scholarly journals A FIJI macro for quantifying pattern in extracellular matrix

2021 ◽  
Vol 4 (3) ◽  
pp. e202000880
Author(s):  
Esther Wershof ◽  
Danielle Park ◽  
David J Barry ◽  
Robert P Jenkins ◽  
Antonio Rullan ◽  
...  
Keyword(s):  
Extracellular Matrix ◽  
Fractal Dimension ◽  
Quantitative Analysis ◽  
Comprehensive Description ◽  
End Points ◽  
Wide Range ◽  
Automated Pipeline ◽  
Cytoskeletal Networks ◽  
Alignment Length ◽  
Imagej Plugin

Diverse extracellular matrix patterns are observed in both normal and pathological tissue. However, most current tools for quantitative analysis focus on a single aspect of matrix patterning. Thus, an automated pipeline that simultaneously quantifies a broad range of metrics and enables a comprehensive description of varied matrix patterns is needed. To this end, we have developed an ImageJ plugin called TWOMBLI, which stands for The Workflow Of Matrix BioLogy Informatics. This pipeline includes metrics of matrix alignment, length, branching, end points, gaps, fractal dimension, curvature, and the distribution of fibre thickness. TWOMBLI is designed to be quick, versatile and easy-to-use particularly for non-computational scientists. TWOMBLI can be downloaded from https://github.com/wershofe/TWOMBLI together with detailed documentation and tutorial video. Although developed with the extracellular matrix in mind, TWOMBLI is versatile and can be applied to vascular and cytoskeletal networks. Here we present an overview of the pipeline together with examples from a wide range of contexts where matrix patterns are generated.

scholarly journals A FIJI Macro for quantifying pattern in extracellular matrix

2019 ◽  
Author(s):  
Esther Wershof ◽  
Danielle Park ◽  
David J Barry ◽  
Robert P Jenkins ◽  
Antonio Rullan ◽  
...  
Keyword(s):  
Extracellular Matrix ◽  
Quantitative Analysis ◽  
Comprehensive Description ◽  
Link Type ◽  
Wide Range ◽  
Automated Pipeline ◽  
Imagej Plugin

AbstractDiverse extracellular matrix patterns are observed in both normal and pathological tissue. However, most current tools for quantitative analysis focus on a single aspect of matrix patterning. Thus, an automated pipeline that simultaneously quantifies a broad range of metrics and enables a comprehensive description of varied matrix patterns is needed. To this end we have developed an ImageJ plugin called TWOMBLI, which stands for The Workflow Of Matrix BioLogy Informatics. TWOMBLI is designed to be quick, versatile and easy-to-use particularly for non-computational scientists. TWOMBLI can be downloaded from https://github.com/wershofe/TWOMBLI together with detailed documentation. Here we present an overview of the pipeline together with examples from a wide range of contexts where matrix patterns are generated.

Precision and bias in quantitative EDS: ASTM results

1992 ◽  
Vol 50 (2) ◽  
pp. 1654-1655
Author(s):  
John J. Friel
Keyword(s):  
Stainless Steel ◽  
Quantitative Analysis ◽  
Mechanical Alloy ◽  
Dead Time ◽  
Test Program ◽  
Round Robin Test ◽  
Wide Range ◽  
American Society ◽  
Takeoff Angle ◽  
Standardless Analysis

Committee E-04 on Metallography of the American Society for Testing and Materials (ASTM) conducted an interlaboratory round robin test program on quantitative energy dispersive spectroscopy (EDS). The test program was designed to produce data on which to base a precision and bias statement for quantitative analysis by EDS. Nine laboratories were sent specimens of two well characterized materials, a type 308 stainless steel, and a complex mechanical alloy from Inco Alloys International, Inconel® MA 6000. The stainless steel was chosen as an example of a straightforward analysis with no special problems. The mechanical alloy was selected because elements were present in a wide range of concentrations; K, L, and M lines were involved; and Ta was severely overlapped with W. The test aimed to establish limits of precision that could be routinely achieved by capable laboratories operating under real world conditions. The participants were first allowed to use their own best procedures, but later were instructed to repeat the analysis using specified conditions: 20 kV accelerating voltage, 200s live time, ∼25% dead time and ∼40° takeoff angle. They were also asked to run a standardless analysis.

Phytochemical evaluation of leaf extracts of Naringi crenulata (roxb.) Nicolson

2016 ◽  
Vol 5 (11) ◽  
pp. 5110
Author(s):  
Sartaj Ahmad Allayie ◽  
Mushtaq Ahmed Parray* ◽  
Bilal Ahmad Bhat ◽  
S. Hemalatha
Keyword(s):  
Quantitative Analysis ◽  
Solvent System ◽  
Great Promise ◽  
Phytochemical Analysis ◽  
Bioactive Constituents ◽  
Leaf Extracts ◽  
Traditional Medicines ◽  
The People ◽  
Wide Range ◽  
Rf Values

The use of traditional medicines holds a great promise as an easily available source as effective medicinal agents to cure a wide range of ailments among the people particularly in tropical developing countries like India. The present study investigates the qualitative and quantitative analysis of the major bioactive constituents of N. crenulata leaf extracts. The extractive values of aqueous, acetone and chloroform extracts were found to be 11.34, 4.24 and 6.06 respectively. Qualitative phytochemical analysis of these three solvent extracts confirm the presence of Alkaloids, Saponins, Flavonoids and Phenolic compounds in all the three extracts; however, these phytochemicals were more significant in aqueous extract. Quantitative analysis was carried out using TLC method by different solvent system. Amongst various solvent systems, Butanol: acetic acid: water (9: 0.9: 0.1 v/v/v) shows maximum resolution and number of spots produced at long UV (365 nm) and under iodine vapours. The TLC chromatograms constituted different coloured phytochemical compounds with different Rf values. It can be conveniently used to evaluate the quality of different area samples. This indicates that the leaves can be useful for treating different diseases because the therapeutic activity of a plant is due to the presence of particular class of compounds and thus can serve as potential sources of useful drugs in future.

LATTICE DYNAMICS OF THE BINARY APERIODIC CHAINS OF ATOMS I: FRACTAL DIMENSION OF PHONON SPECTRA

1995 ◽  
Vol 09 (12) ◽  
pp. 1429-1451 ◽  
Author(s):  
WŁODZIMIERZ SALEJDA
Keyword(s):  
Fractal Dimension ◽  
Lattice Dynamics ◽  
Nearest Neighbor ◽  
Average Distance ◽  
Local Maximum ◽  
Fractal Dimensions ◽  
Dimension Formula ◽  
Phonon Spectra ◽  
Wide Range ◽  
Silver Mean

The microscopic harmonic model of lattice dynamics of the binary chains of atoms is formulated and studied numerically. The dependence of spring constants of the nearest-neighbor (NN) interactions on the average distance between atoms are taken into account. The covering fractal dimensions [Formula: see text] of the Cantor-set-like phonon spec-tra (PS) of generalized Fibonacci and non-Fibonaccian aperiodic chains containing of 16384≤N≤33461 atoms are determined numerically. The dependence of [Formula: see text] on the strength Q of NN interactions and on R=mH/mL, where mH and mL denotes the mass of heavy and light atoms, respectively, are calculated for a wide range of Q and R. In particular we found: (1) The fractal dimension [Formula: see text] of the PS for the so-called goldenmean, silver-mean, bronze-mean, dodecagonal and Severin chain shows a local maximum at increasing magnitude of Q and R>1; (2) At sufficiently large Q we observe power-like diminishing of [Formula: see text] i.e. [Formula: see text], where α=−0.14±0.02 and α=−0.10±0.02 for the above specified chains and so-called octagonal, copper-mean, nickel-mean, Thue-Morse, Rudin-Shapiro chain, respectively.

Study of the low cycle fatigue of 12Cr18Ni10Ti steel based on fractal analysis and artificial intelligence approaches

2021 ◽  
Vol 87 (9) ◽  
pp. 59-67
Author(s):  
A. A. Khlybov ◽  
Yu. G. Kabaldin ◽  
M. S. Anosov ◽  
D. A. Ryabov ◽  
D. A. Shatagin
Keyword(s):  
Neural Network ◽  
Growth Rate ◽  
Fractal Dimension ◽  
Low Temperatures ◽  
Main Crack ◽  
Fatigue Loading ◽  
Wide Range ◽  
Lower Temperature ◽  
Number Of Cycles ◽  
Dimension Index

The evolution of the structure and assessment of the age limit of steel 12Cr18Ni10Ti upon fatigue loading is considered using neural network modeling and approaches of fractal analysis of the microstructure. An algorithm for processing images of the microstructures has been developed to improve their quality. An indicator of the fractal dimension of the image is used as a quantitative indicator for assessing the evolution of the microstructure of the surface metal layer. A quantitative assessment of the structures at different stress amplitudes is carried out in a wide range of low temperatures using the fractal dimension index. Correlation of the fractal dimension index with the run of the sample material is shown. The appearance of the main crack was observed in the range of 0.7 - 0.8 from the number of cycles to failure, after which the crack growth rate increased. At a lower temperature, the main crack is formed later, but further loading results in a higher crack growth rate. Formation of the secondary phases in austenitic steel at a lower temperature occurred at earlier stages than that at a temperature of t = +20°C, which led to hardening of the material. An artificial neural network (ANN) has been developed and trained for assessing structural changes in metal proceeding from the fractal dimensionality of the microstructure images at different stages of fatigue loading. The developed neural network made it possible to estimate with a sufficiently high accuracy the number of cycles before damage of the sample and the residual life of the material. Thus, the developed ANN can be used to assess the current state of the material in a wide range of low temperatures.

scholarly journals A method to construct the dynamic landscape of a bio-membrane with experiment and simulation

2022 ◽  
Vol 13 (1) ◽  
Author(s):  
Albert A. Smith ◽  
Alexander Vogel ◽  
Oskar Engberg ◽  
Peter W. Hildebrand ◽  
Daniel Huster
Keyword(s):  
Molecular Dynamics ◽  
Nmr Relaxation ◽  
Dynamics Simulation ◽  
Comprehensive Description ◽  
Correlation Times ◽  
Wide Range ◽  
Dynamic Landscape ◽  
C Nmr ◽  
Analysis Of Motion

AbstractBiomolecular function is based on a complex hierarchy of molecular motions. While biophysical methods can reveal details of specific motions, a concept for the comprehensive description of molecular dynamics over a wide range of correlation times has been unattainable. Here, we report an approach to construct the dynamic landscape of biomolecules, which describes the aggregate influence of multiple motions acting on various timescales and on multiple positions in the molecule. To this end, we use 13C NMR relaxation and molecular dynamics simulation data for the characterization of fully hydrated palmitoyl-oleoyl-phosphatidylcholine bilayers. We combine dynamics detector methodology with a new frame analysis of motion that yields site-specific amplitudes of motion, separated both by type and timescale of motion. In this study, we show that this separation allows the detailed description of the dynamic landscape, which yields vast differences in motional amplitudes and correlation times depending on molecular position.

scholarly journals Effect of Grain Size on Microscopic Pore Structure and Fractal Characteristics of Carbonate-Based Sand and Silicate-Based Sand

2021 ◽  
Vol 5 (4) ◽  
pp. 152
Author(s):  
Shao-Heng He ◽  
Zhi Ding ◽  
Hai-Bo Hu ◽  
Min Gao
Keyword(s):  
Grain Size ◽  
Fractal Dimension ◽  
Pore Structure ◽  
Pore Size ◽  
Quartz Sand ◽  
Glass Bead ◽  
Fractal Theory ◽  
Calcareous Sand ◽  
Wide Range ◽  
Fractal Characteristics

In this study, a series of nuclear magnetic resonance (NMR) tests was conducted on calcareous sand, quartz sand, and glass bead with a wide range of grain sizes, to understand the effect of grain size on the micro-pore structure and fractal characteristics of the carbonate-based sand and silicate-based sand. The pore size distribution (PSD) of the tested materials were obtained from the NMR T2 spectra, and fractal theory was introduced to describe the fractal properties of PSD. Results demonstrate that grain size has a significant effect on the PSD of carbonate-based sand and silicate-based sand. As grain size increases, the PSD of sands evolves from a binary structure with two peaks to a ternary structure with three peaks. The increase in the grain size can cause a remarkable increase in the maximum pore size. It is also found that the more irregular the particle shape, the better the continuity between the large and medium pores. In addition, grain size has a considerable effect on the fractal dimension of the micro-pore structure. The increase of grain size can lead to a significant increase in the heterogeneity and fractal dimension in PSD for calcareous sand, quartz sand and glass bead.

scholarly journals Extragalactic Supergiants

2016 ◽  
Vol 12 (S329) ◽  
pp. 297-304
Author(s):  
Miguel A. Urbaneja ◽  
Rolf P. Kudritzki
Keyword(s):  
Quantitative Analysis ◽  
Chemical Composition ◽  
Optical Spectra ◽  
Host Galaxies ◽  
High Quality ◽  
Distant Galaxies ◽  
Wide Range

AbstractBlue supergiant stars of B and A spectral types are amongst the visually brightest non-transient astronomical objects. Their intrinsic brightness makes it possible to obtain high quality optical spectra of these objects in distant galaxies, enabling the study not only of these stars in different environments, but also to use them as tools to probe their host galaxies. Quantitative analysis of their optical spectra provide tight constraints on their evolution in a wide range of metallicities, as well as on the present-day chemical composition, extinction laws and distances to their host galaxies. We review in this contribution recent results in this field.

A New Way To Detect Noncovalently Bonded Complexes of Biomolecules from Liquid Micro-Droplets by Laser Mass Spectrometry

2006 ◽  
Vol 59 (2) ◽  
pp. 109 ◽  
Author(s):  
Nina Morgner ◽  
Hans-Dieter Barth ◽  
Bernhard Brutschy
Keyword(s):  
Mass Spectrometry ◽  
Quantitative Analysis ◽  
Liquid Phase ◽  
Laser Pulses ◽  
Laser Mass Spectrometry ◽  
Native Solution ◽  
On Demand ◽  
Ir Laser ◽  
Intensity Threshold ◽  
Wide Range

A new version of laser mass-spectrometry is presented, which allows the quantitative analysis of specific biocomplexes in native solution. On-demand micro droplets, injected into vacuum, are irradiated by mid IR-laser pulses. Above a certain intensity threshold they explode due to the transmitted energy, setting free a fraction of the charged biomolecules which are then mass-analyzed. Amounts of analyte in the attomolar range may be detected with the ion intensity being linear over a wide range of molarity. Evidence is given that this method is soft, tolerant against various buffers, reflects properties of the liquid phase, and suitable for studying noncovalently bonded specific complexes. This is highlighted by results from antibiotics specifically binding into the minor groove of duplex DNA.

Differential fractal dimension is associated with extracellular matrix remodeling in developing bovine corpus luteum

2019 ◽  
Vol 516 (3) ◽  
pp. 888-893 ◽  
Author(s):  
Paola Francini Fávero ◽  
Victor Augusto Vieira de Lima ◽  
Priscila Helena dos Santos ◽  
Ana Paula Marques Andrade ◽  
Leonardo Oliveira Mendes ◽  
...  
Keyword(s):  
Extracellular Matrix ◽  
Fractal Dimension ◽  
Corpus Luteum ◽  
Extracellular Matrix Remodeling ◽  
Matrix Remodeling ◽  
Bovine Corpus Luteum
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