The use of cluster and discriminant analysis in the investigations of the role of trace metals in the pathogenesis of Parkinson’s disease

Chwiej, Joanna

doi:10.1016/j.jtemb.2009.11.002

Cited by 18 publications

(15 citation statements)

References 54 publications

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“…As can be seen from the existing literature, multivariate methods, also known as chemometrics, are frequently used in the analysis of elemental data especially in the field of life sciences [24,[33][34][35][36][37][38][39][40][41]. For example, hierarchical cluster analysis was successfully applied for the prediction of cancerrelated Cu-binding proteins, which can serve as a source for mechanistic-molecular studies of Cu-dependent processes in cancer [42].…”

Section: Discussionmentioning

confidence: 99%

“…In turn, discriminant analysis was adapted inter alia, for characterization of metal profiles within serum in Alzheimer's disease [34] and gouty arthritis [44] as well as identification of metal biomarkers of different cancers in human tissues [39,45,46]. In the literature, there are also many examples of the chemometric method application in the research utilizing X-ray fluorescencebased techniques [24,36,38,47,48]. Both multivariate methods, which were used in the study, proved that the elemental composition of examined organs is so unique that enables to correctly classify them into the groups that were separated during analysis or defined a priori.…”

Section: Discussionmentioning

confidence: 99%

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Organ Metallome Processed with Chemometric Methods Enable the Determination of Elements that May Serve as Markers of Exposure to Iron Oxide Nanoparticles in Male Rats

Rugieł

Dróżdż

Matusiak

et al. 2020

Biol Trace Elem Res

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The systemic influence of iron oxide nanoparticles on the elemental homeostasis of key organs was examined in male rats. In tissues taken at different intervals from nanoparticles injection, the dynamics of elemental changes was analyzed. The organ metallome was studied using total reflection X-ray fluorescence. The obtained data were processed with advanced cluster and discriminant analyses-to classify the tissues according to their organs of origin and to distinguish accurately the nanoparticletreated and normal rats. Additionally, in the case of liver and heart, it was possible to determine the elements of highest significance for different treatments, which may serve as markers of exposure to iron oxide nanoparticles.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Organ Metallome Processed with Chemometric Methods Enable the Determination of Elements that May Serve as Markers of Exposure to Iron Oxide Nanoparticles in Male Rats

Rugieł

Dróżdż

Matusiak

et al. 2020

Biol Trace Elem Res

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“…Hence, PCA has been used for feature reduction and classificatory methods then employed to distinguish between AD, mild cognitive impairment (MCI), and control cases [80]. By contrast, a combination of HCA and discriminant analysis was used to distinguish among concentrations of various elements in the substantia nigra of Parkinson's disease (PD) and controls using X-ray fluorescent microscopy [23]. Various methods of classifying MRI data have been compared including O-PLS, DTA, ANN, and SVM, slightly better results being achieved using SVM and O-PLS [2,65].…”

Section: Discussionmentioning

confidence: 99%

The quantitative analysis of neurodegenerative disease: classification, noda, constellations, and multivariate geometry

Armstrong¹

2018

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A variety of methods are available for the quantitative description and analysis of neurodegenerative disease. If neurodegenerative disease exists as a series of distinct disorders, then classificatory methods such as hierarchical cluster analysis (HCA) and decision tree analysis (DTA) can be used to classify cases into groups more objectively. If neurodegenerative disease consists of overlapping phenotypes, then the Braun-Blanquet 'nodal' system and 'constellation diagrams' implicitly recognise intermediate cases and reveal their relationships to the main groupings. By contrast, if cases are more continuously distributed without easily distinguishable disease entities, then methods based on spatial geometry, such as a triangular system or principal components analysis (PCA), may be more appropriate as they display cases spatially according to their similarities and differences. This review compares the different methods and concludes that as a result of the heterogeneity and overlap commonly present plus the multiplicity of possible descriptive variables, methods such as PCA are likely to be particularly useful in the quantitative analysis of neurodegenerative disease. A more general application of such methods, however, has implications for studies of disease risk factors and pathogenesis and in clinical trials.

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“…In between these two extreme cases, X-ray microscopy (XM) is a valuable tool to the field of neuroscience, with increasing application. [15][16][17][18][19][20] Up to now the most studies using different X-ray microscopes were performed on tissues isolated from different brain tumors by using X-ray fluorescence imaging at low resolution, with pixel size of 15 μm. 21 Even more importantly, before this work the only GBM samples investigated by XFM used cell culture cell lines such as U87MG cells.…”

Section: Discussionmentioning

confidence: 99%

Structural and elemental changes in glioblastoma cells in situ: complementary imaging with high resolution visible light- and X-ray microscopy

Dučić

Paunesku

Chen

et al. 2017

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The glioblastoma (GBM) is characterized by a short median survival and an almost 100% tumor related mortality. GBM cells exhibit highly invasive behavior whose mechanisms are not yet fully understood. The present study explores application of X-ray and visible light microscopy to display the elemental and structural images of cells from 3 patient derived GMB samples and an established GMB cell line. Slight differences in elemental concentrations, in actin cytoskeleton organization and cell morphology were noted between all cells types by X-ray fluorescence and full field soft X-ray microscopy, as well as the Structured Illumination Super-resolution Microscope (SIM). Different sample preparation approaches were used to match each imaging technique. While preparation for SIM included cell fixation and staining, intact frozen hydrated cells were used for the trace element imaging by hard X-ray fluorescence and exploration of the structural features by soft X-ray absorption tomography. Each technique documented differences between samples with regard to morphology and elemental composition and underscored the importance of use of multiple patient derived samples for detailed GBM study.

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The use of cluster and discriminant analysis in the investigations of the role of trace metals in the pathogenesis of Parkinson’s disease

Cited by 18 publications

References 54 publications

Organ Metallome Processed with Chemometric Methods Enable the Determination of Elements that May Serve as Markers of Exposure to Iron Oxide Nanoparticles in Male Rats

Organ Metallome Processed with Chemometric Methods Enable the Determination of Elements that May Serve as Markers of Exposure to Iron Oxide Nanoparticles in Male Rats

The quantitative analysis of neurodegenerative disease: classification, noda, constellations, and multivariate geometry

Structural and elemental changes in glioblastoma cells in situ: complementary imaging with high resolution visible light- and X-ray microscopy

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