scholarly journals A Workflow for Rapid Unbiased Quantification of Fibrillar Feature Alignment in Biological Images

2021 ◽  
Vol 3 ◽  
Author(s):  
Stefania Marcotti ◽  
Deandra Belo de Freitas ◽  
Lee D Troughton ◽  
Fiona N Kenny ◽  
Tanya J Shaw ◽  
...  
Keyword(s):  
Fourier Transforms ◽  
Image Feature ◽  
Global Alignment ◽  
Length Scale ◽  
Desktop Computer ◽  
Length Scales ◽  
Advantages And Disadvantages ◽  
Segmentation Methods ◽  
Wide Range ◽  
Feature Alignment

Measuring the organization of the cellular cytoskeleton and the surrounding extracellular matrix (ECM) is currently of wide interest as changes in both local and global alignment can highlight alterations in cellular functions and material properties of the extracellular environment. Different approaches have been developed to quantify these structures, typically based on fiber segmentation or on matrix representation and transformation of the image, each with its own advantages and disadvantages. Here we present AFT − Alignment by Fourier Transform, a workflow to quantify the alignment of fibrillar features in microscopy images exploiting 2D Fast Fourier Transforms (FFT). Using pre-existing datasets of cell and ECM images, we demonstrate our approach and compare and contrast this workflow with two other well-known ImageJ algorithms to quantify image feature alignment. These comparisons reveal that AFT has a number of advantages due to its grid-based FFT approach. 1) Flexibility in defining the window and neighborhood sizes allows for performing a parameter search to determine an optimal length scale to carry out alignment metrics. This approach can thus easily accommodate different image resolutions and biological systems. 2) The length scale of decay in alignment can be extracted by comparing neighborhood sizes, revealing the overall distance that features remain anisotropic. 3) The approach is ambivalent to the signal source, thus making it applicable for a wide range of imaging modalities and is dependent on fewer input parameters than segmentation methods. 4) Finally, compared to segmentation methods, this algorithm is computationally inexpensive, as high-resolution images can be evaluated in less than a second on a standard desktop computer. This makes it feasible to screen numerous experimental perturbations or examine large images over long length scales. Implementation is made available in both MATLAB and Python for wider accessibility, with example datasets for single images and batch processing. Additionally, we include an approach to automatically search parameters for optimum window and neighborhood sizes, as well as to measure the decay in alignment over progressively increasing length scales.

scholarly journals A Workflow for Rapid Unbiased Quantification of Fibrillar Feature Alignment in Biological Images

2021 ◽  
Author(s):  
Stefania Marcotti ◽  
Deandra Belo de Freitas ◽  
Lee D Troughton ◽  
Fiona N Kenny ◽  
Tanya J Shaw ◽  
...  
Keyword(s):  
Fourier Transforms ◽  
Image Feature ◽  
Global Alignment ◽  
Length Scale ◽  
Desktop Computer ◽  
Length Scales ◽  
Advantages And Disadvantages ◽  
Segmentation Methods ◽  
Wide Range ◽  
Feature Alignment

Measuring the organisation of the cellular cytoskeleton and the surrounding extracellular matrix (ECM) is currently of wide interest as changes in both local and global alignment can highlight alterations in cellular functions and material properties of the extracellular environment. Different approaches have been developed to quantify these structures, typically based on fibre segmentation or on matrix representation and transformation of the image, each with its own advantages and disadvantages. Here we present AFT −Alignment by Fourier Transform, a workflow to quantify the alignment of fibrillar features in microscopy images exploiting 2D Fast Fourier Transforms (FFT). Using pre- existing datasets of cell and ECM images, we demonstrate our approach and compare and contrast this workflow with two other well-known ImageJ algorithms to quantify image feature alignment. These comparisons reveal that AF T has a number of advantages due to its grid-based FFT approach. 1) Flexibility in defining the window and neighbourhood sizes allows for performing a parameter search to determine an optimal length scale to carry out alignment metrics. This approach can thus easily accommodate different image resolutions and biological systems. 2) The length scale of decay in alignment can be extracted by comparing neighbourhood sizes, revealing the overall distance that features remain anisotropic. 3) The approach is ambivalent to the signal source, thus making it applicable for a wide range of imaging modalities and is dependent on fewer input parameters than segmentation methods. 4) Finally, compared to segmentation methods, this algorithm is computationally inexpensive, as high-resolution images can be evaluated in less than a second on a standard desktop computer. This makes it feasible to screen numerous experimental perturbations or examine large images over long length scales. Implementation is made available in both MATLAB and Python for wider accessibility, with example datasets for single images and batch processing. Additionally, we include an approach to automatically search parameters for optimum window and neighbourhood sizes, as well as to measure the decay in alignment over progressively increasing length scales.

scholarly journals Subject-specific multiscale modeling of aortic valve biomechanics

2021 ◽  
Author(s):  
G. Rossini ◽  
A. Caimi ◽  
A. Redaelli ◽  
E. Votta
Keyword(s):  
Aortic Valve ◽  
Boundary Conditions ◽  
Narrow Range ◽  
Radial Strain ◽  
Length Scale ◽  
Length Scales ◽  
Anatomical Features ◽  
Wide Range ◽  
Subject Specific ◽  
Cell Strains

AbstractA Finite Element workflow for the multiscale analysis of the aortic valve biomechanics was developed and applied to three physiological anatomies with the aim of describing the aortic valve interstitial cells biomechanical milieu in physiological conditions, capturing the effect of subject-specific and leaflet-specific anatomical features from the organ down to the cell scale. A mixed approach was used to transfer organ-scale information down to the cell-scale. Displacement data from the organ model were used to impose kinematic boundary conditions to the tissue model, while stress data from the latter were used to impose loading boundary conditions to the cell level. Peak of radial leaflet strains was correlated with leaflet extent variability at the organ scale, while circumferential leaflet strains varied over a narrow range of values regardless of leaflet extent. The dependency of leaflet biomechanics on the leaflet-specific anatomy observed at the organ length-scale is reflected, and to some extent emphasized, into the results obtained at the lower length-scales. At the tissue length-scale, the peak diastolic circumferential and radial stresses computed in the fibrosa correlated with the leaflet surface area. At the cell length-scale, the difference between the strains in two main directions, and between the respective relationships with the specific leaflet anatomy, was even more evident; cell strains in the radial direction varied over a relatively wide range ($$0.36-0.87$$ 0.36 - 0.87 ) with a strong correlation with the organ length-scale radial strain ($$R^{2}= 0.95$$ R 2 = 0.95 ); conversely, circumferential cell strains spanned a very narrow range ($$0.75-0.88$$ 0.75 - 0.88 ) showing no correlation with the circumferential strain at the organ level ($$R^{2}= 0.02$$ R 2 = 0.02 ). Within the proposed simulation framework, being able to account for the actual anatomical features of the aortic valve leaflets allowed to gain insight into their effect on the structural mechanics of the leaflets at all length-scales, down to the cell scale.

scholarly journals Derivation of Canopy Resistance in Turbulent Flow from First-Order Closure Models

Water ◽  
2018 ◽  
Vol 10 (12) ◽  
pp. 1782 ◽  
Author(s):  
Wei-Jie Wang ◽  
Wen-Qi Peng ◽  
Wen-Xin Huai ◽  
Gabriel Katul ◽  
Xiao-Bo Liu ◽  
...  
Keyword(s):  
Friction Factor ◽  
Free Surface Flows ◽  
Hydrodynamic Resistance ◽  
Small Scale ◽  
Length Scale ◽  
Length Scales ◽  
First Order ◽  
Closure Models ◽  
Wide Range ◽  
The Mean

Quantification of roughness effects on free surface flows is unquestionably necessary when describing water and material transport within ecosystems. The conventional hydrodynamic resistance formula empirically shows that the Darcy–Weisbach friction factor f~(r/hw)1/3 describes the energy loss of flowing water caused by small-scale roughness elements characterized by size r (<<hw), where hw is the water depth. When the roughness obstacle size becomes large (but <hw) as may be encountered in flow within canopies covering wetlands or river ecosystem, the f becomes far more complicated. The presence of a canopy introduces additional length scales above and beyond r/hw such as canopy height hv, arrangement density m, frontal element width D, and an adjustment length scale that varies with the canopy drag coefficient Cd. Linking those length scales to the friction factor f frames the scope of this work. By adopting a scaling analysis on the mean momentum equation and closing the turbulent stress with a first-order closure model, the mean velocity profile, its depth-integrated value defining the bulk velocity, as well as f can be determined. The work here showed that f varies with two dimensionless groups that depend on the canopy submergence depth and a canopy length scale. The relation between f and these two length scales was quantified using first-order closure models for a wide range of canopy and depth configurations that span much of the published experiments. Evaluation through experiments suggests that the proposed model can be imminently employed in eco-hydrology or eco-hydraulics when using the De Saint-Venant equations.

Experiments on turbulence in a rotating fluid

1975 ◽  
Vol 68 (4) ◽  
pp. 639-672 ◽  
Author(s):  
A. Ibbetson ◽  
D. J. Tritton
Keyword(s):  
Rotation Rate ◽  
Rotation Axis ◽  
Turbulence Energy ◽  
Length Scale ◽  
Grid Turbulence ◽  
Rotating Fluid ◽  
Mean Flow ◽  
Length Scales ◽  
Wide Range ◽  
Energy Sink

Experiments have been carried out to investigate the effect of rotation of the whole system on decaying turbulence, generally similar to grid turbulence, generated in air in an annular container on a rotating table. Measurements to determine the structure of the turbulence were made during its decay, mean quantities being determined by a mixture of time and ensemble averaging. Quantities measured (as functions of time after the turbulence generation) were turbulence intensities perpendicular to and parallel to the rotation axis, spectra of these two components with respect to a wavenumber perpendicular to the rotation axis, and some correlation coefficients, selected to detect differences in length scales perpendicular and parallel to the rotation axis. The intensity measurements were made for a wide range of rotation rates; the other measurements were made at a single rotation rate (selected to give a Rossby number varying during the decay from about 1 to small values) and, for comparison, at zero rotation. Subsidiary experiments were carried out to measure the spin-up time of the system, and to determine whether the turbulence produced any mean flow relative to the container.A principal result is that increasing the rotation rate produces faster decay of the turbulence; the nature of the additional energy sink is an important part of the interpretation. Other features of the results are as follows: the measurements with-outrotation can be satisfactorily related to wind-tunnel measurements; even with rotation, the ratio of the intensities in the two directions remains substantially constant; the normalized spectra for the rotating and the non-rotating cases show surprising similarity but do contain slight systematic differences, consistent with the length scales indicated by the correlations; rotation produces a large increase in the length scale parallel to the rotation axis and a smaller increase in that perpendicular to it; the turbulence produces no measurable mean flow.A model for the interpretation of the results is developed in terms of the action of inertial waves in carrying energy to the boundaries of the enclosure, where it is dissipated in viscous boundary layers. The model provides satisfactory explanations of the overall decay of the turbulence and of the decay of individual spectral components. Transfer of energy between wavenumbers plays a much less significant role in the dynamics of decay than in a non-rotating fluid. The relationship of the model to the interpretation of the length-scale difference in terms of the Taylor-Proudman theorem is discussed.The model implies that the overall dimensions of the system enter in an important way into the dynamics. This imposes a serious limitation on the application of the results to the geophysical situations at which experiments of this type are aimed.The paper includes some discussion of the possibility of energy transfer from the turbulence to a mean motion (the ‘vorticity expulsion’ hypothesis). It is possible, on the basis of the observations, to exclude this process as the additional turbulence energy sink. But this does not provide any evidence either for or against the hypothesis in the conditions for which it has been postulated.

The Management of Post-Tonsillectomy Morbidity in Patients With Sleep Apnoea

2019 ◽  
Vol 70 (10) ◽  
pp. 3738-3740
Keyword(s):  
Day Surgery ◽  
Sleep Apnoea ◽  
Integrative Approach ◽  
Multicenter Studies ◽  
Therapeutic Modalities ◽  
Advantages And Disadvantages ◽  
Obstructive Sleep ◽  
Wide Range ◽  
The Impact ◽  
Surgery Center

The Tonsillectomy in children or adults is an intervention commonly encountered in the ENT (Ear Nose and Throat) and Head and Neck surgeon practice. The current tendency is to perform this type of surgery in major ambulatory surgery centers. Two objectives are thus pursued: first of all, the increase of the patient quality of life through the reintegration into the family as quickly as possible and secondly, the expenses associated with continuous hospitalization are reduced. Any tertiary (multidisciplinary) sleep center must ensure the complete diagnosis and treatment (including surgery) of sleep respiratory disorders. Under these conditions the selection of patients and especially the implementation of the specific protocols in order to control the postoperative complications it becomes essential. The present paper describes our experience of tonsillectomy as treatment for selected patients with chronic rhonchopathy (snoring) and mild to moderate obstructive sleep apnoea. It was presented the impact of antibiotics protocols in reducing the main morbid outcomes following tonsillectomy, in our day surgery center. The obtained results can also be a prerequisite for the integrative approach of the patients with sleep apnoea who were recommended surgical treatment. Considering the wide range of therapeutic modalities used in sleep apnoea, each with its specific advantages and disadvantages, more extensive and multicenter studies are needed. Keywords: post-tonsillectomy morbidity, day surgery center, sleep disorders

scholarly journals Advancements in Assessments of Bio-Tissue Engineering and Viable Cell Delivery Matrices Using Bile Acid-Based Pharmacological Biotechnologies

Nanomaterials ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1861
Author(s):  
Armin Mooranian ◽  
Melissa Jones ◽  
Corina Mihaela Ionescu ◽  
Daniel Walker ◽  
Susbin Raj Wagle ◽  
...  
Keyword(s):  
Tissue Engineering ◽  
Viable Cell ◽  
Cell Delivery ◽  
Artificial Organ ◽  
Bioartificial Pancreas ◽  
Advantages And Disadvantages ◽  
Wide Range ◽  
Bioartificial Organs ◽  
Significant Interest ◽  
Modern Technologies

The utilisation of bioartificial organs is of significant interest to many due to their versatility in treating a wide range of disorders. Microencapsulation has a potentially significant role in such organs. In order to utilise microcapsules, accurate characterisation and analysis is required to assess their properties and suitability. Bioartificial organs or transplantable microdevices must also account for immunogenic considerations, which will be discussed in detail. One of the most characterized cases is the investigation into a bioartificial pancreas, including using microencapsulation of islets or other cells, and will be the focus subject of this review. Overall, this review will discuss the traditional and modern technologies which are necessary for the characterisation of properties for transplantable microdevices or organs, summarizing analysis of the microcapsule itself, cells and finally a working organ. Furthermore, immunogenic considerations of such organs are another important aspect which is addressed within this review. The various techniques, methodologies, advantages, and disadvantages will all be discussed. Hence, the purpose of this review is providing an updated examination of all processes for the analysis of a working, biocompatible artificial organ.

scholarly journals Ureido Functionalization through Amine-Urea Transamidation under Mild Reaction Conditions

Polymers ◽  
2021 ◽  
Vol 13 (10) ◽  
pp. 1583
Author(s):  
Natalia Guerrero-Alburquerque ◽  
Shanyu Zhao ◽  
Daniel Rentsch ◽  
Matthias M. Koebel ◽  
Marco Lattuada ◽  
...  
Keyword(s):  
Aqueous Media ◽  
Reaction Times ◽  
Reaction Rates ◽  
Secondary Amines ◽  
Isocyanic Acid ◽  
Advantages And Disadvantages ◽  
Major Disadvantage ◽  
Wide Range ◽  
Potential Alternative ◽  
Full Conversion

Ureido-functionalized compounds play an indispensable role in important biochemical processes, as well as chemical synthesis and production. Isocyanates, and KOCN in particular, are the preferred reagents for the ureido functionalization of amine-bearing compounds. In this study, we evaluate the potential of urea as a reagent to graft ureido groups onto amines at relatively low temperatures (<100 °C) in aqueous media. Urea is an inexpensive, non-toxic and biocompatible potential alternative to KOCN for ureido functionalization. From as early as 1864, urea was the go-to reagent for polyurea polycondensation, before falling into disuse after the advent of isocyanate chemistry. We systematically re-investigate the advantages and disadvantages of urea for amine transamidation. High ureido-functionalization conversion was obtained for a wide range of substrates, including primary and secondary amines and amino acids. Reaction times are nearly independent of substrate and pH, but excess urea is required for practically feasible reaction rates. Near full conversion of amines into ureido can be achieved within 10 h at 90 °C and within 24 h at 80 °C, and much slower reaction rates were determined at lower temperatures. The importance of the urea/amine ratio and the temperature dependence of the reaction rates indicate that urea decomposition into an isocyanic acid or a carbamate intermediate is the rate-limiting step. The presence of water leads to a modest increase in reaction rates, but the full conversion of amino groups into ureido groups is also possible in the absence of water in neat alcohol, consistent with a reaction mechanism mediated by an isocyanic acid intermediate (where the water assists in the proton transfer). Hence, the reaction with urea avoids the use of toxic isocyanate reagents by in situ generation of the reactive isocyanate intermediate, but the requirement to separate the excess urea from the reaction product remains a major disadvantage.

A Compliant Transmission Mechanism With Intermittent Contacts for Cycle-Doubling

2006 ◽  
Vol 129 (1) ◽  
pp. 114-121 ◽  
Author(s):  
Nilesh D. Mankame ◽  
G. K. Ananthasuresh
Keyword(s):  
Finite Element ◽  
Conceptual Design ◽  
Finite Element Simulations ◽  
Nonlinear Finite Element ◽  
Transmission Mechanism ◽  
Input Frequency ◽  
Length Scales ◽  
Wide Range ◽  
Macro Scale ◽  
Functional Prototype

A novel compliant transmission mechanism that doubles the frequency of a cyclic input is presented in this paper. The compliant cycle-doubler is a contact-aided compliant mechanism that uses intermittent contact between itself and a rigid surface. The conceptual design for the cycle-doubler was obtained using topology optimization in our earlier work. In this paper, a detailed design procedure is presented for developing the topology solution into a functional prototype. The conceptual design obtained from the topology solution did not account for the effects of large displacements, friction, and manufacturing-induced features such as fillet radii. Detailed nonlinear finite element analyses and experimental results from quasi-static tests on a macro-scale prototype are used in this paper to understand the influence of the above factors and to guide the design of the functional prototype. Although the conceptual design is based on the assumption of quasi-static operation, the modified design is shown to work well in a dynamic setting for low operating frequencies via finite element simulations. The cycle-doubler design is a monolithic elastic body that can be manufactured from a variety of materials and over a range of length scales. This makes the design scalable and thus adaptable to a wide range of operating frequencies. Explicit dynamic nonlinear finite element simulations are used to verify the functionality of the design at two different length scales: macro (device footprint of a square of 170mm side) at an input frequency of 7.8Hz; and meso (device footprint of a square of 3.78mm side) at an input frequency of 1kHz.

scholarly journals High-Fidelity Simulations of a Linear HPT Vane Cascade Subject to Varying Inlet Turbulence

2017 ◽  
Author(s):  
Richard Pichler ◽  
Richard D. Sandberg ◽  
Gregory Laskowski ◽  
Vittorio Michelassi
Keyword(s):  
Heat Flux ◽  
Turbulence Intensity ◽  
Side Surface ◽  
Suction Side ◽  
Transition Process ◽  
Length Scale ◽  
Length Scales ◽  
Inflow Turbulence ◽  
High Turbulence ◽  
Turbulence Length

The effect of inflow turbulence intensity and turbulence length scales have been studied for a linear high-pressure turbine vane cascade at Reis = 590,000 and Mis = 0.93, using highly resolved compressible large-eddy simulations employing the WALE turbulence model. The turbulence intensity was varied between 6% and 20% while values of the turbulence length scales were prescribed between 5% and 20% of axial chord. The analysis focused on characterizing the inlet turbulence and quantifying the effect of the inlet turbulence variations on the vane boundary layers, in particular on the heat flux to the blade. The transition location on the suction side of the vane was found to be highly sensitive to both turbulence intensity and length scale, with the case with turbulence intensity 20% and 20% length scale showing by far the earliest onset of transition and much higher levels of heat flux over the entire vane. It was also found that the transition process was highly intermittent and local, with spanwise parts of the suction side surface of the vane remaining laminar all the way to the trailing edge even for high turbulence intensity cases.

Application of neural networks in membrane separation

2020 ◽  
Vol 36 (2) ◽  
pp. 265-310 ◽  
Author(s):  
Morteza Asghari ◽  
Amir Dashti ◽  
Mashallah Rezakazemi ◽  
Ebrahim Jokar ◽  
Hadi Halakoei
Keyword(s):  
Neural Networks ◽  
Chemical Engineering ◽  
Membrane Separation ◽  
Mechanistic Model ◽  
Computing Time ◽  
Permeate Flux ◽  
Practical Applications ◽  
Advantages And Disadvantages ◽  
Wide Range ◽  
Physical And Chemical

AbstractArtificial neural networks (ANNs) as a powerful technique for solving complicated problems in membrane separation processes have been employed in a wide range of chemical engineering applications. ANNs can be used in the modeling of different processes more easily than other modeling methods. Besides that, the computing time in the design of a membrane separation plant is shorter compared to many mass transfer models. The membrane separation field requires an alternative model that can work alone or in parallel with theoretical or numerical types, which can be quicker and, many a time, much more reliable. They are helpful in cases when scientists do not thoroughly know the physical and chemical rules that govern systems. In ANN modeling, there is no requirement for a deep knowledge of the processes and mathematical equations that govern them. Neural networks are commonly used for the estimation of membrane performance characteristics such as the permeate flux and rejection over the entire range of the process variables, such as pressure, solute concentration, temperature, superficial flow velocity, etc. This review investigates the important aspects of ANNs such as methods of development and training, and modeling strategies in correlation with different types of applications [microfiltration (MF), ultrafiltration (UF), nanofiltration (NF), reverse osmosis (RO), electrodialysis (ED), etc.]. It also deals with particular types of ANNs that have been confirmed to be effective in practical applications and points out the advantages and disadvantages of using them. The combination of ANN with accurate model predictions and a mechanistic model with less accurate predictions that render physical and chemical laws can provide a thorough understanding of a process.

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