pinecone/core-2020-05-10-deduplication huggingface dataset:
Mathematical modeling of postmenopausal osteoporosis and its treatment by the anti-catabolic drug denosumab

Denosumab, a fully human monoclonal antibody, has been approved for the treatment of postmenopausal osteoporosis. The therapeutic effect of denosumab rests on its ability to inhibit osteoclast differentiation. Here, we present a computational approach on the basis of coupling a pharmacokinetics model of denosumab with a pharmacodynamics model for quantifying the effect of denosumab on bone remodeling. The pharmacodynamics model comprises an integrated systems biology-continuum micromechanics approach, including a bone cell population model, considering the governing biochemical factors of bone remodeling (including the action of denosumab), and a multiscale micromechanics-based bone mechanics model, for implementing the mechanobiology of bone remodeling in our model. Numerical studies of postmenopausal osteoporosis show that denosumab suppresses osteoclast differentiation, thus strongly curtailing bone resorption. Simulation results also suggest that denosumab may trigger a short-term bone volume gain, which is, however, followed by constant or decreasing bone volume. This evolution is accompanied by a dramatic decrease of the bone turnover rate by more than one order of magnitude. The latter proposes dominant occurrence of secondary mineralization (which is not anymore impeded through cellular activity), leading to higher mineral concentration per bone volume. This explains the overall higher bone mineral density observed in denosumab-related clinical studies
Emulating facial biomechanics using multivariate partial least squares surrogate models

This is the author’s final, accepted and refereed manuscript to the article. Locked until 2015-05-06A detailed biomechanical model of the human face driven by a network of muscles is a useful tool in
relating the muscle activities to facial deformations. However, lengthy computational times often hinder
its applications in practical settings. The objective of this study is to replace precise but computationally
demanding biomechanical model by a much faster multivariate meta-model (surrogate model), such that a
significant speedup (to real-time interactive speed) can be achieved. Using a multilevel fractional factorial
design, the parameter space of the biomechanical system was probed from a set of sample points chosen
to satisfy maximal rank optimality and volume filling. The input–output relationship at these sampled points
was then statistically emulated using linear and nonlinear, cross-validated, partial least squares regression
models. It was demonstrated that these surrogate models can mimic facial biomechanics efficiently and
reliably in real-time.Copyright © 2014 John Wiley & Sons, Ltd. http://onlinelibrary.wiley.com/journal/10.1002/%28ISSN%292040-794
Calibrating corneal material model parameters using only inflation data : an ill-posed problem

Goldmann applanation tonometry (GAT) is a method used to estimate the intraocular pressure by measuring
the indentation resistance of the cornea. A popular approach to investigate the sensitivity of GAT results
to material and geometry variations is to perform numerical modelling using the finite element method,
for which a calibrated material model is required. These material models are typically calibrated using
experimental inflation data by solving an inverse problem. In the inverse problem, the underlying material
constitutive behaviour is inferred from the measured macroscopic response (chamber pressure versus apical
displacement). In this study, a biomechanically motivated elastic fibre-reinforced corneal material model is
chosen. The inverse problem of calibrating the corneal material model parameters using only experimental
inflation data is demonstrated to be ill-posed, with small variations in the experimental data leading to large
differences in the calibrated model parameters. This can result in different groups of researchers, calibrating
their material model with the same inflation test data, drawing vastly different conclusions about the effect
of material parameters on GAT results. It is further demonstrated that multiple loading scenarios, such as
inflation as well as bending, would be required to reliably calibrate such a corneal material model.http://onlinelibrary.wiley.com/journal/10.1002/(ISSN)2040-79472015-07-30hj201
Computational model of collagen turnover in carotid arteries during hypertension

This is the peer reviewed version of the following article: Saez, P., Peña, E., Tarbell, J., Martínez, M. Computational model of collagen turnover in carotid arteries during hypertension. "International journal for numerical methods in biomedical engineering - Online", Febrer 2015, vol. 31, núm. 2, p. 1-25, which has been published in final form at https://doi.org/10.1002/cnm.2705. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.t is well known that biological tissues adapt their properties because of different mechanical and chemical stimuli. The goal of this work is to study the collagen turnover in the arterial tissue of hypertensive patients through a coupled computational mechano-chemical model. Although it has been widely studied experimen- tally, computational models dealing with the mechano-chemical approach are not. The present approach can be extended easily to study other aspects of bone remodeling or collagen degradation in heart diseases. The model can be divided into three different stages. First, we study the smooth muscle cell synthesis of differ- ent biological substances due to over-stretching during hypertension. Next, we study the mass-transport of these substances along the arterial wall. The last step is to compute the turnover of collagen based on the amount of these substances in the arterial wall which interact with each other to modify the turnover rate of collagen. We simulate this process in a finite element model of a real human carotid artery. The final results show the well-known stiffening of the arterial wall due to the increase in the collagen content.Peer ReviewedPostprint (author's final draft
Influence of material property variability on the mechanical behaviour of carotid atherosclerotic plaques: A 3D fluid-structure interaction analysis

Mechanical analysis has been shown to be complementary to luminal stenosis in assessing atherosclerotic plaque vulnerability. However, patient-specific material properties are not available and the effect of material properties variability has not been fully quantified. Media and fibrous cap (FC) strips from carotid endarterectomy samples were classified into hard, intermediate and soft according to their incremental Young's modulus. Lipid and intraplaque haemorrhage/thrombus strips were classified as hard and soft. Idealised geometry-based 3D fluid-structure interaction analyses were performed to assess the impact of material property variability in predicting maximum principal stress (Stress-P1) and stretch (Stretch-P1). When FC was thick (1000 or 600 µm), Stress-P1 at the shoulder was insensitive to changes in material stiffness, whereas Stress-P1 at mid FC changed significantly. When FC was thin (200 or 65 µm), high stress concentrations shifted from the shoulder region to mid FC, and Stress-P1 became increasingly sensitive to changes in material properties, in particular at mid FC. Regardless of FC thickness, Stretch-P1 at these locations was sensitive to changes in material properties. Variability in tissue material properties influences both the location and overall stress/stretch value. This variability needs to be accounted for when interpreting the results of mechanical modelling.This research is supported by BHF PG/11/74/29100, HRUK RG2638/14/16, National Natural Science Foundation of China 81270386 and 81170291 and the NIHR Cambridge Biomedical Research Centre. Mr Yuan is supported by China Scholarship Council (CSC) Cambridge Scholarship.This is the final version of the article. It first appeared from Wiley via http://dx.doi.org/10.1002/cnm.272
Does increasing applied load lead to contact changes indicative of knee osteoarthritis? A subject-specific FEA study

This study investigated whether increased loading (representing obesity) in the extended knee and flexed knee led to increased stresses in areas of typical medial and lateral osteoarthritis cartilage lesions, respectively. We created two paired sets of subject-specific finite element models; both sets included models of extended knees and of flexed knees. The first set represented normal loading; the second set represented increased loading. All other variables were held constant. The von Mises stresses and contact areas calculated on the tibial cartilage surfaces of the paired models were then compared. In the extended knee models, applying a larger load led to increased stress in the anterior and central regions of the medial tibial cartilage. These are the typical locations of medial osteoarthritis cartilage lesions. Therefore, the results support that increased loading in the extended knee may result in medial osteoarthritis. In the flexed knee models, applying a larger load increased stress in the anterior and central regions of the lateral tibial cartilage. Lateral osteoarthritis cartilage lesions typically occur centrally and posteriorly. Therefore, these results do not support our hypothesis. Shear stress was increased in areas of typical lateral lesions, however, and should be investigated in future studies
Numerical simulation of electrocardiograms for full cardiac cycles in healthy and pathological conditions

International audienceThis work is dedicated to the simulation of full cycles of the electrical activity of the heart and the corresponding body surface potential. The model is based on a realistic torso and heart anatomy, including ventricles and atria. One of the specificities of our approach is to model the atria as a surface, which is the kind of data typically provided by medical imaging for thin volumes. The bidomain equations are considered in their usual formulation in the ventricles, and in a surface formulation on the atria. Two ionic models are used: the Courtemanche-Ramirez-Nattel model on the atria, and the " Minimal model for human Ventricular action potentials " (MV) by Bueno-Orovio, Cherry and Fenton in the ventricles. The heart is weakly coupled to the torso by a Robin boundary condition based on a resistor-capacitor transmission condition. Various ECGs are simulated in healthy and pathological conditions (left and right bundle branch blocks, Bachmann's bundle block, Wolff-Parkinson-White syndrome). To assess the numerical ECGs, we use several qualitative and quantitative criteria found in the medical literature. Our simulator can also be used to generate the signals measured by a vest of electrodes. This capability is illustrated at the end of the article
Computer-aided diagnosis : Detection and localization of prostate cancer within the peripheral zone

This is the peer reviewed version of the following article: Rampun, Y. A., Chen, Z., Malcolm, P., Tiddeman, B., & Zwiggelaar, R. (2015). Computer-aided diagnosis: detection and localization of prostate cancer within the peripheral zone. International Journal for Numerical Methods in Biomedical Engineering., which has been published in final form at http://dx.doi.org/doi:10.1002/cnm.2745. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.We propose a methodology for prostate cancer detection and localization within the peripheral zone based on combining multiple segmentation techniques. We extract four image features using Gaussian and median filters. Subsequently, we use each image feature separately to generate binary segmentations. Finally, we take the intersection of all four binary segmentations, incorporating a model of the peripheral zone, and perform erosion to remove small false-positive regions. The initial evaluation of this method is based on 275 MRI images from 37 patients, and 86% of the slices were classified correctly with 87% and 86% sensitivity and specificity achieved, respectively. This paper makes two contributions: firstly, a novel computer-aided diagnosis approach, which is based on combining multiple segmentation techniques using only a small number of simple image features, and secondly, the development of the proposed method and its application in prostate cancer detection and localization using a single MRI modality with the results comparable with the state-of-the-art multimodality and advanced computer vision methods in the literature. Copyright ? 2015 John Wiley & Sons, LtdauthorsversionPeer reviewe
Non-uniform force allocation for area preservation in spring network
  models

In modelling of elastic objects in a flow such as red blood cells, white
blood cells, or tumour cells, several elastic moduli are involved. One of them
is the area conservation modulus. In this paper, we focus on spring network
models and we introduce a new way of modeling the area preservation modulus. We
take into account the current shape of the individual triangles and find the
proportional allocation of area conservation forces, which would for individual
triangles preserve their shapes. The analysis shows that this approach tends to
regularize the triangulation. We demonstrate this effect on individual
triangles as well as on the complete triangulations
Fast left ventricle tracking using localized anatomical affine optical flow

Fast left ventricle tracking using localized anatomical affine optical flowIn daily clinical cardiology practice, left ventricle (LV) global and regional function assessment is crucial for disease diagnosis, therapy selection, and patient follow-up. Currently, this is still a time-consuming task, spending valuable human resources. In this work, a novel fast methodology for automatic LV tracking is proposed based on localized anatomically constrained affine optical flow. This novel method can be combined to previously proposed segmentation frameworks or manually delineated surfaces at an initial frame to obtain fully delineated datasets and, thus, assess both global and regional myocardial function. Its feasibility and accuracy were investigated in 3 distinct public databases, namely in realistically simulated 3D ultrasound, clinical 3D echocardiography, and clinical cine cardiac magnetic resonance images. The method showed accurate tracking results in all databases, proving its applicability and accuracy for myocardial function assessment. Moreover, when combined to previous state-of-the-art segmentation frameworks, it outperformed previous tracking strategies in both 3D ultrasound and cardiac magnetic resonance data, automatically computing relevant cardiac indices with smaller biases and narrower limits of agreement compared to reference indices. Simultaneously, the proposed localized tracking method showed to be suitable for online processing, even for 3D motion assessment. Importantly, although here evaluated for LV tracking only, this novel methodology is applicable for tracking of other target structures with minimal adaptations.The authors acknowledge funding support from FCT - Fundacao para a Ciência e a Tecnologia, Portugal, and 
the European Social Found, European Union, through the Programa Operacional Capital Humano (POCH) in
the scope of the PhD grants SFRH/BD/93443/2013 (S. Queiros) and SFRH/BD/95438/2013 (P. Morais), and 
by the project ’PersonalizedNOS (01-0145-FEDER-000013)’ co-funded by Programa Operacional Regional
do Norte (Norte2020) through the European Regional Development Fund (ERDF).info:eu-repo/semantics/publishedVersio
Controlling the Error on Target Motion through Real-time Mesh
  Adaptation: Applications to Deep Brain Stimulation

We present an error-controlled mesh refinement procedure for needle insertion
simulation and apply it to the simulation of electrode implantation for deep
brain stimulation, including brain shift. Our approach enables to control the
error in the computation of the displacement and stress fields around the
needle tip and needle shaft by suitably refining the mesh, whilst maintaining a
coarser mesh in other parts of the domain. We demonstrate through academic and
practical examples that our approach increases the accuracy of the displacement
and stress fields around the needle without increasing the computational
expense. This enables real-time simulations. The proposed methodology has
direct implications to increase the accuracy and control the computational
expense of the simulation of percutaneous procedures such as biopsy,
brachytherapy, regional anesthesia, or cryotherapy and can be essential to the
development of robotic guidance.Comment: 21 pages, 14 figure
Implementation of surface tension with wall adhesion effects in a three-dimensional finite element model for fluid flow

This is the pre-peer reviewed version of the following article: Implementation of surface tension with wall adhesion effects in a three-dimensional finite element model for fluid flow, Bellet Michel, Communications in Numerical Methods in Engineering 17, 8 (2001) Pages 563-579, which has been published in final form at http://dx.doi.org/10.1002/cnm.430International audienceThis paper addresses the finite element modelling of surface tension. The external stress vectors associated with surface tension are assumed proportional to the average curvature and oriented along the normal vector to the fluid surface. The issue of estimating the average curvature of a discretized surface is then discussed. It is proposed to use the surface divergence of a field of nodal normal vectors. Special attention is devoted to the calculation of the so-called consistent normal vectors. In the case of a surface composed of linear triangular facets, it is demonstrated that these normals are given at each node by the average of the normals of the surrounding facets, weighted by their surface. In order to account for wall adhesion effects, the method which consists in modifying the normal vectors at nodes in contact is discussed and extended to the three-dimensional case. In order to validate the approach, the three-dimensional finite element resolution of the equilibrium of a drop of liquid on a plane is treated
A beam finite element for through cracked tubular node behaviour modelling

International audienceThis paper deals with the problem of a through-cracked tubular joint behaviour modelling. A new beam finite element has been created, in order to take into account the loss of stiffness of the joint due to through-thickness crack presence. and the coupling between axial force and bending momentum. This allows to study at a low computing time large damaged offshore structures, using beam elements. The mechanical model used to build the finite element is first described. An analytical identification of its internal parameters (eccentricity and stiffness) is then performed, Finally, some results are presented. Copyright (C) 2002 John Wiley Sons, Ltd
Numerical representation of the quality measures of triangles and triangular meshes

In this note a new procedure to represent the quality measure for triangles is proposed. The triangles are identified by their three angles and are represented in a bounded domain, called angle representation region, according to the area co-ordinates, which are common and well known by finite element users. The developed representation can also be used in order to visualize the characteristics of any quality measure. This new procedure is extended to graphically represent triangular meshes in the angle representation region.Peer ReviewedPostprint (author’s final draft
An inflatable fabric beam finite element

International audienceInflatable structures made of modern textile materials with important mechanical characteristics can be inflated at high pressure (up to several hundreds kPa). For such values of the pressure they have a strong mechanical strength. The aim of the paper is to construct a new inflatable beam finite element able to predict the behaviour of inflatable structures made of beam elements. Experiments and analytical studies on inflatable fabric beams at high pressure have shown that their compliance is the sum of the beam compliance and of the yarn compliance. This new finite element is therefore obtained by the equilibrium finite element method and is modified into a displacement finite element. The stiffness matrix takes into account the inflation pressure. Comparisons between experimental and numerical results are shown and prove the accuracy of this new finite element for solving problems of inflatable beams at high pressure
Master-slave approach for the modelling of joints with dependent degrees of freedom in flexible mechanisms

The analysis of multibody systems requires an exact description of the kinematics of the joints involved. In the present work the master–slave approach is employed and endowed with the possibility of including several more complex types of joints. We present the formulation for joints where some relation between the different released degrees of freedom exists such as the screw joint, the rack-and-pinion joint or the cam joint. These joints are implemented in conjunction with geometrically exact beams and an energy-momentum conserving time-stepping algorithmPreprin
A combined implicit-explicit algorithm in time for non-linear finite element analysis

An algorithm combining the numerical execution in time of implicit and explicit methods of solution is presented in this paper. The algorithm swaps between both methods as required for the analysis. The whole mesh is solved for an unique method at once, i.e. there are no partitions of the mesh for separate implicit or explicit treatment of the solution. The combination is in-time, in such a manner that if the implicit method starts diverging the explicit one is initiated by appropriate conditions of transition. The formulation is presented first and its implementation is validated by the analysis of a key numerical example.Peer ReviewedPostprint (author’s final draft
Mesh projection between parametric surfaces

This paper presents a new algorithm to map a given mesh over a source surface onto a target surface. This projection is determined by means of a least-squares approximation of a transformation defined between the loops of boundary nodes of the cap surfaces in the parametric spaces. Once the new mesh is obtained on the parametric space of the target surface, it is mapped to the target surface according to its parameterization. Therefore, in contrast with the usual techniques, the developed algorithm does not require solving any root finding problem to ensure that the projected nodes are on the target surface. Finally, this projection algorithm is extended to three-dimensional cases and included in a sweep meshing tool in order to generate the inner layers of elements in the physical space.Peer ReviewedPostprint (author’s final draft
An efficient domain-decomposition pseudo-spectral method for solving elliptic differential equations

In this paper, a new numerical scheme based on non-overlapping domain decompositions and integrated Chebyshev approximations for solving elliptic differential equations is presented. The distinguishing feature of the present scheme is that it achieves a Cp continuous solution across the interfaces (p is the order of the differential equation). Several test problems are employed to verify the method. The obtained results indicate that the achievement of higher-order smoothness leads to a significant improvement in accuracy