Multivariate analysis of a data matrix containing A-DNA and B-DNA dinucleoside monophosphate steps: Multidimensional Ramachandran plots for nucleic acids

1998 ◽  
Vol 19 (7) ◽  
pp. 695-715 ◽  
Author(s):  
M. L. M. Beckers ◽  
L. M. C. Buydens
Keyword(s):  
Multivariate Analysis ◽  
Nucleic Acids ◽  
Data Matrix ◽  
Ramachandran Plots

scholarly journals Indication of high lipid content in epithelial-mesenchymal transitions of breast tissues

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Siti Norbaini Sabtu ◽  
S. F. Abdul Sani ◽  
L. M. Looi ◽  
S. F. Chiew ◽  
Dharini Pathmanathan ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Raman Spectroscopy ◽  
Multivariate Analysis ◽  
Nucleic Acids ◽  
Raman Spectra ◽  
Cancer Progression ◽  
Component Analysis ◽  
Breast Cancer Tissue ◽  
Metabolic Changes ◽  
Cancer Tissue

AbstractThe epithelial-mesenchymal transition (EMT) is a crucial process in cancer progression and metastasis. Study of metabolic changes during the EMT process is important in seeking to understand the biochemical changes associated with cancer progression, not least in scoping for therapeutic strategies aimed at targeting EMT. Due to the potential for high sensitivity and specificity, Raman spectroscopy was used here to study the metabolic changes associated with EMT in human breast cancer tissue. For Raman spectroscopy measurements, tissue from 23 patients were collected, comprising non-lesional, EMT and non-EMT formalin-fixed and paraffin embedded breast cancer samples. Analysis was made in the fingerprint Raman spectra region (600–1800 cm−1) best associated with cancer progression biochemical changes in lipid, protein and nucleic acids. The ANOVA test followed by the Tukey’s multiple comparisons test were conducted to see if there existed differences between non-lesional, EMT and non-EMT breast tissue for Raman spectroscopy measurements. Results revealed that significant differences were evident in terms of intensity between the non-lesional and EMT samples, as well as the EMT and non-EMT samples. Multivariate analysis involving independent component analysis, Principal component analysis and non-negative least square were used to analyse the Raman spectra data. The results show significant differences between EMT and non-EMT cancers in lipid, protein, and nucleic acids. This study demonstrated the capability of Raman spectroscopy supported by multivariate analysis in analysing metabolic changes in EMT breast cancer tissue.

Multivariate Analysis of Mixed Lipid Aggregate Phase Transitions Monitored Using Raman Spectroscopy

2017 ◽  
Vol 72 (1) ◽  
pp. 102-113 ◽  
Author(s):  
Sharon L. Neal
Keyword(s):  
Raman Spectroscopy ◽  
Multivariate Analysis ◽  
Minor Component ◽  
Data Matrix ◽  
Melting Transition ◽  
Spectral Features ◽  
Temperature Dependent ◽  
Spectral Parameters ◽  
Spectral Matrix ◽  
Lipid Response

The phase behavior of aqueous 1,2-dimyristoyl-sn-glycero-3-phosphorylcholine (DMPC)/1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC) mixtures between 8.0 ℃ and 41.0 ℃ were monitored using Raman spectroscopy. Temperature-dependent Raman matrices were assembled from series of spectra and subjected to multivariate analysis. The consensus of pseudo-rank estimation results is that seven to eight components account for the temperature-dependent changes observed in the spectra. The spectra and temperature response profiles of the mixture components were resolved by applying a variant of the non-negative matrix factorization (NMF) algorithm described by Lee and Seung (1999). The rotational ambiguity of the data matrix was reduced by augmenting the original temperature-dependent spectral matrix with its cumulative counterpart, i.e., the matrix formed by successive integration of the spectra across the temperature index (columns). Successive rounds of constrained NMF were used to isolate component spectra from a significant fluorescence background. Five major components exhibiting varying degrees of gel and liquid crystalline lipid character were resolved. Hydrogen-bonded water networks exhibiting varying degrees of organization are associated with the lipid components. Spectral parameters were computed to compare the chain conformation, packing, and hydration indicated by the resolved spectra. Based on spectral features and relative amounts of the components observed, four components reflect long chain lipid response. The fifth component could reflect the response of the short chain lipid, DHPC, but there were no definitive spectral features confirming this assignment. A minor component of uncertain assignment that exhibits a striking response to the DMPC pre-transition and chain melting transition also was recovered. While none of the spectra resolved exhibit features unequivocally attributable to a specific aggregate morphology or step in the gelation process, the results are consistent with the evolution of mixed phase bicelles (nanodisks) and small amounts of worm-like DMPC/DHPC aggregates, and perhaps DHPC micelles, at low temperature to suspensions of branched and entangled worm-like aggregates above the DMPC gel phase transition and perforated multi-lamellar aggregates at high temperature.

Investigating temperature-induced structural changes of lead halide perovskites by in situ X-ray powder diffraction

2019 ◽  
Vol 52 (5) ◽  
pp. 1104-1118
Author(s):  
Rocco Caliandro ◽  
Davide Altamura ◽  
Benny Danilo Belviso ◽  
Aurora Rizzo ◽  
Sofia Masi ◽  
...  
Keyword(s):  
Multivariate Analysis ◽  
Structural Changes ◽  
Lattice Distortion ◽  
Data Matrix ◽  
Cubic Phase ◽  
X Ray Diffraction ◽  
Temperature Variations ◽  
Temperature Changes ◽  
X Ray

In situ X-ray diffraction experiments offer a unique opportunity to investigate structural dynamics at atomic resolution, by collecting several patterns in an appropriate time sequence (data matrix) while varying the applied stimulus (e.g. temperature changes). Individual measurements can be processed independently by refinement procedures that are based on prior knowledge of the average structure of each crystal phase present in the sample. If the refinement converges, parameters of the average structural model can be assessed and studied as a function of the stimulus variations. An alternative approach consists in applying a multivariate analysis to the data matrix as a whole. Methods such as principal component analysis (PCA) and phase-sensitive detection perform fast, blind and model-independent calculations that can be used for on-site analysis to identify trends in data actually related to the applied stimulus. Both classical and multivariate approaches are here applied to the in situ X-ray diffraction pair distribution function (PDF) setup on two samples of the hybrid perovskite methylammonium (MA) lead iodide obtained by different synthetic routes, subjected to temperature variations. The PDF refinement allows assessing the occurrence of temperature-induced rotations of the PbI6 octahedra and variations in the relative amount of MAPbI3 and intermediate PbI2–MAI–DMSO (dimethyl sulfoxide) crystal phases. A change in the orientation of the methylammonium molecule with temperature is also characterized. Results of the multivariate analysis tools, which include a newly introduced space-dependent variant of PCA, are described, interpreted and validated against simulated data, and their specificity and relation to refinement results are highlighted. The interaction between nearby octahedra is identified as the driving force for the tetragonal-to-cubic phase transition, and three fundamental trends in data having different temperature behaviours are unveiled: (i) irreversible weight-fraction variations of the MAPbI3 and PbI2–MAI–DMSO phases; (ii) reversible structural changes related to the MAPbI3 crystalline phase and its lattice distortion in the ab plane, having the same frequency as the temperature variations; (iii) reversible lattice distortion along the c axis, occurring at twice the frequency of the temperature changes.

Effect of mass segment size on polymer ToF-SIMS multivariate analysis using a universal data matrix

2019 ◽  
Vol 478 ◽  
pp. 465-477 ◽  
Author(s):  
Robert M.T. Madiona ◽  
David A. Winkler ◽  
Benjamin W. Muir ◽  
Paul J. Pigram
Keyword(s):  
Multivariate Analysis ◽  
Data Matrix ◽  
Segment Size ◽  
Tof Sims

scholarly journals Optinalysis: A New Approach of Multivariate Analysis through A Looking-Glass

2019 ◽  
Author(s):  
Kabir Bindawa Abdullahi
Keyword(s):  
Multivariate Analysis ◽  
T Test ◽  
Data Matrix ◽  
Data Types ◽  
New Approach ◽  
Alternative Approach ◽  
Simple Alternative ◽  
Algorithmic Analysis ◽  
Looking Glass ◽  
One Way Anova

Optinalysis, as a method of symmetry detection, is a new advanced computational algorithm that intrametrically (within elements) or intermetrically (between elements) computes and compares two or more multivariate sequences in an unclustered or clustered manner as a mirror-like reflection of each other (optics-like manner), hence the name is driven. Optinalysis is based by the principles of reflection and moment about a symmetrical line which detects symmetry that reflects a similarity measurement. Optinalysis is suitable for quantitative and qualitative data types, with or without replications, provided it conform the algorithmic requirements there provided. Optinalysis can be organized for geometrical, geostatistical and statistical analysis in one-way, two-way, or three-way approach. A simulation comparisons shows that Optinalysis is a simple alternative approach of multivariate analysis of sociometric, demographic, socio-demographic, psychometric, ecological, experimental, genomic, nanoparticle and shape morphometric data. Optinalysis of these data matrix shows very similar results or conclusions with some multivariate analysis such as skewness measure, one-way ANOVA, paired t-test, one sample t-test, Tukey’s multiple comparisons, BLAST sequence algorithmic analysis (percentages of identity, similarity, gabs, and positives, and the Needleman-Wunsch score), and Riemannian distance.

scholarly journals PHENETIC AND UNSUPERVISED MULTIVARIATE ANALYSIS SYZYGIUM POLYANTHUM (WIGHT) WALP

2021 ◽  
Vol 52 (1) ◽  
pp. 249-258
Author(s):  
Abdulrahman & et al.
Keyword(s):  
Multivariate Analysis ◽  
Woody Plants ◽  
De Novo ◽  
Morphological Variability ◽  
Principal Component ◽  
Hierarchical Cluster ◽  
Peninsular Malaysia ◽  
Data Matrix ◽  
Documented Information ◽  
Study Species

Myrtaceae family is widely distributed in Asia has been the largest group of plant; mainly trees and few shrubs. Distributed all over the world in tropical and subtropical areas. Syzygium is the largest genus with economical value found all over the Malaysian Peninsular. Evolutionary relationships within the Syzygium is unclear and there are currently no reliable criteria to divide the genus into manageable entities for systematic study. Species of Syzygium is the richest genus of woody plants in South East Asia with approximately 1000 or more species but little is known about the genus. Syzygium polyanthum Wight is one of the favourites Ulam that have been consumed for ages in Peninsular Malaysia and also as herbal medicine. The species is widely misunderstood due to extreme morphological variability, similarity in aroma and flavor. The species is substituted or adulterated with several other species. The study was aimed to construct phenetic tree and unsupervised multivariate analysis from morphological and anatomical the data matrix.  Phenetic analysis, Principal component and hierarchical cluster analysis revealed they are two different cultivars species  but inter variation exited among cultivars of same species.  The above documented information has added new  taxonomic information with regard to the identification of the cultivars in Peninsular Malaysia. The study recommends further study on de novo sequence of Serai kayu and Serai kayu hutan.

Statistical analysis of classification

1966 ◽  
Vol 24 ◽  
pp. 188-189
Author(s):  
T. J. Deeming
Keyword(s):  
Multivariate Analysis ◽  
Statistical Analysis ◽  
Classification Scheme ◽  
Analytical Procedure ◽  
Narrow Band ◽  
Scientific Research ◽  
Maximum Amount ◽  
Amount Of Information

If we make a set of measurements, such as narrow-band or multicolour photo-electric measurements, which are designed to improve a scheme of classification, and in particular if they are designed to extend the number of dimensions of classification, i.e. the number of classification parameters, then some important problems of analytical procedure arise. First, it is important not to reproduce the errors of the classification scheme which we are trying to improve. Second, when trying to extend the number of dimensions of classification we have little or nothing with which to test the validity of the new parameters.Problems similar to these have occurred in other areas of scientific research (notably psychology and education) and the branch of Statistics called Multivariate Analysis has been developed to deal with them. The techniques of this subject are largely unknown to astronomers, but, if carefully applied, they should at the very least ensure that the astronomer gets the maximum amount of information out of his data and does not waste his time looking for information which is not there. More optimistically, these techniques are potentially capable of indicating the number of classification parameters necessary and giving specific formulas for computing them, as well as pinpointing those particular measurements which are most crucial for determining the classification parameters.

Electron Microscopy of Nucleic Acids

1974 ◽  
Vol 32 ◽  
pp. 302-303
Author(s):  
Norman Davidson
Keyword(s):  
Electron Microscopy ◽  
Nucleic Acids ◽  
Basic Protein ◽  
Molecular Biologist ◽  
Topological Properties ◽  
Protein Film ◽  
Polynucleotide Chain

The basic protein film technique for mounting nucleic acids for electron microscopy has proven to be a general and powerful tool for the working molecular biologist in characterizing different nucleic acids. It i s possible to measure molecular lengths of duplex and single-stranded DNAs and RNAs. In particular, it is thus possible to as certain whether or not the nucleic acids extracted from a particular source are or are not homogeneous in length. The topological properties of the polynucleotide chain (linear or circular, relaxed or supercoiled circles, interlocked circles, etc. ) can also be as certained.

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