects associated with K. thyrsites infection. Further studies are suggested where NIR spectroscopy is used in combination with texture analysis and image spectroscopy.

Near-infrared spectroscopy combined with support vector machine for the identification of Tartary buckwheat (Fagopyrum tataricum (L.) Gaertn) adulteration using wavelength selection algorithms

The frequent occurrence of adulterating Tartary buckwheat powder with crop flours in the market necessitates an urgent need for a simple analysis method to ensure the quality of Tartary buckwheat. This study employed near-infrared spectroscopy (NIRS) for the collection of spectral data from Tartary buckwheat samples adulterated with whole wheat, oat, soybean, barley, and sorghum flours. The competitive adaptive reweighted sampling (CARS) and successive projection algorithm (SPA) were deployed to identify informative wavelengths. By integrating support vector machine (SVM) and partial least squares discriminant analysis (PLS-DA), we constructed qualitative models to discern Tartary buckwheat adulteration. The PLS-DA model exhibited prediction accuracies between 89.78 % and 94.22 %, while the mean-centering (MC)-PLS-DA model showcased impressive predictive accuracy of 93.33 %. Notably, the feature-based Autoscales-CARS-CV-SVM model achieved more excellent identification accuracy. These findings exhibit the excellent potential of chemometrics as a powerful tool for detecting food product adulteration.

Towards a Spectral Library of Medicinal and Aromatic Plant species (MAPs): Plant Discrimination and Wavelength Selection

The recognition and identification of Medicinal and Aromatic Plants species (MAPs) is a challenge for researchers and professionals in the field. To address this issue, this study aimed to examine the potential of using hyperspectral remote sensing, chemometrics and Machine Learning in discriminating between MAP species. Specifically, we tested the applicability of UV-Near-infrared Spectroscopy (UV-NIR), PCA and Partial Least-Squares Discriminant Analysis (PLS-DA) as tools for discrimination. The spectral signature data were obtained by UV-near infrared spectroscopy, covering a range of 325–1075 nm. Principal component analysis (PCA) was applied to reduce data dimensionality in order to minimize errors in PLS-DA model. This model was used to build a discriminant model based on the wavelengths obtained from PCA. The results show that it is effective to combine UV-NIR spectral features and PLS-DA to establish a discriminant model for accurately classifying the MAP species. The key wavelengths most involved in the discrimination were found in the NIR region and especially in ranges 516–548 and 628–1070 nm.

Attenuated Total Reflection-Fourier Transform Infrared (ATR-FTIR) Spectroscopy Analysis of Saliva as a Diagnostic Specimen for Rapid Classification of Oral Squamous Cell Carcinoma Using Chemometrics Methods

Background & Aim Recent advancements in analytical techniques have highlighted the potential of Attenuated Total Reflection-Fourier Transform Infrared (ATR-FTIR) spectroscopy as a quick, cost-effective, non-invasive, and efficient tool for cancer diagnosis. This study aims to evaluate the effectiveness of ATR-FTIR spectroscopy in combination with supervised machine learning classification models for diagnosing OSCC using saliva samples. Methods & Materials Eighty unstimulated whole saliva samples from OSCC patients and healthy controls were collected. The ATR-FTIR spectroscopy was performed and spectral data were used to classify healthy and OSCC groups. The data were analyzed using machine learning classification methods such as Partial Least Squares-Discriminant Analysis (PLS-DA) and Support Vector Machine Classification (SVM-C). The classification performance of the models was evaluated by computing sensitivity, specificity, precision, and accuracy. Results The samples were classified into two classes based on their spectral data. The obtained results demonstrate a high level of accuracy in the prediction sets of the PLS-DA and SVM-C models, with accuracy values of 0.960 and 0.962, respectively. The OSCC group sensitivity values for both PLS-DA and SVM-C models was 1.00, respectively. Conclusion The study indicates that ATR-FTIR spectroscopy, combined with chemometrics, is a potential method for the non-invasive diagnosis of OSCC using saliva samples. This method achieved high accuracy and the findings of this study suggest that ATR-FTIR spectroscopy could be further developed for clinical applications in OSCC diagnosis.

Assessing the Metabolic Variations of Invasive and Noninvasive Unilateral Retinoblastoma Patients.

Retinoblastoma (Rb) is a pediatric eye cancer which if diagnosed at later stages can lead to Rb invasion into the choroid, optic nerve, sclera, or beyond, with the potential of undergoing metastasis. Cancer cells, including Rb cells, reprogram their metabolic circuits for their own survival and progression, which provides a great opportunity to monitor the extent of Rb progression based on metabolic differences. Henceforth, the present study aims to map the metabolic variations in patients with invasive (primarily enucleated eyes with high-risk histopathological features) and noninvasive (eyes salvaged with treatment) unilateral retinoblastoma (Rb) using nuclear magnetic resonance (NMR) based serum metabolomics. Quantification of differential metabolites in the serum obtained from 9 patients with invasive and 4 with noninvasive unilateral Rb along with 6 controls (no retinal pathology) was carried out using 1H NMR spectroscopy. A total of 71 metabolites, such as organic acids, amino acids, carbohydrates, and others, were identified in the serum obtained from 9 patients with invasive and 4 with noninvasive unilateral Rb. Partial least-squares discriminant analysis (PLS-DA) models depicted distinct grouping of invasive and noninvasive Rb patients and controls. Differential metabolic fingerprints were observed for invasive and noninvasive Rb patients based on their biostatistical analyses with respect to controls. Remarkable perturbation was observed among various metabolites such as 4-aminobutyrate, 2-phosphoglycerate, O-phosphocholine, proline, Sn-glycero-3-phosphocholine (Sn-GPC), and O-phosphoethanolamine in noninvasive and invasive Rb patients with most of the effects being heightened in the latter group. Metabolic changes unique to invasive and noninvasive Rb patients were also observed. Multivariate receiver operating characteristics (ROC) analysis unveiled the highest accuracy and potency of ROC models 2 and 5 to distinguish the noninvasive and invasive Rb from controls, respectively. Metabolites identified in the serum of patients with invasive and noninvasive Rb may aid in advancing our knowledge about Rb tumor biology. Differential aberrant metabolic variations in patients with invasive Rb compared to those with noninvasive Rb may guide the decision of enucleation versus globe salvage.

Differentiating Pond-Intensive, Paddy-Ecologically, and Free-Range Cultured Crayfish (Procambarus clarkii) Using Stable Isotope and Multi-Element Analysis Coupled with Chemometrics.

The farming pattern of crayfish significantly impacts their quality, safety, and nutrition. Typically, green and ecologically friendly products command higher economic value and market competitiveness. Consequently, intensive farming methods are frequently employed in an attempt to replace these environmentally friendly products, leading to potential instances of commercial fraud. In this study, stable isotope and multi-element analysis were utilized in conjunction with multivariate modeling to differentiate between pond-intensive, paddy-ecologically, and free-range cultured crayfish. The four stable isotope ratios of carbon, nitrogen, hydrogen, and oxygen (δ13C, δ15N, δ2H, δ18O) and 20 elements from 88 crayfish samples and their feeds were determined for variance analysis and correlation analysis. To identify and differentiate three different farming pattern crayfish, unsupervised methods such as hierarchical cluster analysis (HCA) and principal component analysis (PCA) were used, as well as supervised multivariate modeling, specifically partial least squares discriminant analysis (PLS-DA). The HCA and PCA exhibited limited effectiveness in classifying the farming pattern of crayfish, whereas the PLS-DA demonstrated a more robust performance with a predictive accuracy of 90.8%. Additionally, variables such as δ13C, δ15N, δ2H, Mn, and Co exhibited relatively higher contributions in the PLS-DA model, with a variable influence on projection (VIP) greater than 1. This study is the first attempt to use stable isotope and multi-element analysis to distinguish crayfish under three farming patterns. It holds promising potential as an effective strategy for crayfish authentication.

Detection of hypoglycaemia in type 1 diabetes through breath volatile organic compound profiling using gas chromatography-ion mobility spectrometry.

To evaluate the relationship between breath volatile organic compounds (VOCs) and glycaemic states in individuals with type 1 diabetes (T1D), focusing on identifying specific VOCs as biomarkers for hypoglycaemia to offer a non-invasive diabetes-monitoring method. Ten individuals with T1D underwent induced hypoglycaemia in a clinical setting. Breath samples, collected every 10-15 minutes, were analysed using gas chromatography-ion mobility spectrometry (GC-IMS). Correlation analysis and machine learning models, including Partial Least Squares Discriminant Analysis (PLS-DA) and Support Vector Machine classifiers, were used to classify glycaemic states based on VOC profiles. Statistical analysis revealed moderate correlations between specific VOCs (e.g. isoprene, acetone) and venous blood glucose levels. Machine learning models showed high accuracy in classifying glycaemic states, with the best performance achieved by a two-class PLS-DA model showing an accuracy of 93%, sensitivity of 92% and specificity of 94%. Key biomarkers identified included isoprene, acetone, 2-butanone, methanol, ethanol, 2-propanol and 2-pentanone. This study shows the potential of breath VOCs to accurately classify glycaemic states in individuals with T1D. While key biomarkers such as isoprene, acetone and 2-butanone were identified, the analysis emphasizes the importance of using overall VOC patterns rather than individual compounds, which can be markers for multiple conditions. Machine learning models leveraging these patterns achieved high accuracy, sensitivity and specificity. These findings suggest that breath analysis using GC-IMS could be a viable non-invasive method for monitoring glycaemic states and managing diabetes.

Comparative chemometric modeling of fresh and dry cannabis inflorescences using FT-NIR spectroscopy: Quantification and classification insights.

Cannabis sativa L. inflorescences are rich in cannabinoids and terpenes. Traditional chemical analysis methods for cannabinoids and terpenes, such as liquid and gas chromatography (using UV or MS detectors), are expensive and time-consuming. This study explores the use of Fourier transform near-infrared (FT-NIR) spectroscopy combined with chemometric approaches for classifying cannabis chemovars and predicting cannabinoid and terpene concentrations for the first time in freshly harvested (wet) cannabis inflorescence. The study also compares the performance of FT-NIR spectroscopy on wet versus dry cannabis inflorescences. Spectral data from 187 samples across seven cannabis chemovars were analyzed using partial least squares-discriminant analysis (PLS-DA) and partial least squares-regression (PLS-R) models. The PLS-DA models effectively classified chemovars and major classes using only two latent variables (LVs) with minimal overfitting risk, with sensitivity, specificity, and accuracy values approaching 1. Despite the high water content in wet cannabis inflorescence, the PLS-R models demonstrated good to excellent predictive capabilities for nine cannabinoids and eight terpenes using FT-NIR spectra for the first time, achieving cross-validation and prediction R-squared values greater than 0.7, ratio of performance to interquartile range (RPIQ) exceeding 2, and a RMSECV/RMSEC ratio below 1.24. However, the low-cannabidiolic acid submodel and (-)-Δ9-trans-tetrahydrocannabinol model showed poor predictive performance. Some cannabinoid and terpene prediction models in wet cannabis inflorescence exhibited lower predictive capabilities compared with previously published models for dry cannabis inflorescence. These findings suggest that FT-NIR spectroscopy can be a viable rapid on-site analytical tool for growers during the inflorescence flowering stage.

Surface-enhanced Raman spectroscopy for the characterization of xylanases enzyme

Xylanases are essential hydrolytic enzymes which break down the plant cell wall polysaccharide, xylan composed of D-xylose monomers. Surface-enhanced Raman Spectroscopy (SERS) was utilized for the characterization of interaction of xylanases with xylan at varying concentrations. The study focuses on the application of SERS for the characterization of enzymatic activity of xylanases causing hydrolysis of Xylan substrate with increase in its concentration which is substrate for this enzyme in the range of 0.2% to 1.0%. SERS differentiating features are identified which can be associated with xylanases treated with different concentrations of xylan. SERS measurements were performed using silver nanoparticles as SERS substrate to amplify Raman signal intensity for the characterization of xylan treated with xylanases. Principal Component Analysis (PCA) and Partial Least Square Discriminant Analysis (PLS-DA) were applied to analyze the spectral data to analyze differentiation between the SERS spectra of different samples. Mean SERS spectra revealed significant differences in spectral features particularly related to carbohydrate skeletal mode and O-C-O and C–C–C ring deformations. PCA scatter plot effectively differentiates data sets, demonstrating SERS ability to distinguish treated xylanases samples and the PC-loadings plot highlights the variables responsible for differentiation. PLS-DA was employed as a quantitative classification model for treated xylanase enzymes with increasing concentrations of xylan. The values of sensitivity, specificity, and accuracy were found to be 0.98%, 0.99%, and 100% respectively. Moreover, the AUC value was found to be 0.9947 which signifies the excellent performance of PLS-DA model. SERS combined with multivariate techniques, effectively characterized and differentiated xylanase samples as a result of interaction with different concentrations of the Xylan substrate. The identified SERS features can help to characterize xylanases treated with various concentrations of xylan with promising applications in the bio-processing and biotechnology industries.

Pilot Study on the Use of Attenuated Total Reflectance-Fourier Transform Infrared Spectroscopy for Diagnosing and Characterizing Cardiac Amyloidosis.

Amyloidosis diagnosis relies on Congo red staining with immunohistochemistry and immunofluorescence for subtyping but lacks sensitivity and specificity. Laser-microdissection mass spectroscopy offers better accuracy but is complex and requires extensive sample preparation. Attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy offers a promising alternative for amyloidosis characterization. Cardiac tissue sections from nine patients with amyloidosis and 20 heart transplant recipients were analyzed using ATR-FTIR spectroscopy. Partial least squares discriminant analysis (PLS-DA), principal component analysis (PCA), and hierarchical cluster analysis (HCA) models were used to differentiate healthy post-transplant cardiac tissue from amyloidosis samples and identify amyloidosis subtypes [κ light chain (n = 1), λ light chain (n = 3), and transthyretin (n = 5)]. Leave-one-out cross-validation (LOOCV) was employed to assess the performance of the PLS-DA model. Significant spectral differences were found in the 1700-1500 cm-1 and 1300-1200 cm-1 regions, primarily related to proteins. The PLS-DA model explained 85.8% of the variance, showing clear clustering between groups. PCA in the 1712-1711 cm-1, 1666-1646 cm-1, and 1385-1383 cm-1 regions also identified two clear clusters. The PCA and the HCA model in the 1646-1642 cm-1 region distinguished κ light chain, λ light chain, and transthyretin cases. This pilot study suggests ATR-FTIR spectroscopy as a novel, non-destructive, rapid, and inexpensive tool for diagnosing and subtyping amyloidosis. This study was limited by a small dataset and variability in measurements across different instruments and laboratories. The PLS-DA model's performance may suffer from overfitting and class imbalance. Larger, more diverse datasets are needed for validation.

Suitability of different machine learning algorithms for the classification of the proportion of grassland-based forages at herd-level using mid-infrared spectral information from routine milk control

As the call for an international standard for milk from grassland-based production systems continues to grow, so too do the monitoring and evaluation policies surrounding this topic. Individual stipulations by countries and milk producers to market their milk under their own grass-fed labels include a compulsory number of grazing days per year, ranging from 120 d for certain labels to 180 d for others, a specified amount of herbage in the diet or a prescribed dietary proportion of grassland-based forages (GBF) fed and produced on farm. As these multifarious policy and label requirements are laborious and costly to monitor on farm, fast economical proxies would be advantageous to verify the proportion of GBF consumed by the cows in the final product. With this in mind, we employed readily available mid-infrared spectral data (n = 1132 spectra) from routine milk controls to develop binary classification models for 4 main feed groups from a primarily forage-based diet: Total GBF (≥50% n = 955, ≥ 75% n = 599, ≥ 85% n = 356), pasture (≥20% n = 451, ≥ 50% n = 284, ≥ 70% n = 152), fresh herbage (pasture + fresh herbage indoor feeding, ≥ 20% n = 517, ≥ 50% n = 325, ≥ 70% n = 182) and whole plant corn (fresh + conserved) (≥10% n = 646, ≥ 30% n = 187), the latter as a negative control. We compared 4 machine learning methods to assess which statistical model performs best at discriminating these classes. Three of these models have not yet been tested for herd-level dietary proportion classification and all 4 follow completely different approaches: least absolute shrinkage and selection operator (LASSO), partial least squares discriminant analysis (PLS-DA), random forest (RF) and support vector machines (SVM). Seasonality has been a missing element from previous dietary herbage proportion classification models. As grazing and fresh herbage indoor feeding are highly dependent on the season, we developed an indicator to incorporate seasonality in a consistent, unbiased manner into our models. We also tested 3 sets of covariates. The first set included only mid-infrared spectra derived data, the second included mid-infrared spectra derived data plus seasonality indices and the third included mid-infrared spectra derived data, seasonality indices and additional herd specific information (DIM, breed and parity). Of the 4 machine learning algorithms tested for the binary classification of GBF proportion at herd level, LASSO and PLS-DA performed best according to evaluation metrics; however, the RF and SVM models were not far behind the best performing model evaluation metrics in each feed category. Our best performing model, the LASSO model containing seasonality indices and herd specific information, classified total GBF ≥50% with an accuracy of 78.6%, precision of 85.1%, sensitivity of 90.6%, specificity 14.1% and F1 score (harmonic mean of precision and sensitivity) of 87.7%, this was very similar to the PLS-DA model. Our results suggest that in general LASSO and PLS-DA machine learning algorithms perform better for dietary GBF classification than RF or SVM algorithms.

Combination of Near-Infrared Spectroscopy and Multisource Data Fusion for the Geographical Origin Authentication of Panax notoginseng

Panax notoginseng (Burk.) F.H. Chen (P. notoginseng), a precious medicinal herb, provides both considerable values. There is confusion in the market regarding the geographical origins of P. notoginseng. It is of paramount importance to authenticate geographical origins of P. notoginseng, which will facilitate the rational utilization of resources and sustainable development. Principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA) were employed to investigate the influence of the tissue and data fusion strategy for the authentication of P. notoginseng origins. The PLS-DA model employing the main root spectra demonstrated great potential for authenticating P. notoginseng origin. The PLS-DA training and test sets based on feature-level fusion (VIP) spectral data were 100% accurate, indicating excellent potential in authenticating P. notoginseng. The data fusion strategy improved the authentication. The article presents a reliable and efficacious novel methodology for authenticating P. notoginseng origins and a scientific foundation for its quality control.

Haemonchus contortus alters distribution and utilization of protein and amino acids in different tissues of host sheep

The objective was to determine host animal protein/amino acid redistribution and use among the abomasum, duodenum and muscle of sheep infected with Haemonchus contortus. Sixteen male Ujumqin sheep (32.4 ± 3.9 kg) were dewormed and randomly assigned to two groups, infected or not infected with H. contortus (GIN and CON). The GIN group had lower (P < 0.05) dry matter intake, average daily gain, and live body weight than CON, with extensive focal infiltration of lymphocytes in the lamina propria and bottom of the abomasal epithelium. In the abomasum and duodenum, there were 100 and 220 genes, respectively, that were up-regulated, whereas 56 and 149 were down-regulated. In the abomasum, the most enriched KEGG pathways were related to immunity and inflammation reaction, including: viral protein interaction with cytokine and cytokine receptor (P = 0.017), influenza A (P = 0.030), IL-17 signaling pathway (P = 0.030). In the duodenum, KEGG pathways were more enriched in nutrient metabolism, including pancreatic secretion (P < 0.001), protein digestion and absorption (P < 0.001), graft-versus-host disease (P = 0.004). Furthermore, most genes related with the above KEGG pathways were increased in the abomasum but decreased in the duodenum. Amino acid profiles in abomasum and duodenum of CON and GIN groups were clustered in a partial least-squares discriminant analysis model, with significant changes in 36 and 19 metabolites in abomasal and duodenal chyme, respectively. Further confirmed by transcriptome-targeted metabolome association analysis, GIN mainly enhanced metabolism of arginine and sulphur amino acids in abomasum and those metabolic pathways were associated. Meanwhile, GIN mainly decreased pyruvate related amino acid metabolism in duodenum. Moreover, concentrations of Arg (P = 0.036), His (P = 0.027), and Cys (P = 0.046) in longissimus thoracis et lumborum were decreased in GIN, whereas concentrations of Gly (P = 0.012) and Ala (P = 0.046) were increased. In conclusion, H. contortus enhanced metabolism of arginine and sulphur amino acids in the abomasum; decreased pyruvate metabolism in the duodenum; and drove more protein/amino acids for abomasal tissues to resist physical and immune damage, reducing protein and amino acids in duodenum and muscle for support host growth. Specific nutrients (such like arginine, histidine, and cysteine) may play important role in control gastrointestinal nematode infection for ruminant.

Identification and quantification of goat milk adulteration using mid-infrared spectroscopy and chemometrics

The fraudulent adulteration of goat milk with cheaper and more available milk of other species such as cow milk is occurrence. The aims of the present study were to investigate the effect of goat milk adulteration with cow milk on the mid-infrared (MIR) spectrum and further evaluate the potential of MIR spectroscopy to identify and quantify the goat milk adulterated. Goat milk was adulterated with cow milk at 5 different levels including 10%, 20%, 30%, 40%, and 50%. Statistical analysis showed that the adulteration had significant effect on the majority of the spectral wavenumbers. Then, the spectrum was preprocessed with standard normal variate (SNV), multiplicative scattering correction (MSC), Savitzky-Golay smoothing (SG), SG plus SNV, and SG plus MSC, and partial least squares discriminant analysis (PLS-DA) and partial least squares regression (PLSR) were used to establish classification and regression models, respectively. PLS-DA models obtained good results with all the sensitivity and specificity over 0.96 in the cross-validation set. Regression models using raw spectrum obtained the best result, with coefficient of determination (R2), root mean square error (RMSE), and the ratio of performance to deviation (RPD) of cross-validation set were 0.98, 2.01, and 8.49, respectively. The results preliminarily indicate that the MIR spectroscopy is an effective technique to detect the goat milk adulteration with cow milk. In future, milk samples from different origins and different breeds of goats and cows should be collected, and more sophisticated adulteration at low levels should be further studied to explore the potential and effectiveness of milk mid-infrared spectroscopy and chemometrics.

Smart classification of organic and inorganic pineapple juice using dual NIR spectrometers combined with chemometric techniques

The global demand for organic foods, driven by health benefits and consumer preferences, necessitates reliable methods for distinguishing organic products from their inorganic counterparts. This study investigates the application of dual handheld near infrared (NIR) spectroscopy devices, SCiO and Tellspec, combined with chemometric techniques for the nondestructive differentiation of organic and inorganic pineapple juices. The objective was to establish a rapid and robust method to differentiate organic pineapple juice from inorganic juice using unique spectral data from the two devices. Eighty-four pineapple juice samples were analyzed with preprocessing techniques, including mean centering, multiplicative scatter correction, standard normal variate, first derivative, and second derivative applied to the spectral data. Partial least squares discriminant analysis (PLS-DA) was employed for classification, and variable importance in projection (VIP) was used for optimal wavelength selection. The results demonstrated that the Tellspec scanner, particularly with second derivative preprocessing, achieved high accuracy in differentiating organic from inorganic pineapple juice. The fusion of data from both SCiO (740–1070 nm) and Tellspec (900–1700 nm) scanners, without preprocessing, coupled with the PLS-DA model, achieved perfect classification accuracy, sensitivity, and specificity (100 %) in both training and testing sets. This study highlights the potential of integrating dual handheld NIR spectroscopy with chemometrics to effectively and accurately classify organic and inorganic pineapple juices. The findings support using these advanced techniques for quality assurance and authentication in the food industry.

Discrimination of Fungicide-Contaminated Lettuces Based on Maximum Residue Limits Using Spectroscopy and Chemometrics

The fast and effective monitoring of agrochemical residues is essential for assuring food safety, since many agricultural products are sprayed with pesticides and commercialised without waiting for the pre-harvest interval. In this study, we investigated the use of spectral reflectance combined with principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA) to evaluate the discrimination of fungicide-contaminated lettuces, considering three maximum residue limits (MRLs) [3.5, 5, and 7 mg carbon disulphide (CS2) kg−1]. The non-systemic Mancozeb fungicide (dithiocarbamate) was adopted in this research. Spectral reflectance (Vis/NIR) was measured by a hand-held spectrometer connected to a clip probe with an integrating sphere. The lettuce spectra were pre-treated (centring, standard normal variate, and first derivative) before data processing. Our findings suggest that PCA recognised inherent similarities in the fungicide-contaminated lettuce spectra, categorising them into two distinct groups. The PLS-DA models for all MRLs resulted in high accuracy levels, with correct discriminations ranging from 94.5 to 100% for the external validation dataset. Overall, our study demonstrates that spectroscopy combined with discriminating methods is a promising tool for non-destructive and fast discrimination of fungicide-contaminated lettuces. This methodology can be used in industrial food processing, enabling large-scale individual analysis and real-time decision making.