pinecone/core-2020-05-10-deduplication huggingface dataset:
Zonal organization of the climbing fiber projection to the flocculus and nodulus of the rabbit: A combined axonal tracing and acetylcholinesterase histochemical study

The localization and termination of olivocerebellar fibers in the flocculus and nodulus of the rabbit were studied with anterograde axonal transport methods [wheatgerm agglutinin-horseradish peroxidase (WGA-HRP) and tritiated leucine] and correlated with the compartments in the white matter of these lobules delineated with acetylcholinesterase histochemistry (Tan et al. J. Comp. Neurol., 1995, this issue). Olivocerebellar fibers originating from the caudal dorsal cap travel through floccular compartments FC2 and FC4 to terminate as climbing fibers in floccular zones FZII and FZIV. Fibers from the rostral dorsal cap and the ventrolateral outgrowth traverse compartments FC1 and FC3, which are interleaved with compartments FC2 and FC4, and terminate in zones FZI and FZIII. Fibers from the rostral pole of the medial accessory olive traverse the C2 compartment and terminate in the C2 zone. FZI-III extend into the adjoining folium (folium p) of the ventral paraflocculus. The C2 zone continues across folium p into other folia of the ventral paraflocculus and into the dorsal paraflocculus. Four compartments and five zones were distinguished in the nodulus. Medial compartment XC1 contains olivocerebellar fibers from the caudal dorsal cap and subnucleus β that terminate in the XZI zone. Olivocerebellar fibers from the rostral dorsal cap and the ventrolateral outgrowth occupy XC2 and terminate in XZII. The XC4 compartment contains fibers from both the caudal dorsal cap and from the rostral dorsal cap and the ventrolateral outgrowth. The latter terminate in a central portion of the XZIV zone. The dorsomedial cell column projects to the XZIII zone, which is present only in the dorsal part of the nodulus, The rostral, medial accessory olive projects to the XZV zone, which occupies the lateral border of the nodulus. These results confirm and extend the conclusions of Katayama and Nisimaru ([1988] Neurosci. Res. 5:424–438) on the zonal pattern in the olivo-nodular projection in the rabbit. Additional observations were made on the presence of a lateral A zone (Buisseret-Delmas [1988] Neurosci. Res. 5:475–493) in the hemisphere of lobules VI and VII. Retrograde labeling of the nucleo-olivary tract of Legendre and Courville ([1987] Neuroscience 21:877–891) was observed after WGA-HRP injections into the inferior olive including the rostral dorsal cap and the ventrolateral outgrowth. The anatomical and functional implications of these observations are discussed
Zonal organization of the flocculovestibular nucleus projection in the rabbit: A combined axonal tracing and acetylcholinesterase histochemical study

With the use of retrograde transport of horseradish peroxidase we confirmed the observation of Yamamoto and Shimoyama ([1977] Neurosci Lett. 5:279-283) that Purkinje cells of the rabbit flocculus projecting to the medial vestibular nucleus are located in two discrete zones, FZII and FZIV, that alternate with two other Purkinje cell zones, FZI and FZIII, projecting to the superior vestibular nucleus. The retrogradely labeled axons of these Purkinje cells collect in four bundles that occupy the corresponding floccular white matter compartments, FC1–4, that can be delineated with acetylcholinesterase histochemistry (Tan et al. [1995a] J. Comp. Neurol., this issue). Anterograde tracing from small injections of wheat germ agglutin-hoseradish peroxidase in single Purkinje cell zones of the flocculus showed that Purkinje cell axons of FZII travel in FC2 to terminate in the medial vestibular nucleus. Purkinje cell axons from FZI and FZIII occupy the FC2 and FC3 compartments, respectively, and terminate in the superior vestibular nucleus. Purkinje cell axons from all three compartments pass through the floccular peduncle and dorsal group y. In addition, some fibers from FZI and FZII, but not from FZIII, arch through the cerebellar nuclei to join the floccular peduncle more medially. No anterograde tracing experiments were available to determine the projections of the FZIV and C2 zones. The functional implications of these results are discussed
An integral-collocation-based fictitious-domain technique for solving elliptic problems

This paper presents a new fictitious-domain technique for numerically solving elliptic second-order partial-differential equations (PDEs) in complex geometries. The proposed technique is based on the use of integral collocation schemes and Chebyshev polynomials. The boundary conditions on the actual boundary are implemented by means of integration constants. The method works for both Dirichlet and Neumann boundary conditions. Several test problems are considered to verify the technique. Numerical results show that the present method yields spectral accuracy for smooth (analytic) problems.\u
Application of high-order Higdon non-reflecting boundary conditions to linear shallow water models

Communications in Numerical Methods in Engineering, 24, (2008), 1459–1466.The article of record as published may be located at http://dx.doi.org/10.1002/cnm.1044.A shallow water model with linear time-dependent dispersive waves in an unbounded domain is considered. The domain is truncated with artificial boundaries B where a sequence of high-order non-reflecting boundary conditions (NRBCs) proposed by Higdon are applied. Methods devised by Givoli and Neta that afford easy implementation of Higdon NRBCs are refined in order to reduce computational expenses. The new refinement makes the computational effort associated with the boundary treatment quadratic rather than exponential (as in the original scheme) with the order. This allows for implementation of NRBCs of higher orders than previously. A numerical example for a semi-infinite channel truncated on one side is presented. Finite difference schemes are used throughout.A shallow water model with linear time-dependent dispersive waves in an unbounded domain is considered.
The domain is truncated with artiﬁcial boundaries B where a sequence of high-order non-reﬂecting
boundary conditions (NRBCs) proposed by Higdon are applied. Methods devised by Givoli and Neta that
afford easy implementation of Higdon NRBCs are reﬁned in order to reduce computational expenses. The
new reﬁnement makes the computational effort associated with the boundary treatment quadratic rather
than exponential (as in the original scheme) with the order. This allows for implementation of NRBCs of
higher orders than previously. A numerical example for a semi-inﬁnite channel truncated on one side is
presented. Finite difference schemes are used throughout
The use of pseudo-inertia in asymptotic modelling of constraints in boundary value problems

In recent publications, the validity of using positive and negative inertial penalty parameters and the advantage of this approach over the conventional positive penalty function approach have been established for linear eigenvalue problems. This paper shows how this method may be applied to solve a boundary value problem. A steady-state 2-D heat transfer problem is used to demonstrate the method. First, the governing partial differential equation is modified by adding a pseudo-inertial term that results in an equation, which is mathematically identical to the equation governing the free vibration of a membrane. The essential boundary conditions of zero temperature along a specified line are imposed using inertial penalty parameters. The characteristic vibration modes found in this way are used to generate the complementary function to the heat transfer problem. This solution satisfies all natural boundary conditions (adiabatic) and zero temperature conditions using the inertial penalty parameter. To satisfy any additional temperature distribution imposed on the system, two sets of corrector terms are superimposed resulting in the final solution. The results are compared with constrained solutions obtained using the Lagrangian multiplier method and the ordinary penalty method
Effect of induced magnetic field on peristaltic flow of a micropolar
  fluid in an asymmetric channel

Of concern in this paper is an investigation of peristaltic transport of a
physiological fluid in an asymmetric channel under long wave length and
low-Reynolds number assumptions. The flow is assumed to be incompressible,
viscous, electrically conducting micropolar fluid and the effect of induced
magnetic field is taken into account. Exact analytical solutions obtained for
the axial velocity, microrotation component, stream line pattern, magnetic
force function, axial-induced magnetic field as well as the current density
distribution across the channel. The flow phenomena for the pumping
characteristics, trapping and reflux are also investigated. The results
presented reveal that the velocity decreases with the increase of magnetic
field as well as the coupling parameter. Moreover, the trapping fluid can be
eliminated by the application of an external magnetic field. Thus, the study
bears the promise of important applications in physiological systems.Comment: 24 pages, 34 figure
Patient-specific computational biomechanics for simulating adolescent scoliosis surgery : predicted vs clinical correction for a preliminary series of six patients

Scoliosis is a spinal deformity that requires surgical correction in progressive cases.  In order to optimize surgical outcomes, patient-specific finite element models are being developed by our group.  In this paper, a single rod anterior correction procedure is simulated for a group of six scoliosis patients.  For each patient, personalised model geometry was derived from low-dose CT scans, and clinically measured intra-operative corrective forces were applied.  However, tissue material properties were not patient-specific, being derived from existing literature.  Clinically, the patient group had a mean initial Cobb angle of 47.3 degrees, which was corrected to 17.5 degrees after surgery.  The mean simulated post-operative Cobb angle for the group was 18.1 degrees.  Although this represents good agreement between clinical and simulated corrections, the discrepancy between clinical and simulated Cobb angle for individual patients varied between -10.3 and +8.6 degrees, with only three of the six patients matching the clinical result to within accepted Cobb measurement error of +-5 degrees.  The results of this study suggest that spinal tissue material properties play an important role in governing the correction obtained during surgery, and that patient-specific modelling approaches must address the question of how to prescribe patient-specific soft tissue properties for spine surgery simulation
Iterative operator splitting method for capillary formation model in tumor angiogenesis problem: Analysis and application

Iterative operator splitting method is used to solve numerically the mathematical model for capillary formation in tumor angiogenesis problem. The method is based on first splitting the complex problem into simpler sub-problems. Then each sub-equation is combined with iterative schemes. The algorithms are obtained by applying the proposed method to the given model problem. The explicit local error bounds are derived to show consistency. We also explained the stability by constructing the stability functions. The obtained numerical results show that iterative splitting method provides high accuracy and efficiency with respect to other classical methods in the literature
Progress towards the design and numerical analysis of a 3D microchannel biochip separator

This is the pre-peer reviewed version of the article which has been published in final form at: http://dx.doi.org/10.1002/cnm.1439This paper reports the design and numerical analysis of a three-dimensional biochip plasma blood\ud
separator using Computational Fluid Dynamics (CFD) techniques. Based on the initial\ud
configuration of a 2D separator, five 3D microchannel biochip designs are categorically developed\ud
through axial and plenary symmetrical expansions. These include the geometric variations of three\ud
types of the branch side channels (circular, rectangular, disc) and two types of the main channel\ud
(solid and concentric). Ignoring the initial transient behaviour and assuming that steady state flow\ud
has been established, the behaviour of the blood fluid in the devices is algebraically analysed and\ud
numerically modelled. The roles of the relevant microchannel mechanisms, i.e. bifurcation,\ud
constriction and bending channel, on promoting the separation process are analysed based on\ud
modelling results. The differences among the different 3D implementations are compared and\ud
discussed. The advantages of 3D over 2D separator in increasing separation volume and effectively\ud
depleting cell-free layer fluid from the whole cross section circumference are addressed and\ud
illustrated
Immersed boundary model of aortic heart valve dynamics with
  physiological driving and loading conditions

The immersed boundary (IB) method is a mathematical and numerical framework
for problems of fluid-structure interaction, treating the particular case in
which an elastic structure is immersed in a viscous incompressible fluid. The
IB approach to such problems is to describe the elasticity of the immersed
structure in Lagrangian form, and to describe the momentum, viscosity, and
incompressibility of the coupled fluid-structure system in Eulerian form.
Interaction between Lagrangian and Eulerian variables is mediated by integral
equations with Dirac delta function kernels. The IB method provides a unified
formulation for fluid-structure interaction models involving both thin elastic
boundaries and also thick viscoelastic bodies. In this work, we describe the
application of an adaptive, staggered-grid version of the IB method to the
three-dimensional simulation of the fluid dynamics of the aortic heart valve.
Our model describes the thin leaflets of the aortic valve as immersed elastic
boundaries, and describes the wall of the aortic root as a thick, semi-rigid
elastic structure. A physiological left-ventricular pressure waveform is used
to drive flow through the model valve, and dynamic pressure loading conditions
are provided by a reduced (zero-dimensional) circulation model that has been
fit to clinical data. We use this model and method to simulate aortic valve
dynamics over multiple cardiac cycles. The model is shown to approach rapidly a
periodic steady state in which physiological cardiac output is obtained at
physiological pressures. These realistic flow rates are not specified in the
model, however. Instead, they emerge from the fluid-structure interaction
simulation
On a continuum thermodynamics formulation and computational aspects of finite growth in soft tissues

17 pagesInternational audienceIn this paper, we try to settle the bases of a concise modelling of growth within the unified framework of continuum thermodynamics. Special emphasis is placed on the modelling of soft biological tissues at finite strains. For this, we adopt the nowadays well-known kinematic assumption of a multiplicative decomposition of the deformation gradient into an elastic part and a growth part. It is shown how continuum thermodynamics is crucial in setting convenient forms for the coupling between stress and growth in general. The particularization to isotropy simplifies considerably the growth modelling from both the theoretical and the numerical points of view. Simple growth constitutive equations are proposed and embedded into a finite element context. Finally, representative numerical examples examining stress-dependent growth and residual stress arising from growth and resorption close this study
Sequential parameter estimation for fluid-structure problems. Application to hemodynamics

International audienceWe present a robust and computationally efficient parameter estimation strategy for fluid-structure interaction problems. The method is based on a filtering algorithm restricted to the parameter space, known as the reduced order Unscented Kalman Filter. It does not require any adjoint or tangent problems. In addition, it can easily be run in parallel, which is of great interest in fluid-structure problems where the computational cost of the forward simulation is already a challenge in itself. We illustrate our methodology with the estimation of the artery wall stiffness from the wall displacement measurements - as they could be extracted from medical imaging - in a three-dimensional idealized abdominal aortic aneurysm. We also show preliminary results about the estimation of the proximal Windkessel resistance, which is an important parameter for setting appropriate fluid boundary conditions
Real Time Simulation of Surgery by Reduced Order Modelling and X-FEM Techniques

International audienceThis paper describes a novel approach for the simulation of surgery by a combined technique of model order reduction and extended finite element method (X-FEM) methods. Whereas model order reduction techniques employ globally supported (Ritz) shape functions, a combination with X-FEM methods on a locally superimposed patch is developed for cutting simulation without remeshing. This enables to obtain models with very few degrees of freedom that run under real-time constrains even for highly non-linear tissue constitutive equations. To show the performance of the technique, we studied an application to refractive surgery in the cornea
Human skull shape and masticatory induced stress : objective comparison through the use of non-rigid registration

Variation in masticatory induced stress, caused by shape changes in the human skull, is quantified in this
article. A comparison on masticatory induced stress is presented subject to a variation in human skull shape.
Non-rigid registration is employed to obtain appropriate computational domain representations. This procedure
allows the isolation of shape from other variations that could affect the results. An added benefit,
revealed through the use of non-rigid registration to acquire appropriate domain representation, is the possibility
of direct and objective comparison and manipulation. The effect of mapping uncertainty on the
direct comparison is also quantified. As shown in this study, exact difference values are not necessarily
obtained, but a non-rigid map between subject shapes and numerical results gives an objective indication on
the location of differences.http://onlinelibrary.wiley.com/journal/10.1002/(ISSN)2040-7947ai201
Automatic MRI 2D Brain Segmentation using Graph SearchingTechnique

Accurate and efficient segmentation of the whole brain in magnetic resonance (MR) images is a key task in many neuroscience and medical studies either because the whole brain is the final anatomical structure of interest or because the automatic extraction facilitates further analysis. The problem of segmenting brain MRI images has been extensively addressed by many researchers. Despite the relevant achievements obtained, automated segmentation of brain MRI imagery is still a challenging problem whose solution has to cope with critical aspects such as anatomical variability and pathological deformation. In the present paper, we describe and experimentally evaluate a method for segmenting brain from MRI images basing on two-dimensional graph searching principles for border detection. The segmentation of the whole brain over the entire volume is accomplished slice by slice, automatically detecting frames including eyes. The method is fully automatic and easily reproducible by computing the internal main parameters directly from the image data. The segmentation procedure is conceived as a tool of general applicability, although design requirements are especially commensurate with the accuracy required in clinical tasks such as surgical planning and post-surgical assessment. Several experiments were performed to assess the performance of the algorithm on a varied set of MRI images obtaining good results in terms of accuracy and stabilit
Automatic tracking of labeled red blood cells in microchannels

The current study proposes an automatic method for the segmentation and tracking of red blood cells
flowing through a 100- m glass capillary. The original images were obtained by means of a confocal system
and then processed in MATLAB using the Image Processing Toolbox. The measurements obtained with the
proposed automatic method were compared with the results determined by a manual tracking method. The
comparison was performed by using both linear regressions and Bland–Altman analysis. The results have
shown a good agreement between the two methods. Therefore, the proposed automatic method is a powerful
way to provide rapid and accurate measurements for in vitro blood experiments in microchannels.The authors acknowledge the financial support provided by: Student Mobility Placements with the program Lifelong Learning(Erasmus Program), PTDC/SAUBEB/108728/2008, PTDC/SAU-BEB/105650/2008, PTDC/EMEMFE/099109/2008 and PTDC/SAU-ENB/116929/2010 from the FCT (Science and Technology Foundation) and COMPETE, Portugal
Real Time Simulation of Biological Soft Tissues: A PGD Approach

International audienceWe introduce here a novel approach for the numerical simulation of nonlinear, hyperelastic soft tissues at kilohertz feedback rates necessary for haptic rendering. This approach is based upon the use of proper generalized decomposition techniques, a generalization of PODs. Proper generalized decomposition techniques can be considered as a means of a priori model order reduction and provides a physics-based meta-model without the need for prior computer experiments. The suggested strategy is thus composed of an offline phase, in which a general meta-model is computed, and an online evaluation phase in which the results are obtained at real time. Results are provided that show the potential of the proposed technique, together with some benchmark test that shows the accuracy of the method
Endocortical bone loss in osteoporosis: The role of bone surface availability

Age-related bone loss and postmenopausal osteoporosis are due to a dysregulation of bone remodelling in which less bone is reformed than resorbed. This dysregulation of bone remodelling does not occur with equal strength in all bone regions. Loss of bone is more pronounced near the endocortical surface. This leads to thinning of the cortical wall proceeding from the endosteum, a process sometimes called ‘trabecularisation’. In this paper, we investigate the influence of the nonuniform distribution of bone surface within bone tissue for osteoporotic bone losses. We use a spatio-temporal computational model of bone remodelling in which microstructural changes of bone tissue are represented by a phenomenological relationship between bone specific surface and bone porosity. The simulation of an osteoporotic condition by our model shows that the evolution of bone porosity within a bone cross section is significantly influenced by the nonuniform availability of bone surface. Greater bone loss occurs near the endocortical wall, leading to cortical wall thinning and to an expansion of the medullary cavity similar to cross-sectional observations from human femur midshafts. Our model suggests that the rate of cortical wall thinning is fast/slow in the presence/absence of an adjacent trabecular or trabecularised bone compartment