bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sub‐cell shock capturing and spacetime discontinuity tracking for nonlinear conservation laws
Authors: Palaniappan J. , Miller S. T. , Haber R. B. 
Published: June 2008

AbstractWe describe two approaches to resolving shocks and other discontinuities in spacetime discontinuous Galerkin (SDG) methods for nonlinear conservation laws. The first is an adaptation of the sub‐cell shock‐capturing technique, recently introduced by Persson and Peraire, to the special circumstances of SDG solutions constructed on causal spacetime grids. We restrict the stabilization operator to spacetime element interiors, thereby preserving the 𝒪(N) computational complexity and the element‐wise conservation properties of the basic SDG method, and use a special discontinuity indicator to limit the stabilization to elements traversed by discontinuous solution features. The method resolves discontinuities within individual spacetime elements having a sufficiently high‐order basis. Numerical studies demonstrate the combination of sub‐cell shock capturing with h‐adaptive spacetime meshing that circumvents the projection errors inherent to purely spatial remeshing procedures.In a second method, we use adaptive spacetime meshing operations to track the trajectories of singular surfaces while maintaining the quality of the surrounding mesh. We present a series of feasibility studies where we track shocks and contact discontinuities in solutions to the inviscid Euler equations, including an example where the trajectories are not known a priori. The SDG‐tracking method sharply resolves discontinuities without mesh refinement and requires very little stabilization. Copyright © 2008 John Wiley & Sons, Ltd.
Parallel three‐dimensional simulation of the injection molding process
Authors: Araújo B. J. , Teixeira J. C. F. , Cunha A. M. , Groth C. P. T. 
Published: June 2008

AbstractThis paper describes the development of a parallel three‐dimensional unstructured non‐isothermal flow solver for the simulation of the injection molding process. The numerical model accounts for multiphase flow in which the melt and air regions are considered to be a continuous incompressible fluid with distinct physical properties. This aspect avoids the complex reconstruction of the interface. A collocated finite volume method is employed, which can switch between first‐ and second‐order accuracy in both space and time. The pressure implicit with splitting of operators algorithm is used to compute the transient flow variables and couple velocity and pressure. The temperature equation is solved using a transport equation with convection and diffusion terms. An upwind differencing scheme is used for the discretization of the convection term to enforce a bounded solution. In order to capture the sharp interface, a bounded compressive high‐resolution scheme is employed. Parallelization of the code is achieved using the PETSc framework and a single program multiple data message passing model. Predicted numerical solutions for several example problems are considered. The first case validates the solution algorithm for moderate Reynolds number flows using a structured mesh. The second case employs an unstructured hybrid mesh showing the capability of the solver to describe highly viscous flows closer to realistic injection molding conditions. The final case presents the non‐isothermal filling of a thick cavity using three mesh sizes and up to 80 processors to assess parallel performance. The proposed algorithm is shown to have good accuracy and scalability. Copyright © 2008 John Wiley & Sons, Ltd.
The extended hippocampal‐diencephalic memory system: Enriched housing promotes recovery of the flexible use of spatial representations after anterior thalamic lesions
Authors: Wolff Mathieu , Loukavenko Elena A. , Will Bruno E. , Dalrymple‐Alford John C. 
Published: June 2008

AbstractThe anterior thalamic (AT) nuclei constitute an important component of an extended hippocampal‐diencephalic system, and severe persisting memory deficits are normally found after AT damage. This study examined whether postoperative enrichment promotes the recovery of the flexible use of spatial representations in rats with AT lesions. After training to swim from a single constant start position to a submerged platform in a Morris water maze, rats with AT lesions that were housed in standard cages (AT‐Std) performed poorly when required to swim to the platform from novel start positions during probe trials. By contrast, rats with AT lesions but housed in enriched environments (AT‐Enr), like sham‐lesion rats, showed relatively little disruption when tested with novel start positions. AT‐Std rats also initially showed impaired acquisition of the task, whereas AT‐Enr rats learned at a similar rate to that of the Sham‐Std group. Beneficial effects of enrichment were replicated in the subsequent standard water maze procedure that used varying start positions throughout training to acquire a new platform location. Although it is clear that AT damage can severely disrupt episodic‐like memory processes, and appear to be a core part of the interlinked neural systems subserving episodic memory, the current findings strongly encourage study on the adaptive response of the brain to thalamic lesions and prospects for the development of rehabilitation programs in cases of anterograde amnesia associated with diencephalic injury. © 2008 Wiley‐Liss, Inc.
Transport and retention of Escherichia coli in a mixture of quartz, Al‐coated and Fe‐coated sands
Authors: Kim Song‐Bae , Park Seong‐Jik , Lee Chang‐Gu , Kim Hyon‐Chong 
Published: June 2008

AbstractTransport and retention of Escherichia coli through the mixture of quartz, Al‐coated and Fe‐coated sands was examined using column experiments to investigate the effect of geochemical heterogeneity on bacteria transport. The first set of the experiments was performed in quartz, Al‐coated and Fe‐coated sand mixtures (coated sand: 0, 5, 10, 25, 50, 100%) to examine the influence of positively‐charged sand grains on bacteria transport. The second experiments were carried out to observe the impact of pH (range 6·74–8·21) on bacteria transport in the mixture of quartz 50% and Fe‐coated sand 50%. The third experiments were conducted to analyse the effect of ionic strength (0, 50, 100, 200 mM) on bacteria transport in the mixture of quartz 50% and Al‐coated sand 50%. The first experiments show that bacterial mass recoveries were in the range of 3·6–43·4%, decreasing nonlinearly as the content of Al‐ and Fe‐coated sands increased. In the second experiments, the bacterial mass recoveries were in the range of 35·5–79·2%, increasing linearly as the solution pH increased. In the third experiments, the mass recovery was 3·4% at 0 mM. As the ionic strength increased to 50mM, the mass recovery decreased to 0%. When the ionic strength increased further to 100 and 200 mM, no bacterial mass was recovered as in the case of 50 mM. It indicates that in the mixed medium of quartz 50% and Al‐coated sand 50% both positive (increment of bacterial adhesion) and negative (decrement) effects of ionic strength may be counterbalanced, minimizing the impact of ionic strength on the bacterial adhesion. This study helps to understand the role of metal oxides and solution chemistry in the transport of bacteria in geochemically heterogeneous media Copyright © 2008 John Wiley & Sons, Ltd.
Genetic and epigenetic inactivation of T‐cadherin in human hepatocellular carcinoma cells
Authors: Chan David W. , Lee Joyce M.F. , Chan Patrick C.Y. , Ng Irene O.L. 
Published: June 2008

AbstractT‐cadherin is an atypical cadherin and growing evidence has indicated that T‐cadherin exerts tumor‐suppressive effects on cancers of epithelial cell type and also causes positive effects on tumor angiogenesis. Human hepatocellular carcinoma (HCC) is a hypervascular tumor and T‐cadherin has been shown to be overexpressed in intratumoral endothelial cells of HCCs. However, the expression status and functions of T‐cadherin in hepatocytes or HCC cells remain unclear. Here, we demonstrated that T‐cadherin was underexpressed in HCC cells (26.5%, 13/49 cases), but was frequently (77.6%, 38/49) overexpressed in intratumoral endothelial cells immunohistochemically. Semiquantitative RT‐PCR analysis also showed that the T‐cadherin gene was underexpressed in 7 of 11 HCC cell lines. Loss of heterozygosity analysis revealed that 32–38% of the 42 human HCC samples had allelic losses at this locus. Upon pharmacological treatment with demethylating agent 5‐aza‐2′‐deoxycytidine or histone deacetylase inhibitor trichostatin A, T‐cadherin promoter hypermethylation and/or histone deacetylation was frequently observed in HCC samples and cell lines. Functionally, enforced expression of T‐cadherin induced G2/M cell cycle arrest, reduced cell proliferation in low serum medium, suppressed anchorage‐independent growth in soft agar and increased sensitivity to TNFα‐mediated apoptosis in HCC cells. Intriguingly, we found that T‐cadherin significantly suppressed the activity of c‐Jun, a crucial oncoprotein constitutively activated in HCC cells. To conclude, T‐cadherin was differentially expressed in human HCCs. The underexpression of T‐cadherin in HCC cells suggests it may be another critical event in addition to T‐cadherin‐mediated angiogenesis during HCC development. © 2008 Wiley‐Liss, Inc.
A methodology for analyzing curvature in the developing brain from preterm to adult
Authors: Pienaar R. , Fischl B. , Caviness V. , Makris N. , Grant P. E. 
Published: June 2008

AbstractThe character and timing of gyral development is one manifestation of the complex orchestration of human brain development. The ability to quantify these changes would not only allow for deeper understanding of cortical development but also conceivably allow for improved detection of pathologies. This article describes a FreeSurfer‐based image‐processing analysis “pipeline” or methodology that inputs an MRI volume, corrects possible contrast defects, creates surface reconstructions, and outputs various curvature‐based function analyses. A technique of performing neonate reconstructions using FreeSurfer, which has not been possible previously because of inverted image contrast in premyelinated brains, is described. Once surfaces are reconstructed, the analysis component of the pipeline incorporates several surface‐based curvature functions found in literature (principle curvatures, Gaussian, mean curvature, “curvedness,” and Willmore Bending Energy). We consider the problem of analyzing curvatures from different sized brains by introducing a Gaussian‐curvature based variable‐radius filter. Segmented volume data are also analyzed for folding measures: a gyral folding index (gyrification‐white index GWI) and a gray‐white matter junction folding index (WMF). A very simple curvature‐based classifier is proposed that has the potential to discriminate between certain classes of subjects. We also present preliminary results of this curvature analysis pipeline on nine neonate subjects (30.4 weeks through 40.3 weeks Corrected Gestational Age), three children (2, 3, and 7 years), and three adults (33, 37, and 39 years). Initial results demonstrate that curvature measures and functions across our subjects peaked at term, with a gradual decline through early childhood and further decline continuing through to adults. We can also discriminate older neonates, children, and adults based on curvature analysis. Using a variable radius Gaussian‐curvature filter, we also observed that the per‐unit bending energy of neonate brain surfaces was also much higher than the children and adults. © 2008 Wiley Periodicals, Inc. Int J Imaging Syst Technol, 18, 42–68, 2008
A fast spherical inflation method of the cerebral cortex by deformation of a simplex mesh on the polar coordinates
Authors: Kwon Min Jeong , Hahn Jooyoung , Park HyunWook 
Published: June 2008

AbstractThe convoluted shape of the cerebral cortex makes it difficult to analyze and visualize the neuronal activation area. One way of overcoming this problem is to use a spherical inflation method to draw a cerebral cortex on a spherical surface. The task of mapping the cortical surface on a sphere has several obstacles, namely, the overlap between the polygons of the surface, the heavy computation demand, and the geometric distortions inherent in the process. This article proposes a method of mapping the three‐dimensional (3D) cortical surface represented in a simplex mesh to a sphere surface, which does not have any overlap between the polygons and minimizes the geometric distortions as well as the computation time. The proposed method consists of the two steps of preprocessing and refinement. In the preprocessing step, the 3D cortical surface is mapped onto a sphere without any overlap between the polygons by iterative deformation. In the refinement step, the mapped surface is adjusted to minimize its linear distortion. The experimental results show the efficiency and performance of the proposed mapping method. © 2008 Wiley Periodicals, Inc. Int J Imaging Syst Technol, 18, 9–16, 2008
New brain atlas—Mapping the human brain in vivo with 7.0 T MRI and comparison with postmortem histology: Will these images change modern medicine?
Authors: Cho Zang‐Hee , Kim Young‐Bo , Han Jae‐Yong , Min Hoon‐Ki , Kim Kyoung‐Nam , Choi Sang‐Han , Veklerov Eugene , Shepp Larry A. 
Published: June 2008

AbstractHuman brain imaging with magnetic resonance at 7.0 Tesla (T) can reveal the brain's architecture with resolution equivalent to that obtained from thin slices in vitro. In vivo images can provide tissue type identification with a greater clarity than that available in vitro without special stains. The coil design is an 8 or 12 channel phased array antenna tuned for 7.0T. The individual coils are arranged 8 or 12 loops in a “crown” configuration. Image acquisition is 6 minutes for 15 slices of 2 mm thickness with in‐plane resolution of 0.25 mm using a gradient echo pulse sequence. While others have achieved good resolution in human brain imaging, this paper demonstrates a pulse sequence with a specialized radiofrequency coil that achieves an uniformity and resolution not shown in previous studies at 7.0T. Our new images demonstrate very fine details of the midbrain, brainstem, and hippocampal area that have not been previously achieved in living human subjects. © 2008 Wiley Periodicals, Inc. Int J Imaging Syst Technol, 18, 2–8, 2008
Differential transient MEG and fMRI responses to visual stimulation onset rate
Authors: Tuan August S. , Birn Rasmus M. , Bandettini Peter A. , Boynton Geoffrey M. 
Published: June 2008

AbstractWhile recent analysis of functional magnetic resonance imaging (fMRI) data utilize a generalized nonlinear convolution model (e.g., dynamic causal modeling), most conventional analyses of local responses utilize a linear convolution model (e.g., the general linear model). These models assume a linear relationship between the blood oxygenated level dependent (BOLD) signal and the underlying neuronal response. While previous studies have shown that this “neurovascular coupling” process is approximately linear, short stimulus durations are known to produce a larger fMRI response than expected from a linear system. This divergence from linearity between the stimulus time‐course and BOLD signal could be caused by neuronal onset and offset transients, rather than a nonlinearity in the hemodynamics related to BOLD contrast. We tested this hypothesis by measuring MEG and fMRI responses to stimuli with ramped contrast onsets and offsets in place of abrupt transitions. MEG results show that the ramp successfully reduced the transient onset of neural activity. However, the nonlinearity in the fMRI response, while also reduced, remained. Predictions of fMRI responses from MEG signals show a weaker nonlinearity than observed in the actual fMRI data. These results suggest that the fMRI BOLD nonlinearity seen with short duration stimuli is not solely due to transient neuronal activity. © 2008 Wiley Periodicals, Inc. Int J Imaging Syst Technol, 18, 17–28, 2008
Design of irrigation water supply systems using the Q–C feasibility domain concept: I. Introduction and theory
Authors: Sinai Gideon , Dalins Ben‐Zion , Cohen Daniel , Shamir Uri 
Published: June 2008

AbstractThe Q–C Feasibility Domain (QCFD) was defined and proposed as a tool for design of multiquality irrigation water supply systems. It determines all feasible combinations of water discharge and water quality, and can be represented by a point, a line, or an area in a diagram of water discharge versus solute flow rate (a Q–J diagram). The shape of the QCFD is the result of dilution of two or more flows from sources of different water quality. (assuming conservative substances) Several types of QCFDs were analyzed at sources, inner nodes of a network, and of consumer outlets. The effect of water discharge constraints (due to flow limitations in the network) on the QCFDs was formulated and analyzed. Computation of QCFDs of dilution junctions by vector addition of their inflows was described. The method was extended numerically to nonlinear mixing due to dependence of water salinity. Use of this method enables computation of QCFDs for inner nodes in networks, including dilution junctions. The effect of network topology and flow direction was discussed. Application and demonstration will follow in the next paper in this series. Copyright © 2008 John Wiley & Sons, Ltd.
Tail morphology in the Western Diamond‐backed rattlesnake, Crotalus atrox
Authors: Savitzky Alan H. , Moon Brad R. 
Published: June 2008

AbstractThe shaker muscles in the tails of rattlesnakes are used to shake the rattle at very high frequencies. These muscles are physiologically specialized for sustaining high‐frequency contractions. The tail skeleton is modified to support the enlarged shaker muscles, and the muscles have major anatomical modifications when compared with the trunk muscles and with the tail muscles of colubrid snakes. The shaker muscles have been known for many years to consist of three large groups of muscles on each side of the tail. However, the identities of these muscles and their serial homologies with the trunk muscles were not previously known. In this study, we used dissection and magnetic resonance imaging of the tail in the Western Diamond‐backed Rattlesnake, Crotalus atrox, to determine that the three largest muscles that shake the rattle are the M. longissimus dorsi, the M. iliocostalis, and the M. supracostalis lateralis. The architecture of these muscles differs from their serial homologs in the trunk. In addition, the rattlesnake tail also contains three small muscles. The M. semispinalis‐spinalis occurs in the tail, where it is a thin, nonvibratory, postural muscle that extends laterally along the neural spines. An additional muscle, which derives from fusion of the M. interarticularis inferior and M. levator costae, shares segmental insertions with the M. longissimus dorsi and M. iliocostalis. Several small, deep ventral muscles probably represent the Mm. costovertebrocostalis, intercostalis series, and transversohypapophyseus. The architectural rearrangements in the tail skeleton and shaker muscles, compared with the trunk muscles, probably relate to their roles in stabilizing the muscular part of the tail and to shaking the rattle at the tip of the tail. Based on comparisons with the tail muscles of a colubrid snake described in the literature, the derived tail muscle anatomy in rattlesnakes evolved either in the pitvipers or within the rattlesnakes. J. Morphol., 2008. © 2008 Wiley‐Liss, Inc.
Morphology and histology of male and female reproductive systems in the inseminating species Scoloplax distolothrix (Ostariophysi: Siluriformes: Scoloplacidae)
Authors: Spadella Maria Angélica , Oliveira Claudio , Quagio‐Grassiotto Irani 
Published: June 2008

AbstractThe morphology and histology of male and female reproductive systems were examined in Scoloplax distolothrix. Internal insemination was documented in this species by the presence of sperm within the ovaries. Mature males and females have elongated genital papillae, exhibiting a tubular shape in males and a plain heart‐shape with two median protuberances in females. The testes are two elongated structures that converge ventrally, under the intestine, towards the genital papilla. They are joined at the caudal end, forming an ovoid single chamber for sperm storage. Secretory regions were not observed. In the lumen of the testicular tubules, spermatozoa can be tightly packed along their lengths, but do not constitute a spermatozeugmata. The lumen of the sperm storage chamber and spermatic duct are filled with free spermatozoa without the accompanying secretions. The ovaries are bird‐wing shaped, saccular structures that converge ventrally under the intestine, towards the genital papilla. They are joined at the caudal end, forming a tubular chamber possibly destined for oocyte storage. An oviduct with an irregular outline connects the chamber to the tubular region of the genital papilla. No distinct sperm storage structure was found in the ovaries. The unique male and female genital papillae suggest that these structures are associated with the reproductive mode in scoloplacids, representing evidence for insemination. The occurrence of free spermatozoa, without the accompanying secretions and not arranged in a spermatozeugmata can be associated with the presence of a tubular male genital papilla for sperm transfer to the female genital tract. This reinforces the idea that sperm packets are not necessary for all inseminating species. The male reproductive system in scoloplacids is very different from that in auchenipterids, a second catfish family with insemination, which indicates that the occurrence of insemination is not connected to the internal morphology of reproductive organs. J. Morphol., 2008. © 2008 Wiley‐Liss, Inc.
Cardiovascular system of anomuran crabs, genus Lopholithodes
Authors: McGaw Iain J. , Duff Stefanie D. 
Published: June 2008

AbstractThe cardiovascular systems of Puget Sound king crabs, Lopholithodes mandtii, and brown box crabs, Lopholithodes foraminatus, were mapped using corrosion casting techniques. Both species have a similar external morphology and a very similar cardiovascular system. Seven arteries (five arterial systems) arise from the heart. The small anterior aorta exits from the anterior surface of the heart and supplies hemolymph to the eyestalks and brain region. The pathway of the two sets of paired arteries, the anterolateral arteries and hepatic arteries, is close, and they intertwine with one another during their initial course. The anterolateral arteries exit from the anterior dorsal surface of the heart and supply hemolymph to the hypodermis, cardiac stomach, antennal gland, and mandibular muscles, whereas the hepatic arteries branch profusely within the hepatopancreas. The lithodids are believed to have evolved from hermit crab ancestors; indicative of these evolutionary origins the posterior aorta is well developed and supplies hemolymph to the large abdomen and the gonads. Exiting from the ventral surface of the heart, the sternal artery is the largest in the system. It branches to supply the mouthparts, chelae, and pereiopods. The differing arrangement of this vessel compared with that of the pagurid anomurans is due to the more carcinized (crab‐like) morphological features of the lithodid anomurans. The arrangement of vessels supplying the gills is different compared with that of brachyuran crabs; the infrabranchial sinus joins to the afferent gill vessels at their midpoint, rather than along the ventral edge. In general, the circulatory system of the lithodid crabs is somewhat simpler than that of brachyuran crabs, with fewer branching capillary‐like networks. Nevertheless, it is still very complex. In accordance with anatomical descriptions of blue crabs and cancrid crabs it would also seem appropriate to classify the lithodid circulatory system as one that is incompletely closed. J. Morphol., 2008. © 2008 Wiley‐Liss, Inc.