Counter-propagation Artificial Neural Network Research Articles

Deriving general structure–activity/selectivity relationship patterns for different subfamilies of cyclin-dependent kinase inhibitors using machine learning methods

Cyclin-dependent kinases (CDKs) play essential roles in regulating the cell cycle and are among the most critical targets for cancer therapy and drug discovery. The primary objective of this research is to derive general structure–activity relationship (SAR) patterns for modeling the selectivity and activity levels of CDK inhibitors using machine learning methods. To accomplish this, 8592 small molecules with different binding affinities to CDK1, CDK2, CDK4, CDK5, and CDK9 were collected from Binding DB, and a diverse set of descriptors was calculated for each molecule. The supervised Kohonen networks (SKN) and counter propagation artificial neural networks (CPANN) models were trained to predict the activity levels and therapeutic targets of the molecules. The validity of models was confirmed through tenfold cross-validation and external test sets. Using selected sets of molecular descriptors (e.g. hydrophilicity and total polar surface area) we derived activity and selectivity maps to elucidate local regions in chemical space for active and selective CDK inhibitors. The SKN models exhibited prediction accuracies ranging from 0.75 to 0.94 for the external test sets. The developed multivariate classifiers were used for ligand-based virtual screening of 2 million random molecules of the PubChem database, yielding areas under the receiver operating characteristic curves ranging from 0.72 to 1.00 for the SKN model. Considering the persistent challenge of achieving CDK selectivity, this research significantly contributes to addressing the issue and underscores the paramount importance of developing drugs with minimized side effects.

Self-Organizing Maps for Exploration and Classification of Nuclear Magnetic Resonance Spectra for Untargeted Metabolomics of Breast Cancer

Metabolomics has emerged as a powerful tool for identifying biomarkers of disease, and nuclear magnetic resonance (NMR) spectroscopy allows for the simultaneous detection of a wide range of metabolites. However, due to complex interactions within metabolic networks, metabolites often exhibit high correlation and collinearity. To address this challenge, self-organizing maps (SOMs) of Kohonen maps and counter propagation-artificial neural networks (CP-ANN) were employed in this study to model proton nuclear magnetic resonance spectroscopic (1HNMR) data from control samples and breast cancer (BC) patients. Blood serum samples from a control group (n=24) and BC patients (n=18) were used to extract metabolites using methanol and chloroform solvents in optimum extraction conditions. The 1HNMR data was preprocessed by performing phase, baseline, and shift corrections. Subsequently, the preprocessed data was modeled using Kohonen network as an unsupervised technique and CP-ANN as a supervised technique. In this regard, the model built with CP-ANN successfully distinguished between the two classes with an accuracy of 100% for both group and sensitivity of 96% and 100% for control group and BC patients, respectively. Additionally, CP-ANN algorithm demonstrated predictive capabilities by accurately classifying test samples with 90% sensitivity, 98% specificity, and 96% accuracy for control group and 100% sensitivity, 90% specificity, and 96% accuracy for BC patients. Furthermore, analysis of the resulting topological map revealed 14 significant variables (biomarkers) such as sarcosine, lysine, trehalose, tryptophan, and betaine that effectively differentiated between healthy individuals and BC patients.

Cheminformatics and Machine Learning Approaches to Assess Aquatic Toxicity Profiles of Fullerene Derivatives.

Fullerene derivatives (FDs) are widely used in nanomaterials production, the pharmaceutical industry and biomedicine. In the present study, we focused on the potential toxic effects of FDs on the aquatic environment. First, we analyzed the binding affinity of 169 FDs to 10 human proteins (1D6U, 1E3K, 1GOS, 1GS4, 1H82, 1OG5, 1UOM, 2F9Q, 2J0D, 3ERT) obtained from the Protein Data Bank (PDB) and showing high similarity to proteins from aquatic species. Then, the binding activity of 169 FDs to the enzyme acetylcholinesterase (AChE)-as a known target of toxins in fathead minnows and Daphnia magna, causing the inhibition of AChE-was analyzed. Finally, the structural aquatic toxicity alerts obtained from ToxAlert were used to confirm the possible mechanism of action. Machine learning and cheminformatics tools were used to analyze the data. Counter-propagation artificial neural network (CPANN) models were used to determine key binding properties of FDs to proteins associated with aquatic toxicity. Predicting the binding affinity of unknown FDs using quantitative structure-activity relationship (QSAR) models eliminates the need for complex and time-consuming calculations. The results of the study show which structural features of FDs have the greatest impact on aquatic organisms and help prioritize FDs and make manufacturing decisions.

General structure-activity/selectivity relationship patterns for the inhibitors of the chemokine receptors (CCR1/CCR2/CCR4/CCR5) with application for virtual screening of PubChem database

CC chemokine receptors (CCRs) form a crucial subfamily of G protein-linked receptors that play a distinct role in the onset and progression of various life-threatening diseases. The main aim of this research is to derive general structure-activity relationship (SAR) patterns to describe the selectivity and activity of CCR inhibitors. To this end, a total of 7332 molecules related to the inhibition of CCR1, CCR2, CCR4, and CCR5 were collected from the Binding Database and analyzed using machine learning techniques. A diverse set of 450 molecular descriptors was calculated for each molecule, and the molecules were classified based on their therapeutic targets and activities. The variable importance in the projection (VIP) approach was used to select discriminatory molecular features, and classification models were developed using supervised Kohonen networks (SKN) and counter-propagation artificial neural networks (CPANN). The reliability and predictability of the models were estimated using 10-fold cross-validation, an external validation set, and an applicability domain approach. We were able to identify different sets of molecular descriptors for discriminating between active and inactive molecules and model the selectivity of inhibitors towards different CCRs. The sensitivities of the predictions for the external test set for the SKN models ranged from 0.827–0.873. Finally, the developed classification models were used to screen approximately 2 million random molecules from the PubChem database, with average values for areas under the receiver operating characteristic curves ranging from 0.78–0.96 for SKN models and 0.75–0.89 for CPANN models. Communicated by Ramaswamy H. Sarma

Development of in silico classification models for binding affinity to the glucocorticoid receptor

The endocrine disrupting properties of chemicals acting through the glucocorticoid receptor (GR) have attracted considerable interest. Since there are few data for most chemicals on their endocrine properties in silico approaches seem to be the most appropriate tool for screening and prioritizing chemicals for planning further experiments. In this work, we developed classification models for binding affinity to the glucocorticoid receptor using the counterpropagation artificial neural network method. We considered two series of 142 and 182 compounds and their binding affinity to the glucocorticoid receptor as agonists and antagonists, respectively. The compounds belong to different chemical classes. The compounds were represented by a set of descriptors calculated with the DRAGON program. The clustering structure of sets was studied with standard principal component method. A weak separation between binders and non-binders was found. Another classification model was developed using the counterpropagation artificial neural network method (CPANN). The final classification models developed were well balanced and showed a high level of accuracy, with 85.7% of GR agonist and 78.9% of GR antagonist correctly assigned in leave-one-out cross-validation.

Identification of the Origin, Authenticity and Quality of Panax Japonicus Based on a Multistrategy Platform.

Panax Japonicus (PJ) is a widely used Chinese herbal medicine, functional food and tonic. However, its origin has a great influence on the quality of PJ, and with the increasing demand for PJ, fake and inferior products, such as Panax Stipuleanatus (PS), often appear. The identification of the origin and authenticity of PJ is critical for ensuring the quality, safety and effectiveness of drugs. Proposing a strategy to identify the origin, authenticity, and quality of PJ using HPLC fingerprints, chemometrics, and network pharmacology. The chromatographic fingerprint method was established to analyze the origin and authenticity of PJ. Multiple chemometric methods were performed to analyze the fingerprints, including a Hierarchical Cluster Analysis (HCA), Principal Component Analysis (PCA), and Counter Propagation Artificial Neural Network (CP-ANN). Finally, the network pharmacology method was used to construct the "active ingredient-target" network, predict and assist in analyzing potential Qmarkers in PJ. Ward's method was used for the HCA. The results showed that PJ samples from different origins had significant regional differences and could be accurately distinguished from PS. The PCA classification results are consistent with the HCA classification results, further illustrating the model's accuracy. The CP-ANN model can analyze and predict PJ and PS and accurately obtain PJ and PS chemical markers to identify PJ and PS correctly. The network pharmacology of PJ was constructed, and three PJ Q-markers, namely, ginsenoside Ro, ginsenoside Rb1, and chikusetsu saponin Ⅳa, were identified, which lays a foundation for the establishment of PJ quality standards. This research provides a feasible platform for the quality evaluation of PJ in the future.

Predictive Models for Compound Binding to Androgen and Estrogen Receptors Based on Counter-Propagation Artificial Neural Networks.

Endocrine-disrupting chemicals (EDCs) are exogenous substances that interfere with the normal function of the human endocrine system. These chemicals can affect specific nuclear receptors, such as androgen receptors (ARs) or estrogen receptors (ER) α and β, which play a crucial role in regulating complex physiological processes in humans. It is now more crucial than ever to identify EDCs and reduce exposure to them. For screening and prioritizing chemicals for further experimentation, the use of artificial neural networks (ANN), which allow the modeling of complicated, nonlinear relationships, is most appropriate. We developed six models that predict the binding of a compound to ARs, ERα, or ERβ as agonists or antagonists, using counter-propagation artificial neural networks (CPANN). Models were trained on a dataset of structurally diverse compounds, and activity data were obtained from the CompTox Chemicals Dashboard. Leave-one-out (LOO) tests were performed to validate the models. The results showed that the models had excellent performance with prediction accuracy ranging from 94% to 100%. Therefore, the models can predict the binding affinity of an unknown compound to the selected nuclear receptor based solely on its chemical structure. As such, they represent important alternatives for the safety prioritization of chemicals.

Development of new QSAR models for water, sediment, and soil half-life.

Checking the persistence of a chemical in the environment is extremely important. Regulations like REACH, the European one on chemicals, require the measurements or estimates of the half-life of the chemical in water, sediment, and soil. The use of non-testing methods, like quantitative structure-activity relationship (QSAR) models, is encouraged because it reduces costs and time. To our knowledge, there are very few freely available models for these properties and some are for specific chemical classes. Here, we present three new semi-quantitative models, one for each of the required environmental compartments (water, sediment, and soil). Using literature and REACH registration data, we developed three new counter-propagation artificial neural network models using the CPANNatNIC tool. We calculated the VEGA descriptors, and selected the relevant ones using an internal method in R based on the forward selection technique. The best model for each compartment was implemented in two open-source stand-alone tools, the VEGA platform, and the JANUS tool (https://www.vegahub.eu/). These models were also used by ECHA to build their PBT profiler available in the OECD QSAR toolbox (https://qsartoolbox.org/). Screening and prioritization are also our main target. The models perform well, with R2 always above 0.8 in training and validation. The only exception is the validation set of the soil compartment, with R2 0.68, that is above 0.8 only for compounds inside the applicability domain (automatically calculated by the system). The root mean square error (RMSE) is good, 0.34 or less in log units (again, for soil validation it is higher but it reaches 0.21 when considering only the compounds in the applicability domain). Compared with one of the most widely used tools, BIOWIN3, the proposed models give better results in terms of R2 and RMSE. For the classification, the performance is better for water and soil, and comparable or lower for sediment.

Damage Classification Using Supervised Self-Organizing Maps in Structural Health Monitoring.

Improvements in computing capacity have allowed computers today to execute increasingly complex tasks. One of the main benefits of these improvements is the possibility of developing machine learning algorithms, of which the fields of application are extensive and varied. However, an area in which this type of algorithms acquires an increasing relevance is structural health monitoring (SHM), where inspection strategies and guided wave-based approaches make the evaluation of the structural conditions of an aircraft, vessel or building among others possible, by detecting and classifying existing damages. The use of sensors, data acquisition systems (DAQ) and computation has also allowed these damage detection and classification tasks to be carried out automatically. Despite today’s advances, it is still necessary to continue with the development of more robust, reliable, and low-cost structural health monitoring systems. For this reason, this work contemplates three key points: (i) the configuration of a data acquisition system for signal gathering from an an active piezoelectric (PZT) sensor network; (ii) the development of a damage classification methodology based on signal processing techniques (normalization and PCA), from which the models that describe the structural conditions of the plate are built; and (iii) the use of machine learning algorithms, more specifically, three variants of the self-organizing maps called CPANN (counterpropagation artificial neural network), SKN (supervised Kohonen) and XYF (X–Y fused Kohonen). The data obtained allowed one to carry out an experimental validation of the damage classification methodology, to determine the presence of damages in two aluminum plates of different sizes, where masses were added to change the vibrational responses captured by the sensor network and a composite (CFRP) plate with real damages, such as delamination and cracks. This classification methodology allowed one to obtain excellent results by validating the usefulness of the SKN and XYF networks in damage classification tasks, showing overall accuracies of 73.75% and 72.5%, respectively, according to the cross-validation process. These percentages are higher than those obtained in comparison with other neural networks such as: kNN, discriminant analysis, classification trees, partial least square discriminant analysis, and backpropagation neural networks, when the cross-validation process was applied.

A Novel Strategy for Improving the Counter Propagation Artificial Neural Networks in Classification Tasks

Counter-Propagation-Artificial-Neural-Networks (C P-ANNs) have been applied in several domains due to their learning and classification abilities. Regardless of their strength, the CP-ANNs still have some limitations in pattern recognition tasks when they encounter ambiguities during the learning process, which leads to the inaccurate classification of the Kohonen-Self-Organizing-Map (K-SOM). This problem has an impact on the performance of the CP-ANNs. Therefore, this paper proposes a novel strategy to improve the CP-ANNs by the Gram-Schmidt algorithm (GSHM) as a pre-processing step of the original data without changing their architecture. Three datasets examples from various domains, such as correlation, crop, and fertilizer, were employed for experimental validation. To obtain the results, we relied on two simulations. The first simulation uses CP-ANNs, and the datasets are inputted into the network without any prior pre-processing. The second simulation uses MCP-ANNs, and the datasets are pre-processed through the GSHM block. Experiment results show that the proposed MCP-ANNs recognize all patterns with a classification accuracy of 100% versus 62.5% for CP-ANNs in the Correlation Dataset. Furthermore, the proposed MCP-ANNs reduce the execution time and training parameter values in all datasets versus CP-ANNs. Thus, the proposed approach based on the GSHM algorithm significantly improves the performance of the CP-ANNs.

Characteristic profiling of Aconiti Lateralis Radix for distinguishing it from compatible herbal pair using UPLC-Q-TOF-MS coupled with chemometrics.

A method combining ultra-high-performance liquid chromatograph/quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS) and chemometrics was established to evaluate the differences in chemical composition between Aconiti Lateralis Radix (Fuzi in Chinese) before and after combination with Glycyrrhizae Radix et Rhizoma (Gancao in Chinese). UPLC-Q-TOF-MS was used to characterize the chemical components before and after the combination of Fuzi with Gancao, and genetic algorithm selection variables were applied to extract important variables. Partial least square discriminant analysis was used to verify the reliability of the variables obtained by genetic algorithm selection in differentiating Fuzi and combinations with Gancao, and nine potential chemical markers were obtained. The changes in content of chemical markers in Fuzi before and after combination were visualized using a heat map and hierarchical cluster analysis. Based on the chemical markers, characteristic profiling of UPLC-Q-TOF-MS data was developed, then unsupervised principal components analysis and a supervised counter-propagation artificial neural network were used to validate the characteristic profiling approach and showed that it performed well in differentiating between Fuzi and combinations with Gancao.

Artificial neural network for quantitative and qualitative determination of the viscosity of nanofluids by ATR-FTIR spectrometry

The multivariate data analysis refers to the process by which determination and classification of new unknown samples are made by accurate and economically practicable methods. In this paper, new analytical methods were utilized as a fast analytical method for regression and classification of polyacrylamide-nano silica (PAM-SiO2) as an influential factor in the rheological performance of the nanofluids, utilizing attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy and chemometric methods. The effect of nanoparticle concentration on the viscosity measurement was determined. The spectral data were used for determination of viscosity value according to back-propagation artificial neural network (BP-ANN) algorithm. The root mean square errors (RMSEs) of model and test set in BP-ANN method were 0.051, and 3.548, respectively. In classification model, the ATR-FTIR spectral data were applied for analysis by using the counter-propagation artificial neural networks (CP-ANN) for classification of PAM-SiO2 nanofluids. The samples were classified based on the effect of nanoparticle concentration on viscosity values. The correct classification of the four classes was obtained by using CP-ANN modelling procedure. This work attempts to propose an analytical method to regression and classification viscosity of real-world data sets.

Application of spatio-temporal data in site-specific maize yield prediction with machine learning methods

In order to meet the requirements of sustainability and to determine yield drivers and limiting factors, it is now more likely that traditional yield modelling will be carried out using artificial intelligence (AI). The aim of this study was to predict maize yields using AI that uses spatio-temporal training data. The paper has advanced a new method of maize yield prediction, which is based on spatio-temporal data mining. To find the best solution, various models were used: counter-propagation artificial neural networks (CP-ANNs), XY-fused Querynetworks (XY-Fs), supervised Kohonen networks (SKNs), neural networks with Rectangular Linear Activations (ReLU), extreme gradient boosting (XGBoost), support-vector machine (SVM), and different subsets of the independent variables in five vegetation periods. Input variables for modelling included: soil parameters (pH, P2O5, K2O, Zn, clay content, ECa, draught force, Cone index), micro-relief averages, and meteorological parameters for the 63 treatment units in a 15.3 ha research field. The best performing method (XGBoost) reached 92.1% and 95.3% accuracy on the training and the test sets. Additionally, a novel method was introduced to treat individual units in a lattice system. The lattice-based smoothing performed an additional increase in Area under the curve (AUC) to 97.5% over the individual predictions of the XGBoost model. The models were developed using 48 different subsets of variables to determine which variables consistently contributed to prediction accuracy. By comparing the resulting models, it was shown that the best regression model was Extreme Gradient Boosting Trees, with 92.1% accuracy (on the training set). In addition, the method calculates the influence of the spatial distribution of site-specific soil fertility on maize grain yields. This paper provides a new method of spatio-temporal data analyses, taking the most important influencing factors on maize yields into account.

Clinical lipidomics analysis reveals biomarkers of lipid peroxidation in serum from patients with rheumatoid arthritis

Rheumatoid arthritis (RA) is a common chronic inflammatory disorder characterized by inflammation of the synovium which causes joint damage, chronic pain, and disability. Changes in lipid profile are seen before overt RA disease manifestations suggesting that lipids contribute to the inflammation-driven metabolic changes in tumor necrosis factor. Currently, the pathogenesis of RA is unclear. Moreover, it is important to search for lipids biomarkers for early diagnosis of the disease. Herein, we compared the lipid profile of healthy individuals and RA patients to provide evidence for the diagnosis and management of persons with RA. Serum samples were collected from 511 RA patients and 396 health controls (HC). The samples were analyzed by ultra-performance liquid chromatography Q-Exactive mass spectrometry. Potential lipid biomarkers were screened and validated using the partial least squares discriminant analysis (PLS-DA), orthogonal partial least squares-discriminant analysis (OPLS-DA), random forest, binary logistic regression (BLR), receiver operating characteristic (ROC) and counter propagation artificial neural network (CP-ANN) analysis. A total of 36 differential lipid metabolites were identified, including phosphatidylethanolamine (PE), triglyceride (TG), acylcarnitine (ACar) and phosphatidylcholine (PC). Among them, PE 16:0-18:2, TG 18:0-18:1-18:2 and PE 18:2-18:2 were identified as specific biomarkers for differential diagnosis of RA. ROC analysis showed that the biomarkers had a sensitivity of 68% with a specificity of 63% in discriminating RA from HC individuals. The resulting CP-ANN can be used to identify unknown RA samples with predictive accuracy of 97% as determined through cross validation. The external validation accuracy of CP-ANN was 100% in all evaluated cases. The three lipid serum biomarkers were associated with the disease activity in RA. These lipid biomarkers showed that lipid peroxidation is disrupted in RA.

Detection of fraud in lime juice using pattern recognition techniques and FT-IR spectroscopy.

The lime juice is one of the products that has always fallen victim to fraud by manufacturers for reducing the cost of products. The aim of this research was to determine fraud in distributed lime juice products from different factories in Iran. In this study, 101 samples were collected from markets and also prepared manually and finally derived into 5 classes as follows: two natural classes (Citrus limetta, Citrus aurantifolia), including 17 samples, and three reconstructed classes, including 84 samples (made from Spanish concentrate, Chinese concentrate, and concentrate containing adulteration compounds). The lime juice samples were freeze‐dried and analyzed using FT‐IR spectroscopy. At first, principal component analysis (PCA) was applied for clustering, but the samples were not thoroughly clustered with respect to their original groups in score plots. To enhance the classification rates, different chemometric algorithms including variable importance in projection (VIP), partial least square‐discriminant analysis (PLS‐DA), and counter propagation artificial neural networks (CPANN) were used. The best discriminatory wavenumbers related to each class were selected using the VIP‐PLS‐DA algorithm. Then, the CPANN algorithm was used as a nonlinear mapping tool for classification of the samples based on their original groups. The lime juice samples were correctly designated to their original groups in CPANN maps and the overall accuracy of the model reached up to 0.96 and 0.87 for the training and validation procedures. This level of accuracy indicated the FT‐IR spectroscopy coupled with VIP‐PLS‐DA and CPANN methods can be used successfully for detection of authenticity of lime juice samples.

Advanced multivariate techniques for the classification and pollution of marine sediments due to aquaculture

Aquaculture production has globally increased and its environmental impact is not well understood and assessed yet. Therefore, in this work nine metals and metalloids (Cu, Cd, Pb, Hg, Ni, Fe, Mn, Zn and As) and three nutrients (P, N and C) that seem to accumulate in marine sediments, were determined under the fish cages (zero distance) and about 50 and 100 m away from them, in three aquacultures in Greece. The analysis of these data is crucial due to the negative impact of the intensive aquaculture activities on fish population, human health and marine environment. This study investigated the environmental impact associated with aquaculture cages on marine sediments, using Supervised Artificial Neural Networks (ANNs) in parallel with Classification Trees (CTs). Optimised models were constructed in order to detect the significance of each variable, predict the origin of the sediment samples and successfully visualise their results. Three popular ANN architectures, as multi-layer perceptrons (MLPs), radial basis function (RBF) and counter propagation artificial neural networks (CP-ANNs) were used to assess the impact of the intensive aquaculture activities on marine sediments. In addition, more traditional multivariate chemometric techniques like CTs were applied to the same data set for comparison purposes. The modelling study showed that P, N, Cu, Cd were the most critical (and polluting) factors of those metals studied. Moreover, single-element models achieved elevated predictive percentages. The results were justified due to the usual practices used for fish feeding or cages maintenance.

Rapid and practical qualitative and quantitative evaluation of non-fumigated ginger and sulfur-fumigated ginger via Fourier-transform infrared spectroscopy and chemometric methods

A strategy was developed to distinguish and quantitate nonfumigated ginger (NS-ginger) and sulfur-fumigated ginger (S-ginger), based on Fourier transform near infrared spectroscopy (FT-NIR) and chemometrics. FT-NIR provided a reliable method to qualitatively assess ginger samples and batches of S-ginger (41) and NS-ginger (39) were discriminated using principal component analysis and orthogonal partial least squares discriminant analysis of FT-NIR data. To generate quantitative methods based on partial least squares (PLS) and counter propagation artificial neural network (CP-ANN) from the FT-NIR, major gingerols were quantified using high performance liquid chromatography (HPLC) and the data used as a reference. Finally, PLS and CP-ANN were deployed to predict concentrations of target compounds in S- and NS-ginger. The results indicated that FT-NIR can provide an alternative to HPLC for prediction of active components in ginger samples and was able to work directly on solid samples.

Analysis and evaluation of nucleosides, nucleobases, and amino acids in safflower from different regions based on ultra high performance liquid chromatography coupled with triple-quadrupole linear ion-trap tandem mass spectrometry.

Safflower has both medicinal and edible values but research on its nutrient composition is still lacking. This study was established for the quantitative determination of 28 nucleosides, nucleobases, and amino acids based on the ultra-performance liquid chromatography coupled with triple-quadrupole linear ion-trap tandem mass spectrometry. Analysis of 30 batches of safflower from different producing areas indicated that the contents of l-proline, l-asparagine, l(+)-arginine, l-serine, l-histidine, uracil, guanosine, and uridine was high in safflower. Principle component analysis and cluster analysis found that samples from different regions could be distinguished well, and samples from the same area could be clustered into one class, different geographical environments may cause the differences of nucleosides, nucleobases, and amino acids in safflower. The analysis of principal component analysis, cluster analysis, and counter propagation artificial neural network show similar results. Then the content of nucleosides, nucleobases, and essential amino acids were compared, and found that the content in safflower from Gansu was higher than those from other regions, and there was a little difference between the samples from Xinjiang, Sichuan, and Yunnan. This research revealed the composition of nucleosides, nucleobases, and amino acids in safflower, and provided a theoretical basis for utilization of safflower.

Designating the geographical origin of Iranian almond and red jujube oils using fluorescence spectroscopy and l1-penalized chemometric methods

Assessment of the geographical origin of medical plants (MP) has received a lot of attention in traditional medicine for determination of the quality of the products and detection of food/drug adulteration. In the present contribution, the sparse version of N-way partial least square discriminant analysis (sNPLS-DA) has been used for classification of almond and red jujube oil samples using their excitation-emission (EEM) fluorescence spectra, for the first time. Seven types of almond seeds and six species of red jujube samples were collected from mountains and hills in Fars and Khorasan provinces in Iran, respectively. The sNPLS-DA algorithm with l1-norm constraint was utilized for calculation of sparse loading vectors. This method merges variable selection and modeling steps into one phase, and due to sparse loading vectors, models are easily interpretable. The number of latent variables and non-zero elements in the first and second loading spaces for the sNPLS-DA models in this work was optimized using a central composite design (CCD) approach. The optimized models were used for classification of almond and red jujube oil samples according to their geographical origins in Iran. The average accuracies of the sNPLS-DA models were 0.95 and 0.89 for bootstrapping cross validation and 0.97 and 1.00 for external validation for almond and red jujube samples, respectively. The performance of the sNPLS-DA models was compared with PLS-DA, parallel factor analysis (PARAFAC), counter propagation artificial neural networks (CPANN), and supervised Kohonen networks (SKN). The results of the optimized sNPLS-DA models were superior to PARAFAC-DA and comparable to those of CPANN and SKN models. The results in this work reveal that the sNPLS-DA method can be used as a reliable and interpretable tool for quality control and classification of food samples using their EEM fluorescence data.

Hydrophilic interaction chromatography combined with ultrasound-assisted ionic liquid dispersive liquid–liquid microextraction for determination of underivatized neurotransmitters in dementia patients’ urine samples

A sensitive, rapid, precise and specific analytical method of hydrophilic interaction ultra-performance liquid chromatography coupled with triple-quadrupole linear ion-trap tandem mass spectrometry (HILIC-UHPLC–QTRAP®/MS2) combined with a high-efficiency and easy sample preparation technology of ultrasound-assisted ionic liquid dispersive liquid–liquid microextraction (UA-IL-DLLME) was developed to investigate neurotransmitters (NTs) in mild cognitive impairment, mild dementia and moderate dementia patients’ urine samples. Firstly, the UA-IL-DLLME parameters were optimized using Plackett–Burman screening and rotatable central composite design, and the main optimal conditions were obtained: ultrasound power of 307 W, ultrasound time of 4.3 min and agitation time of 4.8 min. Secondly, HILIC-UHPLC–QTRAP®/MS2 method was developed to simultaneously determine 15 underivatized NTs in urine samples. The analysis results of clinical samples showed that some NTs such as γ-aminobutyric acid (GABA), acetylcholine (Ach) and glutamic acid (Glu) presented significant differences in different dementia stages. Finally, multivariate analysis based on the combination of principal component analysis and supervised counter propagation artificial neural network was developed for comprehensive analysis of the obtained clinical data sets. As a result, GABA and Glu were simultaneously presented meaningful contribution for classification of samples, and might be considered as potential differential compounds to the urine samples from cluster patients with different dementia stages. In summary, the presented strategy of preparation, analysis and statistics might be used to investigate NTs in different clinical biological fluids.