scholarly journals Partial Least-Squares Discriminant Analysis and Ensemble-Based Flexible Docking of PD-1/PD-L1 Inhibitors: A Pilot Study

ACS Omega ◽  
2020 ◽  
Vol 5 (41) ◽  
pp. 26914-26923
Author(s):  
Zuyin Kuang ◽  
Yu Heng ◽  
Shuheng Huang ◽  
Tingting Shi ◽  
Linxin Chen ◽  
...  
Keyword(s):  
Discriminant Analysis ◽  
Pilot Study ◽  
Least Squares ◽  
Partial Least Squares ◽  
Flexible Docking

Sparse Partial-least-squares Discriminant Analysis for Different Geographical Origins of Salvia miltiorrhiza by 1 H-NMR-based Metabolomics

2013 ◽  
Vol 25 (1) ◽  
pp. 50-58 ◽  
Author(s):  
Miaomiao Jiang ◽  
Chunhua Wang ◽  
Yu Zhang ◽  
Yifan Feng ◽  
Yuefei Wang ◽  
...  
Keyword(s):  
Discriminant Analysis ◽  
Least Squares ◽  
Partial Least Squares ◽  
Salvia Miltiorrhiza ◽  
H Nmr

scholarly journals 1H-NMR spectroscopy identifies potential biomarkers in serum metabolomic signatures for early stage esophageal squamous cell carcinoma

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e8151 ◽  
Author(s):  
Yan-Yan Liu ◽  
Zhong-Xian Yang ◽  
Li-Min Ma ◽  
Xu-Qing Wen ◽  
Huan-Lin Ji ◽  
...  
Keyword(s):  
Squamous Cell Carcinoma ◽  
Discriminant Analysis ◽  
Nmr Spectroscopy ◽  
Esophageal Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Least Squares ◽  
Partial Least Squares ◽  
Early Stage ◽  
H Nmr ◽  
Potential Biomarkers

Background Esophageal squamous cell carcinoma (ESCC) is one of the most prevalent types of upper gastrointestinal malignancies. Here, we used 1H nuclear magnetic resonance spectroscopy (1H-NMR) to identify potential serum biomarkers in patients with early stage ESCC. Methods Sixty-five serum samples from early stage ESCC patients (n = 25) and healthy controls (n = 40) were analysed using 1H-NMR spectroscopy. We distinguished between different metabolites through principal component analysis, partial least squares-discriminant analysis, and orthogonal partial least squares-discriminant analysis (OPLS-DA) using SIMCA-P+ version 14.0 software. Receiver operating characteristic (ROC) analysis was conducted to verify potential biomarkers. Results Using OPLS-DA, 31 altered serum metabolites were successfully identified between the groups. Based on the area under the ROC curve (AUROC), and the biomarker panel with AUROC of 0.969, six serum metabolites (α-glucose, choline, glutamine, glutamate, valine, and dihydrothymine) were selected as potential biomarkers for early stage ESCC. Dihydrothymine particularly was selected as a new feasible biomarker associated with tumor occurrence. Conclusions 1H-NMR spectroscopy may be a useful tumour detection approach in identifying useful metabolic ESCC biomarkers for early diagnosis and in the exploration of the molecular pathogenesis of ESCC.

scholarly journals Human Melanoma-Cell Metabolic Profiling: Identification of Novel Biomarkers Indicating Metastasis

2020 ◽  
Vol 21 (7) ◽  
pp. 2436 ◽  
Author(s):  
Mariangela Kosmopoulou ◽  
Aikaterini F. Giannopoulou ◽  
Aikaterini Iliou ◽  
Dimitra Benaki ◽  
Aristeidis Panagiotakis ◽  
...  
Keyword(s):  
Discriminant Analysis ◽  
High Resolution ◽  
Least Squares ◽  
Partial Least Squares ◽  
Cell Lines ◽  
High Performance ◽  
Principal Component ◽  
Metastatic Tumor ◽  
Human Melanoma ◽  
Melanoma Metastasis

Melanoma is the most aggressive type of skin cancer, leading to metabolic rewiring and enhancement of metastatic transformation. Efforts to improve its early and accurate diagnosis are largely based on preclinical models and especially cell lines. Hence, we herein present a combinational Nuclear Magnetic Resonance (NMR)- and Ultra High Performance Liquid Chromatography-High-Resolution Tandem Mass Spectrometry (UHPLC-HRMS/MS)-mediated untargeted metabolomic profiling of melanoma cells, to landscape metabolic alterations likely controlling metastasis. The cell lines WM115 and WM2664, which belong to the same patient, were examined, with WM115 being derived from a primary, pre-metastatic, tumor and WM2664 clonally expanded from lymph-node metastases. Metabolite samples were analyzed using NMR and UHPLC-HRMS. Multivariate statistical analysis of high resolution NMR and MS (positive and negative ionization) results was performed by Principal Component Analysis (PCA), Partial Least Squares-Discriminant Analysis (PLS-DA) and Orthogonal Partial Least Squares-Discriminant Analysis (OPLS-DA), while metastasis-related biomarkers were determined on the basis of VIP lists, S-plots and Student’s t-tests. Receiver Operating Characteristic (ROC) curves of NMR and MS data revealed significantly differentiated metabolite profiles for each cell line, with WM115 being mainly characterized by upregulated levels of phosphocholine, choline, guanosine and inosine. Interestingly, WM2664 showed notably increased contents of hypoxanthine, myo-inositol, glutamic acid, organic acids, purines, pyrimidines, AMP, ADP, ATP and UDP(s), thus indicating the critical roles of purine, pyrimidine and amino acid metabolism during human melanoma metastasis.

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