Plasma metabolomics profiles and breast cancer risk.

BACKGROUND: Breast cancer (BC) is the most common cancer in women and incidence rates are increasing; metabolomics may be a promising approach for identifying the drivers of the increasing trends that cannot be explained by changes in known BC risk factors. METHODS: We conducted a nested case-control study (median followup 6.3 years) within the New York site of the Breast Cancer Family Registry (BCFR) (n = 40 cases and 70 age-matched controls). We conducted a metabolome-wide association study using untargeted metabolomics coupling hydrophilic interaction liquid chromatography (HILIC) and C18 chromatography with high-resolution mass spectrometry (LC-HRMS) to identify BC-related metabolic features. RESULTS: We found eight metabolic features associated with BC risk. For the four metabolites negatively associated with risk, the adjusted odds ratios (ORs) ranged from 0.31 (95% confidence interval (CI): 0.14, 0.66) (L-Histidine) to 0.65 (95% CI: 0.43, 0.98) (N-Acetylgalactosamine), and for the four metabolites positively associated with risk, ORs ranged from 1.61 (95% CI: 1.04, 2.51, (m/z: 101.5813, RT: 90.4, 1,3-dibutyl-1-nitrosourea, a potential carcinogen)) to 2.20 (95% CI: 1.15, 4.23) (11-cis-Eicosenic acid). These results were no longer statistically significant after adjusting for multiple comparisons. Adding the BC-related metabolic features to a model, including age, the Breast and Ovarian Analysis of Disease Incidence and Carrier Estimation Algorithm (BOADICEA) risk score improved the accuracy of BC prediction from an area under the curve (AUC) of 66% to 83%. CONCLUSIONS: If replicated in larger prospective cohorts, these findings offer promising new ways to identify exposures related to BC and improve BC risk prediction.

Mass spectrometry (MS)-based metabolomics of plasma and urine in dry eye disease (DED)-induced rat model.

Dry eye disease (DED) is an ophthalmic disease associated with poor quality and quantity of tears, and the number of patients is steadily increasing. The aim of this study was to determine plasma and urine metabolites obtained from DED scopolamine animal model where dry eye conditions (DRY) are induced. It was also of interest to examine whether DED (scopolamine) rat model was exacerbated by treatment with benzalkonium chloride (BAC). Subsequently, plasma and urine metabolites were analyzed using liquid chromatography (LC) and gas chromatography (GC)-mass spectrometry (MS), respectively. Data demonstrated that DED indicators such as tear volume, tear breakup time (TBUT), and corneal damage in the DED groups (DRY and BAC group) differed from those of control (CON). Similar results were noted in inflammatory factors such as interleukin (IL-1ß), IL-6, and tumor necrosis factor (TNF)-α. In the partial least squares-discriminant analysis (PLS-DA) score plots, the three groups were distinctly separated from each other. In addition, the related metabolites were also associated with these distinct separations as evidenced by 9 and 14 in plasma and urine, respectively. Almost all of the selected metabolites were decreased in the DRY group compared to CON, and the BAC group was lower than the DRY. In plasma and urine, lysophosphatidylcholine/lysophosphatidylethanolamine, organic acids, amino acids, and sugars varied between three groups, and these metabolites were related to inflammation and oxidative stress. Data suggest that treatment with scopolamine with/without BAC-induced DED and affected the level of systemic metabolites involved in inflammation and oxidative stress.

Comparison of the diagnostic effectiveness of ultrasound imaging coupled with three mathematical models for discriminating thyroid nodules.

BACKGROUND: The overlapping nature of thyroid lesions visualized on ultrasound (US) images could result in misdiagnosis and missed diagnoses in clinical practice. PURPOSE: To compare the diagnostic effectiveness of US coupled with three mathematical models, namely logistic regression (Logistics), partial least-squares discriminant analysis (PLS-DA), and support vector machine (SVM), in discriminating between malignant and benign thyroid nodules. MATERIAL AND METHODS: A total of 588 thyroid nodules (287 benign and 301 malignant) were collected, among which 80% were utilized for constructing the mathematical models and the remaining 20% were used for internal validation. In addition, an external validation cohort comprising 160 nodules (80 benign and 80 malignant) was employed to validate the accuracy of these mathematical models. RESULTS: Our study demonstrated that all three models exhibited effective predictive capabilities for distinguishing between benign and malignant nodules, whose diagnostic effectiveness surpassed that of the TI-RADS classification, particularly in terms of true negative diagnoses. SVM achieved a higher diagnostic rate for malignant thyroid nodules (93.8%) compared to Logistics (91.5%) and PLS-DA (91.6%). PLS-DA exhibited higher diagnostic rates for benign thyroid nodules (91.9%) compared to Logistics (86.7%) and SVM (88.7%). Both the area under the receiver operating characteristic curve (AUC) values of PLS-DA (0.917) and SVM (0.913) were higher than that of Logistics (0.891). CONCLUSION: Our findings indicate that SVM had significantly higher rates of true positive diagnoses and PLS-DA exhibited significantly higher rates of true negative diagnoses. All three models outperformed the TI-RADS classification in discriminating between malignant and benign thyroid nodules.

Detection of carbon nanotubes in bovine raw milk through Fourier transform Raman spectroscopy.

The potential use of carbon-based methodologies for drug delivery and reproductive biology in cows raises concerns about residues in milk and food safety. This study aimed to assess the potential of Fourier transform Raman spectroscopy and discriminant analysis using partial least squares (PLS-DA) to detect functionalized multiwalled carbon nanotubes (MWCNT) in bovine raw milk. Oxidized MWCNT were diluted in milk at different concentrations from 25.00 to 0.01 µg/mL. Raman spectroscopy measurements and PLS-DA were performed to identify low concentrations of MWCNT in milk samples. The PLS-DA model was characterized by the analysis of the variable importance in projection (VIP) scores. All the training samples were correctly classified by the model, resulting in no false-positive or false-negative classifications. For test samples, only one false-negative result was observed, for 0.01 µg/mL MWCNT dilution. The association between Raman spectroscopy and PLS-DA was able to identify MWCNT diluted in milk samples up to 0.1 µg/mL. The PLS-DA model was built and validated using a set of test samples and spectrally interpreted based on the highest VIP scores. This allowed the identification of the vibrational modes associated with the D and G bands of MWCNT, as well as the milk bands, which were the most important variables in this analysis.

Quality evaluation of Lonicerae Japonicae Flos from different origins based on high-performance liquid chromatography (HPLC) fingerprinting and multicomponent quantitative analysis combined with chemical pattern recognition.

INTRODUCTION: Lonicerae Japonicae Flos (LJF) is widely used in food and traditional Chinese medicine. To meet demand, Lonicera japonica Thunb. is widely cultivated in many provinces of China. However, reported studies on the quality evaluation of LJF only used a single or a few active components as indicators, which could not fully reflect the quality of LJF. OBJECTIVES: In the present study, we aimed to develop a methodology for comprehensively evaluating the quality of LJF from different origins based on high-performance liquid chromatography (HPLC) fingerprinting and multicomponent quantitative analysis combined with chemical pattern recognition. MATERIALS AND METHODS: The HPLC method was developed for fingerprint analysis and was used to determine the contents of 19 components of LJF. To distinguish between samples and identify differential components, similarity analysis, hierarchical cluster analysis, principal component analysis, and orthogonal partial least squares discriminant analysis were performed. RESULTS: The HPLC fingerprint was established. Using the developed method, the contents of 19 components recognized in the fingerprint analysis were determined. Samples from different origins could be effectively distinguished. CONCLUSIONS: HPLC fingerprinting and multicomponent quantitative analysis combined with chemical pattern recognition is an efficient method for evaluating LJF.

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

INTRODUCTION: 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. OBJECTIVES: 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. MATERIALS AND METHODS: 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. RESULTS: 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. CONCLUSIONS: These findings suggest that FT-NIR spectroscopy can be a viable rapid on-site analytical tool for growers during the inflorescence flowering stage.

Sensor for Rapid In-Field Classification of Cannabis Samples Based on Near-Infrared Spectroscopy.

A rugged handheld sensor for rapid in-field classification of cannabis samples based on their THC content using ultra-compact near-infrared spectrometer technology is presented. The device is designed for use by the Austrian authorities to discriminate between legal and illegal cannabis samples directly at the place of intervention. Hence, the sensor allows direct measurement through commonly encountered transparent plastic packaging made from polypropylene or polyethylene without any sample preparation. The measurement time is below 20 s. Measured spectral data are evaluated using partial least squares discriminant analysis directly on the device's hardware, eliminating the need for internet connectivity for cloud computing. The classification result is visually indicated directly on the sensor via a colored LED. Validation of the sensor is performed on an independent data set acquired by non-expert users after a short introduction. Despite the challenging setting, the achieved classification accuracy is higher than 80%. Therefore, the handheld sensor has the potential to reduce the number of unnecessarily confiscated legal cannabis samples, which would lead to significant monetary savings for the authorities.

Chlorophyll Fluorescence Imaging for Environmental Stress Diagnosis in Crops.

The field of plant phenotype is used to analyze the shape and physiological characteristics of crops in multiple dimensions. Imaging, using non-destructive optical characteristics of plants, analyzes growth characteristics through spectral data. Among these, fluorescence imaging technology is a method of evaluating the physiological characteristics of crops by inducing plant excitation using a specific light source. Through this, we investigate how fluorescence imaging responds sensitively to environmental stress in garlic and can provide important information on future stress management. In this study, near UV LED (405 nm) was used to induce the fluorescence phenomenon of garlic, and fluorescence images were obtained to classify and evaluate crops exposed to abiotic environmental stress. Physiological characteristics related to environmental stress were developed from fluorescence sample images using the Chlorophyll ratio method, and classification performance was evaluated by developing a classification model based on partial least squares discrimination analysis from the image spectrum for stress identification. The environmental stress classification performance identified from the Chlorophyll ratio was 14.9% in F673/F717, 25.6% in F685/F730, and 0.209% in F690/F735. The spectrum-developed PLS-DA showed classification accuracy of 39.6%, 56.2% and 70.7% in Smoothing, MSV, and SNV, respectively. Spectrum pretreatment-based PLS-DA showed higher discrimination performance than the existing image-based Chlorophyll ratio.

Unsupervised Clustering-Assisted Method for Consensual Quantitative Analysis of Methanol-Gasoline Blends by Raman Spectroscopy.

Methanol-gasoline blends have emerged as a promising and environmentally friendly bio-fuel option, garnering widespread attention and promotion globally. The methanol content within these blends significantly influences their quality and combustion performance. This study explores the qualitative and qualitative analysis of methanol-gasoline blends using Raman spectroscopy coupled with machine learning methods. Experimentally, methanol-gasoline blends with varying methanol concentrations were artificially configured, commencing with initial market samples. For qualitative analysis, the partial least squares discriminant analysis (PLS-DA) model was employed to classify the categories of blends, demonstrating high prediction performance with an accuracy of nearly 100% classification. For the quantitative analysis, a consensus model was proposed to accurately predict the methanol content. It integrates member models developed on clustered variables, using the unsupervised clustering method of the self-organizing mapping neural network (SOM) to accomplish the regression prediction. The performance of this consensus model was systemically compared to that of the PLS model and uninformative variable elimination (UVE)-PLS model. Results revealed that the unsupervised consensus model outperformed other models in predicting the methanol content across various types of methanol gasoline blends. The correlation coefficients for prediction sets consistently exceeded 0.98. Consequently, Raman spectroscopy emerges as a suitable choice for both qualitative and quantitative analysis of methanol-gasoline blend quality. This study anticipates an increasing role for Raman spectroscopy in analysis of fuel composition.

Differential Chemical Components Analysis of Periplocae Cortex, Lycii Cortex, and Acanthopanacis Cortex Based on Mass Spectrometry Data and Chemometrics.

Background:Periplocae Cortex (PC), Acanthopanacis Cortex (AC), and Lycii Cortex (LC), as traditional Chinese medicines, are all dried root bark, presented in a roll, light and brittle, easy to break, have a fragrant scent, etc. Due to their similar appearances, it is tough to distinguish them, and they are often confused and adulterated in markets and clinical applications. To realize the identification and quality control of three herbs, in this paper, Ultra Performance Liquid Chromatography-Quadrupole Time of Flight Mass Spectrometry Expression (UHPLC-QTOF-MSE) combined with chemometric analysis was used to explore the different chemical compositions. Methods: LC, AC, and PC were analyzed by UHPLC-QTOF-MSE, and the quantized MS data combined with Principal Component Analysis (PCA) and Partial Least Squares Discriminant Analysis (PLS-DA) were used to explore the different chemical compositions with Variable Importance Projection (VIP) > 1.0. Further, the different chemical compositions were identified according to the chemical standard substances, related literature, and databases. Results: AC, PC, and LC can be obviously distinguished in PCA and PLS-DA analysis with the VIP of 2661 ions > 1.0. We preliminarily identified 17 differential chemical constituents in AC, PC, and LC with significant differences (p < 0.01) and VIP > 1.0; for example, Lycium B and Periploside H2 are LC and PC's proprietary ingredients, respectively, and 2-Hydroxy-4-methoxybenzaldehyde, Periplocoside C, and 3,5-Di-O-caffeoylquinic acid are the shared components of the three herbs. Conclusions: UHPLC-QTOF-MSE combined with chemometric analysis is conducive to exploring the differential chemical compositions of three herbs. Moreover, the proprietary ingredients, Lycium B (LC) and Periploside H2 (PC), are beneficial in strengthening the quality control of AC, PC, and LC. In addition, limits on the content of shared components can be set to enhance the quality control of LC, PC, and AC.

Characterization of Flavor Profile of Sauced Pork from Different Regions of China Based on E-Nose, E-Tongue and Gas Chromatography-Ion Mobility Spectroscopy.

This study aimed to investigate the volatile flavor compounds and tastes of six kinds of sauced pork from the southwest and eastern coastal areas of China using gas chromatography-ion mobility spectroscopy (GC-IMS) combined with an electronic nose (E-nose) and electronic tongue (E-tongue). The results showed that the combined use of the E-nose and E-tongue could effectively identify different kinds of sauced pork. A total of 52 volatile flavor compounds were identified, with aldehydes being the main flavor compounds in sauced pork. The relative odor activity value (ROAV) showed that seven key volatile compounds, including 2-methylbutanal, 2-ethyl-3, 5-dimethylpyrazine, 3-octanone, ethyl 3-methylbutanoate, dimethyl disulfide, 2,3-butanedione, and heptane, contributed the most to the flavor of sauced pork (ROAV ≥1). Multivariate data analysis showed that 13 volatile compounds with the variable importance in projection (VIP) values > 1 could be used as flavor markers to distinguish six kinds of sauced pork. Pearson correlation analysis revealed a significant link between the E-nose sensor and alcohols, aldehydes, terpenes, esters, and hetero-cycle compounds. The results of the current study provide insights into the volatile flavor compounds and tastes of sauced pork. Additionally, intelligent sensory technologies can be a promising tool for discriminating different types of sauced pork.

Traceability of Microplastic Fragments from Waste Plastic Express Packages Using Near-Infrared Spectroscopy Combined with Chemometrics.

The pollution from waste plastic express packages (WPEPs), especially microplastic (MP) fragments, caused by the blowout development of the express delivery industry has attracted widespread attention. On account of the variety of additives, strong complexity, and high diversity of plastic express packages (PEPs), the multi-class classification of WPEPs is a typical large-class-number classification (LCNC). The traceability and identification of microplastic fragments from WPEPs is very challenging. An effective chemometric method for large-class-number classification would be very beneficial for the comprehensive treatment of WPEP pollution through the recycling and reuse of waste plastic express packages, including microplastic fragments and plastic debris. Rather than using the traditional one-against-one (OAO) and one-against-all (OAA) dichotomies, an exhaustive and parallel half-against-half (EPHAH) decomposition, which overcomes the defects of the OAO's classifier learning limitations and the OAA's data proportion imbalance, is proposed for feature selection. EPHAH analysis, combined with partial least squares discriminant analysis (PLS-DA) for large-class-number classification, was performed on 750 microplastic fragments of polyethylene WPEPs from 10 major courier companies using near-infrared (NIR) spectroscopy. After the removal of abnormal samples through robust principal component analysis (RPCA), the root mean square error of cross-validation (RMSECV) value for the model was reduced to 0.01, which was 21.5% lower than that including the abnormal samples. The best models of PLS-DA were obtained using SNV combined with SG-17 smoothing and 2D (SNV+SG-17+2D); the latent variables (LVs), the error rates of Monte Carlo cross-validation (ERMCCVs), and the final classification accuracies were 6.35, 0.155, and 88.67% for OAO-PLSDA; 5.37, 0.103, and 87.33% for OAA-PLSDA; and 3.12, 0.054, and 96.00% for EPHAH-PLSDA. The results showed that the EPHAH strategy can completely learn the complex LCNC decision boundaries for 10 classes, effectively break the tie problem, and greatly improve the voting resolution, thereby demonstrating significant superiority to both the OAO and OAA strategies in terms of classification accuracy. Meanwhile, PLS-DA further maximized the covariance and data interpretation abilities between the potential variables and categories of microplastic debris, thereby establishing an ideal performance identification model with a recognition rate of 96.00%.

LC/MS-based discrimination between plasma and urine metabolomic changes following exposure to ultraviolet radiation by using data modelling.

INTRODUCTION: This study sought to compare between metabolomic changes of human urine and plasma to investigate which one can be used as best tool to identify metabolomic profiling and novel biomarkers associated to the potential effects of ultraviolet (UV) radiation. METHOD: A pilot study of metabolomic patterns of human plasma and urine samples from four adult healthy individuals at before (S1) and after (S2) exposure (UV) and non-exposure (UC) were carried out by using liquid chromatography-mass spectrometry (LC-MS). RESULTS: The best results which were obtained by normalizing the metabolites to their mean output underwent to principal components analysis (PCA) and Orthogonal Partial least squares-discriminant analysis (OPLS-DA) to separate pre-from post-of exposure and non-exposure of UV. This separation by data modeling was clear in urine samples unlike plasma samples. In addition to overview of the scores plots, the variance predicted-Q2 (Cum), variance explained-R2X (Cum) and p-value of the cross-validated ANOVA score of PCA and OPLS-DA models indicated to this clear separation. Q2 (Cum) and R2X (Cum) values of PCA model for urine samples were 0.908 and 0.982, respectively, and OPLS-DA model values were 1.0 and 0.914, respectively. While these values in plasma samples were Q2 = 0.429 and R2X = 0.660 for PCA model and Q2 = 0.983 and R2X = 0.944 for OPLS-DA model. LC-MS metabolomic analysis showed the changes in numerous metabolic pathways including: amino acid, lipids, peptides, xenobiotics biodegradation, carbohydrates, nucleotides, Co-factors and vitamins which may contribute to the evaluation of the effects associated with UV sunlight exposure. CONCLUSIONS: The results of pilot study indicate that pre and post-exposure UV metabolomics screening of urine samples may be the best tool than plasma samples and a potential approach to predict the metabolomic changes due to UV exposure. Additional future work may shed light on the application of available metabolomic approaches to explore potential predictive markers to determine the impacts of UV sunlight.

A screening test proposal for congenital defects based on maternal serum metabolomics profile.

BACKGROUND: Historically, noninvasive techniques are only able to identify chromosomal anomalies that accounted for <50% of all congenital defects; the other congenital defects are diagnosed via ultrasound evaluations in the later stages of pregnancy. Metabolomic analysis may provide an important improvement, potentially addressing the need for novel noninvasive and multicomprehensive early prenatal screening tools. A growing body of evidence outlines notable metabolic alterations in different biofluids derived from pregnant women carrying fetuses with malformations, suggesting that such an approach may allow the discovery of biomarkers common to most fetal malformations. In addition, metabolomic investigations are inexpensive, fast, and risk-free and often generate high performance screening tests that may allow early detection of a given pathology. OBJECTIVE: This study aimed to evaluate the diagnostic accuracy of an ensemble machine learning model based on maternal serum metabolomic signatures for detecting fetal malformations, including both chromosomal anomalies and structural defects. STUDY DESIGN: This was a multicenter observational retrospective study that included 2 different arms. In the first arm, a total of 654 Italian pregnant women (334 cases with fetuses with malformations and 320 controls with normal developing fetuses) were enrolled and used to train an ensemble machine learning classification model based on serum metabolomics profiles. In the second arm, serum samples obtained from 1935 participants of the New Zealand Screening for Pregnancy Endpoints study were blindly analyzed and used as a validation cohort. Untargeted metabolomics analysis was performed via gas chromatography-mass spectrometry. Of note, 9 individual machine learning classification models were built and optimized via cross-validation (partial least squares-discriminant analysis, linear discriminant analysis, naïve Bayes, decision tree, random forest, k-nearest neighbor, artificial neural network, support vector machine, and logistic regression). An ensemble of the models was developed according to a voting scheme statistically weighted by the cross-validation accuracy and classification confidence of the individual models. This ensemble machine learning system was used to screen the validation cohort. RESULTS: Significant metabolic differences were detected in women carrying fetuses with malformations, who exhibited lower amounts of palmitic, myristic, and stearic acids; N-α-acetyllysine; glucose; L-acetylcarnitine; fructose; para-cresol; and xylose and higher levels of serine, alanine, urea, progesterone, and valine (P<.05), compared with controls. When applied to the validation cohort, the screening test showed a 99.4%±0.6% accuracy (specificity of 99.9%±0.1% [1892 of 1894 controls correctly identified] with a sensitivity of 78%±6% [32 of 41 fetal malformations correctly identified]). CONCLUSION: This study provided clinical validation of a metabolomics-based prenatal screening test to detect the presence of congenital defects. Further investigations are needed to enable the identification of the type of malformation and to confirm these findings on even larger study populations.

Machine Learning for Prediction, Classification, and Identification of Immobilized Enzymes for Biocatalysis.

BACKGROUND: Enzyme immobilization is a beneficial component involved in biocatalytic strategies. Understanding and evaluating the enzyme immobilization system plays an important role in the successful development and implementation of the biocatalysis route. Ensuring the implementation of a successful enzyme immobilization process is vital for realizing a highly functioning and well suited biocatalytic process within pharmaceutical development. AIM: To develop a method which can accurately and objectively identify and classify differences within enzyme immobilization systems, sample preparation methods, and data collection parameters. METHODS: Raman hyperspectral imaging was used to obtain a total of eight spectral data sets from enzyme immobilization samples. Partial least squares discriminant analysis (PLS-DA) was used to classify and identify the samples based on their differences. RESULTS: Several two-class, four-class, and eight-class PLS-DA models were built to classify the different sample data sets. All models reached between 92-100% accuracy after cross-validation and external validation, illustrating great success of the models for identifying differences between the samples. CONCLUSION: Raman hyperspectral imaging with machine learning can be used to investigate, interpret, and classify different data collection parameters, sample preparation methods, and enzyme immobilization supports, providing crucial insight into enzyme immobilization process development.

Metabolite profiling analysis of hepatitis B virus-induced liver cirrhosis patients with minimal hepatic encephalopathy using gas chromatography-time-of-flight mass spectrometry and ultra-performance liquid chromatography-quadrupole-time-of-flight mass spectrometry.

This study used gas chromatography-time-of-flight mass spectrometry (GC-TOFMS) and ultra-performance liquid chromatography-quadrupole TOFMS (UPLC-QTOFMS) metabonomic analytical techniques in combination with bioinformatics and pattern recognition analysis methods to analyze the serum metabolite profiling of hepatitis B virus (HBV)-induced liver cirrhosis patients with minimal hepatic encephalopathy (MHE), to find the specific biomarkers of MHE, to reveal the pathogenesis of MHE, and to determine a promising approach for early diagnosis of MHE. Serum samples of 100 normal controls (NC group), 29 HBV-induced liver cirrhosis patients with MHE (MHE group), and 24 HBV-induced liver cirrhosis patients without MHE [comprising 12 cases of compensated cirrhosis (CS group) and 12 cases of decompensated cirrhosis (DS group)] were collected and employed into GC-TOFMS and UPLC-QTOFMS platforms for serum metabolite detection; the outcome data were then analyzed using principal component analysis and orthogonal partial least squares-discriminant analysis (OPLS-DA). There were no significant differential metabolites between the NC group and the CS group. A series of key differential metabolites were detected. According to the variable influence in projection values and P-values, 60 small-molecule metabolites were considered to be dysregulated in the MHE group (compared to the NC group); 27 of these 60 dysregulated differential metabolites were considered to be the potential biomarkers (see Table 4, marked in bold); 66 small-molecule metabolites were considered to be dysregulated in the DS group (compared to the NC group); 34 of these 66 dysregulated differential metabolites were considered to be the potential biomarkers (see Table 5, marked in bold). According to the fold-change values, 9 of these 27 metabolites, namely valine, oxalic acid, erythro-sphingosine, 4,7,10,13,16,19-docosahexaenoic acid, isoleucine, allo-isoleucine, thyroxine, rac-octanoyl carnitine, and tocopherol (vitamin E), were downregulated in the MHE group (compared to the NC group); the other 18, namely adenine, glycochenodeoxycholic acid, fucose, allothreonine, glycohyocholic acid, glycoursodeoxycholic acid, tyrosine, taurocheno-deoxycholate, phenylalanine, 2-hydroxy-3-methyl-butanoic acid, hydroxyacetic acid, taurocholate, sorbitol, rhamnose, tauroursodeoxycholate, tolbutamide, pyroglutamic acid, and malic acid, were upregulated; 6 of these 34 metabolites were downregulated in the DS group (compared to the NC group), and the other 28 were upregulated, as shown in Table 5. (a) GC-TOFMS and UPLC-QTOFMS metabonomic analytical platforms can detect a range of metabolites in the serum; this might be of great help to study the pathogenesis of MHE and may provide a new approach for the early diagnosis of MHE. (b) Metabonomics analysis in combination with pattern recognition analysis might have great potential to distinguish the HBV-induced liver cirrhosis patients who have MHE from the normal healthy population and HBV-induced liver cirrhosis patients without MHE.

Disease Incidence and Severity of Cercospora Leaf Spot in Sugar Beet Assessed by Multispectral Unmanned Aerial Images and Machine Learning.

Disease incidence (DI) and metrics of disease severity are relevant parameters for decision making in plant protection and plant breeding. To develop automated and sensor-based routines, a sugar beet variety trial was inoculated with Cercospora beticola and monitored with a multispectral camera system mounted to an unmanned aerial vehicle (UAV) over the vegetation period. A pipeline based on machine learning methods was established for image data analysis and extraction of disease-relevant parameters. Features based on the digital surface model, vegetation indices, shadow condition, and image resolution improved classification performance in comparison with using single multispectral channels in 12 and 6% of diseased and soil regions, respectively. With a postprocessing step, area-related parameters were computed after classification. Results of this pipeline also included extraction of DI and disease severity (DS) from UAV data. The calculated area under disease progress curve of DS was 2,810.4 to 7,058.8%.days for human visual scoring and 1,400.5 to 4,343.2%.days for UAV-based scoring. Moreover, a sharper differentiation of varieties compared with visual scoring was observed in area-related parameters such as area of complete foliage (AF), area of healthy foliage (AH), and mean area of lesion by unit of foliage ([Formula: see text]). These advantages provide the option to replace the laborious work of visual disease assessments in the field with a more precise, nondestructive assessment via multispectral data acquired by UAV flights.[Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Novel fluorescence spectroscopy method coupled with N-PLS-R and PLS-DA models for the quantification of cannabinoids and the classification of cannabis cultivars.

INTRODUCTION: Cannabis sativa L. inflorescences are rich in secondary metabolites, particularly cannabinoids. The most common techniques for elucidating cannabinoid composition are expensive technologies, such as high-pressure liquid chromatography (HPLC). OBJECTIVES: We aimed to develop and evaluate the performance of a novel fluorescence spectroscopy-based method coupled with N-way partial least squares regression (N-PLS-R) and partial least squares discriminant analysis (PLS-DA) models to replace the expensive chromatographic methods for preharvest cannabinoid quantification. METHODOLOGY: Fresh medicinal cannabis inflorescences were collected and ethanol extracts were prepared. Their excitation-emission spectra were measured using fluorescence spectroscopy and their cannabinoid contents were determined by HPLC-PDA. Subsequently, N-PLS-R and PLS-DA models were applied to the excitation-emission matrices (EEMs) for cannabinoid concentration prediction and cultivar classification, respectively. RESULTS: The N-PLS-R model was based on a set of EEMs (n = 82) and provided good to excellent quantification of (-)-Δ9-trans-tetrahydrocannabinolic acid, cannabidiolic acid, cannabigerolic acid, cannabichromenic acid, and (-)-Δ9-trans-tetrahydrocannabinol (R2 CV and R2 pred  > 0.75; RPD > 2.3 and RPIQ > 3.5; RMSECV/RMSEC ratio < 1.4). The PLS-DA model enabled a clear distinction between the four major classes studied (sensitivity, specificity, and accuracy of the prediction sets were all ≥0.9). CONCLUSIONS: The fluorescence spectral region (excitation 220-400 nm, emission 280-550 nm) harbors sufficient information for accurate prediction of cannabinoid contents and accurate classification using a relatively small data set.

Hyperspectral Analysis for Discriminating Herbicide Site of Action: A Novel Approach for Accelerating Herbicide Research.

In agricultural weed management, herbicides are indispensable, yet innovation in their modes of action (MOA)-the general mechanisms affecting plant processes-has slowed. A finer classification within MOA is the site of action (SOA), the specific biochemical pathway in plants targeted by herbicides. The primary objectives of this study were to evaluate the efficacy of hyperspectral imaging in the early detection of herbicide stress and to assess its potential in accelerating the herbicide development process by identifying unique herbicide sites of action (SOA). Employing a novel SOA classification method, eight herbicides with unique SOAs were examined via an automated, high-throughput imaging system equipped with a conveyor-based plant transportation at Purdue University. This is one of the earliest trials to test hyperspectral imaging on a large number of herbicides, and the study aimed to explore the earliest herbicide stress detection/classification date and accelerate the speed of herbicide development. The final models, trained on a dataset with nine treatments with 320 samples in two rounds, achieved an overall accuracy of 81.5% 1 day after treatment. With the high-precision models and rapid screening of numerous compounds in only 7 days, the study results suggest that hyperspectral technology combined with machine learning can contribute to the discovery of new herbicide MOA and help address the challenges associated with herbicide resistance. Although no public research to date has used hyperspectral technology to classify herbicide SOA, the successful evaluation of herbicide damage to crops provides hope to accelerate the progress of herbicide development.

Comparing Machine Learning and PLSDA Algorithms for Durian Pulp Classification Using Inline NIR Spectra.

The aim of this study was to evaluate and compare the performance of multivariate classification algorithms, specifically Partial Least Squares Discriminant Analysis (PLS-DA) and machine learning algorithms, in the classification of Monthong durian pulp based on its dry matter content (DMC) and soluble solid content (SSC), using the inline acquisition of near-infrared (NIR) spectra. A total of 415 durian pulp samples were collected and analyzed. Raw spectra were preprocessed using five different combinations of spectral preprocessing techniques: Moving Average with Standard Normal Variate (MA+SNV), Savitzky-Golay Smoothing with Standard Normal Variate (SG+SNV), Mean Normalization (SG+MN), Baseline Correction (SG+BC), and Multiplicative Scatter Correction (SG+MSC). The results revealed that the SG+SNV preprocessing technique produced the best performance with both the PLS-DA and machine learning algorithms. The optimized wide neural network algorithm of machine learning achieved the highest overall classification accuracy of 85.3%, outperforming the PLS-DA model, with overall classification accuracy of 81.4%. Additionally, evaluation metrics such as recall, precision, specificity, F1-score, AUC ROC, and kappa were calculated and compared between the two models. The findings of this study demonstrate the potential of machine learning algorithms to provide similar or better performance compared to PLS-DA in classifying Monthong durian pulp based on DMC and SSC using NIR spectroscopy, and they can be applied in the quality control and management of durian pulp production and storage.