Ghost Cells Research Articles

Erratum to: Parallel vertex approximate gradient discretization of hybrid dimensional Darcy flow and transport in discrete fracture networks

This paper proposes a parallel numerical algorithm to simulate the flow and the transport in a discrete fracture network taking into account the mass exchanges with the surrounding matrix. The discretization of the Darcy fluxes is based on the Vertex Approximate Gradient finite volume scheme adapted to polyhedral meshes and to heterogeneous anisotropic media, and the transport equation is discretized by a first-order upwind scheme combined with an Euler explicit integration in time. The parallelization is based on the single program, multiple data (SPMD) paradigm and relies on a distribution of the mesh on the processes with one layer of ghost cells in order to allow for a local assembly of the discrete systems. The linear system for the Darcy flow is solved using different linear solvers and preconditioners implemented in the PETSc and Trilinos libraries. The convergence of the scheme is validated on two original analytical solutions with one and four intersecting fractures. Then, the parallel efficiency of the algorithm is assessed on up to 512 processes with different types of meshes, different matrix fracture permeability ratios, and different levels of complexity of the fracture network.

Parallel numerical modeling of hybrid-dimensional compositional non-isothermal Darcy flows in fractured porous media

This paper introduces a new discrete fracture model accounting for non-isothermal compositional multiphase Darcy flows and complex networks of fractures with intersecting, immersed and non-immersed fractures. The so called hybrid-dimensional model using a 2D model in the fractures coupled with a 3D model in the matrix is first derived rigorously starting from the equi-dimensional matrix fracture model. Then, it is discretized using a fully implicit time integration combined with the Vertex Approximate Gradient (VAG) finite volume scheme which is adapted to polyhedral meshes and anisotropic heterogeneous media. The fully coupled systems are assembled and solved in parallel using the Single Program Multiple Data (SPMD) paradigm with one layer of ghost cells. This strategy allows for a local assembly of the discrete systems. An efficient preconditioner is implemented to solve the linear systems at each time step and each Newton type iteration of the simulation. The numerical efficiency of our approach is assessed on different meshes, fracture networks, and physical settings in terms of parallel scalability, nonlinear convergence and linear convergence.

Оценка генотоксичности парацетамола и его комбинации с верапамилом <i>in vivo</i>

Парацетамол в дозах 30 и 60 мг/кг (внутрь) отдельно или в сочетании с известным комутагеном верапамилом (0,25 – 10 мг/кг, внутрь) при однократном или 5-кратном ежедневном введении не проявил цитогенетической активности в клетках костного мозга мышей. Цитогенетический эффект отсутствовал также после однократного введения парацетамола в дозе 300 мг/кг. В тесте ДНК-комет парацетамол при однократном введении в дозах 30 и 60 мг/кг на срок 3 или 24 ч не проявил ДНК-повреждающей активности в клетках костного мозга, печени, почек, селезенки и головного мозга мышей. В дозе 300 мг/кг при экспозиции в течение 3 ч парацетамол индуцировал ДНК-кометы типа «ghost cells» в клетках печени, что было расценено как проявление гепатотоксического эффекта препарата.

A fast and automatic full-potential finite volume solver on Cartesian grids for unconventional configurations

To meet the requirements of fast and automatic computation of subsonic and transonic aerodynamics in aircraft conceptual design, a novel finite volume solver for full potential flows on adaptive Cartesian grids is developed in this paper. Cartesian grids with geometric adaptation are firstly generated automatically with boundary cells processed by cell-cutting and cell-merging algorithms. The nonlinear full potential equation is discretized by a finite volume scheme on these Cartesian grids and iteratively solved in an implicit fashion with a generalized minimum residual (GMRES) algorithm. During computation, solution-based mesh adaptation is also applied so as to capture flow features more accurately. An improved ghost-cell method is proposed to implement the non-penetration wall boundary condition where the velocity-potential of a ghost cell is modified by an analytic method instead. According to the characteristics of the Cartesian grids, the Kutta condition is applied by specially computing the gradients on Kutta-faces without directly assigning the potential jump to cells adjacent wake faces, which can significantly improve the solution converging speed. The feasibility and accuracy of the proposed method are validated by several typical cases of sub/transonic flows around an ONERA M6 wing, a DLR-F4 wing-body, and an unconventional figuration of a blended wing body (BWB). The validation cases demonstrate a fast convergence with fully automatic grid treatment and computation, and the results suggest its capacity in application for aircraft conceptual design.

Facilitating the development of stencil applications using the Heterogeneous Programming Library

SummaryStencil computations are very common in scientific codes. Heterogeneous systems achieve good results solving these problems, but their programming is complex because of the ghost regions required in multi‐device implementations and the difficulty to properly exploit their hardware. The Heterogeneous Programming Library (HPL) is a recent framework that improves the programmability of heterogeneous devices. This paper describes two extensions of HPL focused on stencil computations. The first one allows to automatically update the ghost regions they involve. The second one automates the implementation of the computational kernels of these algorithms. In our evaluation, the first mechanism reduces on average the number of lines of code and the Halstead programming effort of the host code of comparable HPL baselines by 34% and 64.2%, respectively, while the second contribution reduces these metrics by 72% and 79% in the computational kernels, respectively. Also, the first technique has negligible performance overheads, while the second one matches the performance of manually developed kernels. As an added benefit, the facilitation of the development of these codes thanks to these techniques helps programmers experiment with optimizations suited for this applications such as the ghost cell expansion technique, which provides speedups of up to 13% in our experiments.

НЕЙРОПРОТЕКТОРНЫЙ ЭФФЕКТ ЭРИТРОПОЭТИНА ПРИ ЭКСПЕРИМЕНТАЛЬНОЙ ИШЕМИИ СПИННОГО МОЗГА

Aim. To study dynamics of the ethological status and morphological changes in neurons at experimental spinal cord ischemia influenced by erythropoietin (EPO) administration. Materials and Methods. The research was conducted on 54 outbred white rats. Spinal cord ischemia was modeled via total intravasal occlusion of abdominal aorta and its branches. EPO was administered intraperitoneally at a dose of 5000 IU per kg of body weight three times in 3, 24 and 48 hours after induction of lumbar spinal cord ischemia. The ethological status in animals was assessed using the 6-point scale based on the integral indicator of behavioral responses (IIBR). Morphological methods were used to estimate numbers of unchanged neurons, chromatolytic cells, ghost cells, glial cells, and blood vessels in the spinal cord. Results. Experimental spinal cord ischemia induced by total intravasal occlusion of the abdominal aorta and its branches was followed by progressive (from day 3 to day 14) and partially recovering (by day 30) changes in the ethological status manifested by symmetric peripheral paraplegia, apselaphesia of the hind limbs and lumbar spine, fecal and urinary incontinence. Morphological changes of the lumbar spine at spinal ischemia included progressive (from day 3 to day 30) increase in numbers of chromatolytic neurons, ghost cells, glial cells, and small blood vessels; the number of intact neurons was maximally decreased on days 3 and 7 and started recovering on day 30. Conclusion. EPO administration at a total dose of 15000 IU/kg at experimental spinal cord ischemia results in a partial (on day 3) and complete (on days 7-14-30) recovery of animals’ behavioral activity. After EPO has been administered, numbers of normal neurons, glial cells, and small blood vessels in the spinal cord are progressively increasing from day 3 do day 30 of observation while the percentage of chromatolytic neurons and ghost cells is progressively decreasing.

Risk Assessment of ZnO Nanoparticles Revelation on Erythrocyte Membrane

Rapid developments in the cosmetics, food and drug applications Zinc oxide (ZnO) nano materials have resulted in concerns related to the risk of overexposure of human blood. The rationale of this study was to systematically research the influence of nano-ZnO on erythrocyte. The ZnO nanoparticle was prepared by sol-gel method with size of 40 ± 5 nm. The erythrocytes treated with nano-ZnO underwent abnormal sedimentation, aggregation along with dose dependent haemolysis. The ghost cells were investigated by using ultrathin cell section in the case under nano-ZnO. The RBC membrane destruction further confirmed by malondialdehyde (MDA) quantification. The results imply better understanding of the interaction between erythrocytes and nano-ZnO and will help in assessing the risk of nanomaterial toxicity in blood that may have potential toxicity to human being health. The following results suggest that the risk assessment of nano-materials and nano-products should be carried out prior to their wide application although they hold much more inconceivable and remarkable advantages.

Development of Compressible Large-Eddy Simulations Combining High-Order Schemes and Wall Modeling

Compressible large-eddy simulations combining high-order methods with a wall model have been developed in order to compute wall-bounded flows at high Reynolds numbers. The high-order methods consist of low-dissipation and low-dispersion implicit finite volume schemes for spatial discretization on structured grids. In the first part, the procedure used to apply these schemes in near-wall regions is presented. It is based on a ghost cell reconstruction. Its validity is assessed by performing the large-eddy simulation of a turbulent channel flow at a friction Reynolds number of . In the second part, to consider flows at higher Reynolds numbers, a large-eddy simulation approach using a wall model is proposed. The coupling between the wall model and the high-order schemes is described. The performance of the approach is evaluated by simulating a turbulent channel flow at using meshes with grid spacings of , 200, and 300 in the streamwise direction and , 100, and 150 in the wall-normal and spanwise directions (in wall units). The effects of the choice of the point used for data exchange between the wall model and the large-eddy simulation algorithm, as well as of the positions of the ghost cells used for the coupling, are examined by performing additional computations in which these parameters vary. The results are in agreement with direct numerical simulation data. In particular, the turbulent intensities obtained in the logarithmic region of the boundary layers of the channel flow are successfully predicted.

Dynamics of Histological Changes in the Frontal Cortex of the Brain in Rats Subjected to Antenatal Exposure to Alcohol

The aim of the present work was to undertake a comparative study of the effects of prenatal alcoholization of the histological characteristics of neurons in the frontal cortex of the brains of rats of different ages. Experiments were performed on 175 mongrel white rats – the offspring of 25 females given 15% ethanol as drinking solution throughout pregnancy. The cerebral cortex was studied on postnatal days 2–90 using histological, histochemical, and morphometric methods. An increase (on days 2 and 5) followed by a decrease (on days 10 and 90) was seen in cortical thickness, with a decrease in neuron body size (on days 20–90), a decrease in the number of neurons in cortical layer V, a decrease in the number of normochromic cells, and increases in the numbers of hyperchromic shrunken neurons and ghost cells throughout the study period. Antenatal alcoholization in rats induced various histological changes in the frontal cortex, which were long-lasting and progressive during postnatal ontogeny.

Dentinogenic ghost cell tumour: a retrospective study of eight cases with long-term follow-up

Dentinogenic ghost cell tumour: a retrospective study of eight cases with long-term follow-up

Pilomatricoma: A Case Report with a Distinctive Histological Presentation and a Literature Review

Pilomatricoma is an uncommon benign neoplasm commonly affecting the head andneck region of the pediatric patient group. This lesion is clinically described as a wellcircumscribed, slow growing, firm mass with normal overlying skin. It is oftenmisdiagnosed clinically and an accurate diagnosis can only be made by histologicalexamination. Histological features of pilomatricoma are generally consistent, characterizedby a biphasic population of ghost cells and basophilic cells arranged in irregular islandsor sheets. Pilomatricoma is best treated by surgical excision and reports of recurrenceare rare. Here, we report a case of pilomatricoma of the cheek in a female Asian childexhibiting a distinctive histological feature and a literature review of relevant informationof the pilomatricoma is discussed

Development of high-resolution multi-scale modelling system for simulation of coastal-fluvial urban flooding

Abstract. Urban developments in coastal zones are often exposed to natural hazards such as flooding. In this research, a state-of-the-art, multi-scale nested flood (MSN_Flood) model is applied to simulate complex coastal-fluvial urban flooding due to combined effects of tides, surges and river discharges. Cork city on Ireland's southwest coast is a study case. The flood modelling system comprises a cascade of four dynamically linked models that resolve the hydrodynamics of Cork Harbour and/or its sub-region at four scales: 90, 30, 6 and 2 m. Results demonstrate that the internalization of the nested boundary through the use of ghost cells combined with a tailored adaptive interpolation technique creates a highly dynamic moving boundary that permits flooding and drying of the nested boundary. This novel feature of MSN_Flood provides a high degree of choice regarding the location of the boundaries to the nested domain and therefore flexibility in model application. The nested MSN_Flood model through dynamic downscaling facilitates significant improvements in accuracy of model output without incurring the computational expense of high spatial resolution over the entire model domain. The urban flood model provides full characteristics of water levels and flow regimes necessary for flood hazard identification and flood risk assessment.

Parallel multiphase field simulations with OpenPhase

The open-source software project OpenPhase allows the three-dimensional simulation of microstructural evolution using the multiphase field method. The core modules of OpenPhase and their implementation as well as their parallelization for a distributed-memory setting are presented. Especially communication and load-balancing strategies are discussed. Synchronization points are avoided by an increased halo-size, i.e. additional layers of ghost cells, which allow multiple stencil operations without data exchange. Load-balancing is considered via graph-partitioning and sub-domain decomposition. Results are presented for performance benchmarks as well as for a variety of applications, e.g. grain growth in polycrystalline materials, including a large number of phase fields as well as Mg–Al alloy solidification. Program summaryProgram Title: OpenPhaseProgram Files doi:http://dx.doi.org/10.17632/2mnv2fvkkk.1Licensing provisions: GPLv3Programming language: C++Nature of problem: OpenPhase[1] allows the simulation of microstructure evolution during materials processing using the multiphase field method. In order to allow an arbitrary number of phase fields active parameter tracking is used, which can cause load imbalances in parallel computations.Solution method: OpenPhase solves the phase field equations using an explicit finite difference scheme. The parallel version of OpenPhase provides load-balancing using over-decomposition of the computational domain and graph-partitioning. Adaptive sub-domain sizes are used to minimize the computational overhead of the over-decomposition, while allowing appropriate load-balance.Additional comments including Restrictions and Unusual features: The distributed-memory parallelism in OpenPhase uses MPI. Shared-memory parallelism is implemented using OpenMP. The library uses C++11 features and therefore requires GCC version 4.7 or higher. [1] www.openphase.de

Necrotizing Panniculitis as an Uncommon Manifestation of Acute Pancreatitis.

Pancreatic panniculitis is a rare disorder affecting 2–3% of patients with pancreatic disease. The findings are characterized by tender, erythematous, subcutaneous nodules which may undergo spontaneous ulceration with discharge of brownish and viscous material derived from colliquative necrosis of adipocytes. The lesions are usually localized in the lower limbs, although they may also extend to the buttocks and also involve the trunk, upper limbs and scalp. They can precede overt pancreatic disease in 40% of cases. The typical histological features observed in these lesions are characterized by necrotic adipocytes with absent nuclei (better known as ‘ghost cells’) in the context of a predominantly lobular panniculitis.We describe the case of a 78-year-old cirrhotic woman admitted to our department with abdominal pain affecting the upper abdomen and a 3-day fever. On physical examination, multiple tender erythematous nodules, with irregular margins, were present on the pretibial regions of both lower legs, ranging in size from 0.8 to 1.5 cm. Pancreatic amylase and lipase were elevated and abdominal computed tomography revealed acute pancreatitis with oedema, focal gland enlargement of the pancreatic tail and perivisceral inflammation. Histological examination of the lesions was consistent with a diagnosis of necrotizing granulomatous panniculitis.LEARNING POINTSIdentification of the aetiological factors of tender erythematous nodules is challenging.Careful examination and history taking is essential for correct diagnosis and proper treatment.Pancreatic panniculitis should be included in the differential diagnosis as it can indicate developing acute pancreatitis.

A molecular portrait of maternal sepsis from Byzantine Troy.

Pregnancy complications are poorly represented in the archeological record, despite their importance in contemporary and ancient societies. While excavating a Byzantine cemetery in Troy, we discovered calcified abscesses among a woman's remains. Scanning electron microscopy of the tissue revealed 'ghost cells', resulting from dystrophic calcification, which preserved ancient maternal, fetal and bacterial DNA of a severe infection, likely chorioamnionitis. Gardnerella vaginalis and Staphylococcus saprophyticus dominated the abscesses. Phylogenomic analyses of ancient, historical, and contemporary data showed that G. vaginalis Troy fell within contemporary genetic diversity, whereas S. saprophyticus Troy belongs to a lineage that does not appear to be commonly associated with human disease today. We speculate that the ecology of S. saprophyticus infection may have differed in the ancient world as a result of close contacts between humans and domesticated animals. These results highlight the complex and dynamic interactions with our microbial milieu that underlie severe maternal infections.

A review on strategies for decreasing E.coli O157:H7 risk in animals.

Enterohemorrhagic Escherichia coli (EHEC) serotype O157:H7 is a food-borne pathogen that younger children are most prone to this microorganism. Hemolytic Uremic Syndrome (HUS) caused by EHEC, leads to the destruction of red blood cells and kidney failure. The virulence of E.coli O157:H7 is attributed to fimbriae, that facilitate colonization of bacteria within the colon and verotoxins (VT) or Shiga toxins (Stx) that are released into the blood. Although, in most cases, the infection is self-limitedin young children and aged population, it may cause HUS. Therefore, several investigations are performed in order to offer effective therapies and vaccines, which can prevent and treat the infection in appropriate time. As the pathogenesis of this infection is complicated, a multi-targeted strategy is required. Since cattle are the most important reservoir of EHEC and the root of contamination, reducing E.coli O157:H7 at the farm level should decrease the risk of human illness. Several vaccine approaches have been employed with different proper outcomes in animal models, including recombinant proteins (virulence factors such as; Stx1/2, intimin, EspA, fusion proteins of A and B Stx subunits), avirulent ghost cells of EHEC O157:H7, live attenuated bacteria expressing recombinant proteins, recombinant fimbrial proteins. In addition to protein-based vaccines, DNA vaccines have provided proper prevention in the laboratory animal model. This review paper summarizes the previous studies, current status and future perspective of different immunization strategies for eradicating Enterohemorrhagic Escherichia coli O157:H7.

Numerical simulation of complex immersed boundary flow by a radial basis function ghost cell method

A radial basis function ghost cell immersed boundary method of simulating flows around arbitrary complex or multiple immersed boundaries is proposed in this paper. In this method, incompressible Navier-Stokes equations are discretized on fixed Cartesian staggered gridby the finite difference method. A fractional step method is used for time integration, together with third order Runge-Kutta scheme. A high-order TVD MUSCL (total variation diminishing monotonic upstream-centered scheme for conservation law) scheme is used to discretize convective terms. Two salient features are emphasized in the present study. First, boundary conditions at the immersed interface are enforced by a continuous ghost cell method to consider the influence of immersed boundary on the flow field. The immersed bodies are treated as virtual boundaries immersed in the flow. And Navier-Stokes equations are solved in the entire computation domain, including solid domain. Therefore, programming complexity is greatly reduced and the treatment of immersed boundaries is simplified. Second, a polynomial and radial basis function is introduced to implicitly represent and reconstruct arbitrary complex immersed boundaries. Iso-surface distance functions about interface geometries are fitted with some sampling points of body surfaces. It is flexible and robust. Moreover, the information about interface positions on the background grid can be easily identified by the signed distance functions. Based on our in-house developed immersed boundary method solver, typical test cases are simulated to validate the proposed method. The flows around a cylinder at Reynolds numbers of 40, 100 and 200 are first simulated and a grid resolution study is carried out. Good agreement is achieved by comparing with previous numerical results, which shows that this method is accurate and reliable. In the second case of flow around airfoil, the good agreement with previous study shows that the present method has the ability to simulate complex immersed boundary flow. In the last case of flow around array of thirteen cylinders, the ability of present method for multiple immersed boundaries is well proved. And hydrodynamic interaction among multiple bodies is briefly analyzed.

Ghost Cell Odontogenic Carcinoma Arising Denovo with Distant Metastasis: A Case Report and Review of Literature

Ghost Cell Odontogenic Carcinoma (GCOC) is a rare malignant odontogenic tumour of epithelial origin accounting about 0.37% to 2.1% of all odontogenic tumours. They are characterized by the presence of ameloblastic islands along with ghost cells representing aberrant keratinization. The aim of this case report is to present a rare case that was diagnosed in a 37-year-old male patient and to describe the behavior of the tumour.

Scalable Failure Masking for Stencil Computations using Ghost Region Expansion and Cell to Rank Remapping

In order to achieve exascale systems, application resilience needs to be addressed. Some programming models, such as task-DAG (directed acyclic graphs) architectures, currently embed resilience features whereas traditional SPMD (single program, multiple data) and message-passing models do not. Since a large part of the community's code base follows the latter models, it is still required to take advantage of application characteristics to minimize the overheads of fault tolerance. To that end, this paper explores how recovering from hard process/node failures in a local manner is a natural approach for certain applications to obtain resilience at lower costs in faulty environments. In particular, this paper targets enabling online, semitransparent local recovery for stencil computations on current leadership-class systems as well as presents programming support and scalable runtime mechanisms. Also described and demonstrated in this paper is the effect of failure masking, which allows the effective reduct...

下顎に発生した周辺性象牙質形成性幻影細胞腫の1例

下顎に発生した周辺性象牙質形成性幻影細胞腫の1例