bluuebunny/crossref_metadata_2025 huggingface dataset:
Prognostic relevance of cytogenetics determined by fluorescent in situ hybridization in patients having myelofibrosis with myeloid metaplasia
Authors: Strasser‐Weippl Kathrin , Steurer Michael , Kees Mathias , Augustin Florian , Tzankov Alexandar , Dirnhofer Stephan , Fiegl Michael , Simonitsch‐Klupp Ingrid , Gisslinger Heinz , Zojer Niklas , Ludwig Heinz
Published: November 2006

BACKGROUND.

In chronic myelofibrosis (MF), distinct recurrent cytogenetic aberrations have been identified but their true prognostic relevance remains uncertain. In this disease, cytogenetic studies as assessed by conventional metaphase karyotyping are limited due to the inherent difficulties in obtaining adequate bone marrow aspirates and the low proliferative capacity of the clonal cells. Interphase fluorescent in situ hybridization (FISH) can partly overcome these limitations and increase the sensitivity of cytogenetic assessment in MF.

METHODS.

We retrospectively analyzed formalin‐fixed, paraffin embedded bone marrow sections of 107 MF patients by FISH and correlated cytogenetic findings with clinical presentation and survival.

RESULTS.

Chromosomal aberrations were detected in 56% of patients, with 20q− (24.3%) and 13q− (16.8%) being the most frequent ones. Importantly, cytogenetic abnormalities were found in 8/17 patients displaying a normal karyotype as assessed by conventional cytogenetics.

CONCLUSIONS.

Cytogenetic abnormalities in patients with MF can be detected reliably using FISH. Rare abnormalities confer an adverse outcome, but the main recurrent chromosomal aberrations do not correlate with clinical features and prognosis. Cancer 2006. © 2006 American Cancer Society.
The impact of hypogonadism and autonomic dysfunction on fatigue, emotional function, and sexual desire in male patients with advanced cancer
Authors: Strasser Florian , Palmer J. Lynn , Schover Leslie R. , Yusuf S. Wamique , Pisters Katherine , Vassilopoulou‐Sellin Rena , DeGracia Beth , Willey Jie S. , Bruera Eduardo
Published: November 2006

BACKGROUND.

The objective of this study was to determine whether hypogonadism and autonomic dysfunction contribute substantially to cancer‐related fatigue, decreased sexual desire, and depression in male patients with advanced, incurable cancer.

METHODS.

Forty‐eight patients who had received no major antineoplastic intervention for at least 2 weeks were tested for autonomic dysfunction by using Ewing tests. Total and free testosterone levels were measured. Multivariate analyses were performed to test the relation of these factors with the Functional Assessment of Cancer Therapy (FACT) (the Functional Assessment of Anorexia/Cachexia Therapy [FAACT] scale and the Functional Assessment of Chronic Illness Therapy‐Fatigue [FACIT‐F] subscale), the Hospital Anxiety and Depression Scale (HADS), the Edmonton Symptom Assessment Scale, the Sexual Desire Inventory, and sexual function (Cancer Rehabilitation Evaluation System subscale). Common causes for fatigue (anemia, depression, malnutrition, symptom distress, and medications) also were considered.

RESULTS.

Thirty‐eight of 47 patients (81%) had autonomic dysfunction, although it was not associated significantly with the other variables examined. Twenty‐nine of 45 patients (64%) had a low level of free testosterone (hypogonadism), which was correlated with the HADS Anxiety score (P = .002), the FACT Emotional Well‐Being score (P = .02), and the HADS Depression score (P = .04). Hypogonadal men also had lower scores on the FACT Functional Well‐Being scale (P = .01) and the FACIT‐F subscale (P = .05). Men who reported symptoms related to weight loss (FAACT scale) had significantly lower levels of free testosterone (r = 0.34; P = .02) but did not differ from the other group in actual weight loss (P = .22). The total testosterone level was not appropriate for screening of hypogonadism unless the patients had values <100 ng/ mL. Logistic regression analysis failed to reveal a distinct multivariate model of autonomic dysfunction or hypogonadism that predicted clinical outcomes.

CONCLUSIONS.

Hypogonadism is a frequent condition in patients with advanced, incurable cancer and is associated with negative mood, fatigue, and symptoms related to anorexia/cachexia. Cancer 2006. © 2006 American Cancer Society.
Retinal organization in the retinal degeneration 10 (rd10) mutant mouse: A morphological and ERG study
Authors: Gargini Claudia , Terzibasi Eva , Mazzoni Francesca , Strettoi Enrica
Published: November 2006

Retinal degeneration 10 (rd10) mice are a model of autosomal recessive retinitis pigmentosa (RP), identified by Chang et al. in 2002 (Vision Res. 42:517–525). These mice carry a spontaneous mutation of the rod‐phosphodiesterase (PDE) gene, leading to a rod degeneration that starts around P18. Later, cones are also lost. Because photoreceptor degeneration does not overlap with retinal development, and light responses can be recorded for about a month after birth, rd10 mice mimic typical human RP more closely than the well‐known rd1 mutants. The aim of this study is to provide a comprehensive analysis of the morphology and function of the rd10 mouse retina during the period of maximum photoreceptor degeneration, thus contributing useful data for exploiting this novel model to study RP. We analyzed the morphology and survival of retinal cells in rd10 mice of various ages with quantitative immunocytochemistry and confocal microscopy; we also studied retinal function with the electroretinogram (ERG), recorded between P18 and P30. We found that photoreceptor death (peaking around P25) is accompanied and followed by dendritic retraction in bipolar and horizontal cells, which eventually undergo secondary degeneration. ERG reveals alterations in the physiology of the inner retina as early as P18 (before any obvious morphological change of inner neurons) and yet consistently with a reduced band amplification by bipolar cells. Thus, changes in the rd10 retina are very similar to what was previously found in rd1 mutants. However, an overall slower decay of retinal structure and function predicts that rd10 mice might become excellent models for rescue approaches. J. Comp. Neurol. 500:222–238, 2007. © 2006 Wiley‐Liss, Inc.
Proinflammatory cytokine synthesis in the injured mouse spinal cord: Multiphasic expression pattern and identification of the cell types involved
Authors: Pineau Isabelle , Lacroix Steve
Published: November 2006

We have studied the spatial and temporal distribution of six proinflammatory cytokines and identified their cellular source in a clinically relevant model of spinal cord injury (SCI). Our findings show that interleukin‐1β (IL‐1β) and tumor necrosis factor (TNF) are rapidly (<5 and 15 minutes, respectively) and transiently expressed in mice following contusion. At 30–45 minutes post SCI, IL‐1β and TNF‐positive cells could already be seen over the entire spinal cord segment analyzed. Multilabeling analyses revealed that microglia and astrocytes were the two major sources of IL‐1β and TNF at these times, suggesting a role for these cytokines in gliosis. Results obtained from SCI mice previously transplanted with green fluorescent protein (GFP)‐expressing hematopoietic stem cells confirmed that neural cells were responsible for the production of IL‐1β and TNF for time points preceding 3 hours. From 3 hours up to 24 hours, IL‐1β, TNF, IL‐6, and leukemia inhibitory factor (LIF) were strongly upregulated within and immediately around the contused area. Colocalization studies revealed that all populations of central nervous system resident cells, including neurons, synthesized cytokines between 3 and 24 hours post SCI. However, work done with SCI‐GFP chimeric mice revealed that at least some infiltrating leukocytes were responsible for cytokine production from 12 hours on. By 2 days post‐SCI, mRNA signal for all the above cytokines had nearly disappeared. Notably, we also observed another wave of expression for IL‐1β and TNF at 14 days. Overall, these results indicate that following SCI, all classes of neural cells initially contribute to the organization of inflammation, whereas recruited immune cells mostly contribute to its maintenance at later time points. J. Comp. Neurol. 500:267–285, 2007. © 2006 Wiley‐Liss, Inc.
Magnetic resonance imaging and histological studies of corpus callosal and hippocampal abnormalities linked to doublecortin deficiency
Authors: Kappeler Caroline , Dhenain Marc , Phan Dinh Tuy Françoise , Saillour Yoann , Marty Serge , Fallet‐Bianco Catherine , Souville Isabelle , Souil Evelyne , Pinard Jean‐Marc , Meyer Gundela , Encha‐Razavi Ferechté , Volk Andreas , Beldjord Cherif , Chelly Jamel , Francis Fiona
Published: November 2006

Mutated doublecortin (DCX) gives rise to severe abnormalities in human cortical development. Adult Dcx knockout mice show no major neocortical defects but do have a disorganized hippocampus. We report here the developmental basis of these hippocampal abnormalities. A heterotopic band of neurons was identified starting at E17.5 in the CA3 region and progressing throughout the CA1 region by E18.5. At neonatal stages, the CA1 heterotopic band was reduced, but the CA3 band remained unchanged, continuing into adulthood. Thus, in mouse, migration of CA3 neurons is arrested during development, whereas CA1 cell migration is retarded. On the Sv129Pas background, magnetic resonance imaging (MRI) also suggested abnormal dorsal hippocampal morphology, displaced laterally and sometimes rostrally and associated with medial brain structure abnormalities. MRI and cryosectioning showed agenesis of the corpus callosum in Dcx knockout mice on this background and an intermediate, partial agenesis in heterozygote mice. Wild‐type littermates showed no callosal abnormalities. Hippocampal and corpus callosal abnormalities were also characterized in DCX‐mutated human patients. Severe hippocampal hypoplasia was identified along with variable corpus callosal defects ranging from total agenesis to an abnormally thick or thin callosum. Our data in the mouse, identifying roles for Dcx in hippocampal and corpus callosal development, might suggest intrinsic roles for human DCX in the development of these structures. J. Comp. Neurol. 500:239–254, 2007. © 2006 Wiley‐Liss, Inc.
Connections of functional areas in the mustached bat's auditory cortex with the auditory thalamus
Authors: Pearson James M. , Crocker William D. , Fitzpatrick Douglas C.
Published: November 2006

The auditory thalamus is the major target of the inferior colliculus and connects in turn with the auditory cortex. In the mustached bat, biosonar information is represented according to frequency in the central nucleus of the inferior colliculus (ICc) but according to response type in the cortex. In addition, the cortex has multiple areas with neurons of similar response type compared to the single tonotopic representation in the ICc. To investigate whether these transformations occur at the level of the thalamus, we injected anatomical tracers into physiologically defined locations in the mustached bat's auditory cortex. Injections in areas used for target ranging labeled contiguous regions of the auditory thalamus rather than separate patches corresponding to regions that respond to the different harmonic frequencies used for ranging. Injections in the two largest ranging areas produced labeling in separate locations. These results indicate that the thalamus is organized according to response type rather than frequency and that multiple mappings of response types exist. Injections in areas used for target detection labeled thalamic regions that were largely separate from those that interconnect with ranging areas. However, injections in an area used for determining target velocity overlapped with the areas connected to ranging areas and areas involved in target detection. Thus, separation by functional type and multiplication of areas with similar response type occurs by the thalamic level, but connections with the cortex segregate the functional types more completely than occurs in the thalamus. J. Comp. Neurol. 500:401–418, 2007. © 2006 Wiley‐Liss, Inc.
Spatial relationship between synapse loss and β‐amyloid deposition in Tg2576 mice
Authors: Dong Hongxin , Martin Maureen V. , Chambers Shawn , Csernansky John G.
Published: November 2006

Although there is evidence that β‐amyloid impairs synaptic function, the relationship between β‐amyloid and synapse loss is not well understood. In this study we assessed synapse density within the hippocampus and the entorhinal cortex of Tg2576 mice at 6–18 months of age using stereological methods at both the light and electron microscope levels. Under light microscopy we failed to find overall decreases in the density of synaptophysin‐positive boutons in any brain areas selected, but bouton density was significantly decreased within 200 μm of compact β‐amyloid plaques in the outer molecular layer of the dentate gyrus and Layers II and III of the entorhinal cortex at 15–18 months of age in Tg 2576 mice. Under electron microscopy, we found overall decreases in synapse density in the outer molecular layer of the dentate gyrus at both 6–9 and 15–18 months of age, and in Layers II and III of the entorhinal cortex at 15–18 months of age in Tg 2576 mice. However, we did not find overall changes in synapse density in the stratum radiatum of the CA1 subfield. Furthermore, in the two former brain areas we found a correlation between lower synapse density and greater proximity to β‐amyloid plaques. These results provide the first quantitative morphological evidence at the ultrastructure level of a spatial relationship between β‐amyloid plaques and synapse loss within the hippocampus and the entorhinal cortex of Tg2576 mice. J. Comp. Neurol. 500:311–321, 2007. © 2006 Wiley‐Liss, Inc.
Parallel thalamocortical pathways for echolocation and passive sound localization in a gleaning bat, Antrozous pallidus
Authors: Razak Khaleel A. , Shen Weiming , Zumsteg Terese , Fuzessery Zoltan M.
Published: November 2006

We present evidence for parallel auditory thalamocortical pathways that serve two different behaviors. The pallid bat listens for prey‐generated noise (5–35 kHz) to localize prey, while reserving echolocation [downward frequency‐modulated (FM) sweeps, 60–30 kHz] for obstacle avoidance. Its auditory cortex contains a tonotopic map representing frequencies from 6 to 70 kHz. The high‐frequency (BF > 30 kHz) representation is dominated by FM sweep‐selective neurons, whereas most neurons tuned to lower frequencies prefer noise. Retrograde tracer injections into these physiologically distinct cortical regions revealed that the high‐frequency region receives input from the suprageniculate (SG) nucleus, but not the ventral division of the medial geniculate body (MGBv), in all experiments (n = 9). In contrast, the low‐frequency region receives tonotopically organized input from the MGBv in all experiments (n = 16). Labeling in the SG was observed in only two of these experiments. Both cortical regions also receive sparse inputs from medial (MGBm) and parts of the dorsal division (MGBd) outside the SG. These results show that the low‐ and high‐frequency regions of a single tonotopic map receive dominant inputs from different thalamic divisions. Within the low‐frequency region, most neurons are binaurally inhibited, and an orderly map of interaural intensity difference (IID) sensitivity is present. We show that the input to the IID map arises from topographically organized projections from the MGBv. As observed in other species, a frequency‐dependent organization is observed in the lateromedial direction in the MGBv. These data demonstrate that MGBv‐to‐auditory cortex connections are organized with respect to both frequency and binaural selectivity. J. Comp. Neurol. 500:322–338, 2007. © 2006 Wiley‐Liss, Inc.
Rod bipolar cells and horizontal cells form displaced synaptic contacts with rods in the outer nuclear layer of the nob2 retina
Authors: Bayley Philippa R. , Morgans Catherine W.
Published: November 2006

The nob2 mouse carries a null mutation in the Cacna1f gene, which encodes the pore‐forming subunit of the L‐type calcium channel, Cav1.4. The loss of the electroretinogram b‐wave in these mice suggests a severe reduction in transmission between photoreceptors and second‐order neurons in the retina and supports a central role for the Cav1.4 calcium channel at photoreceptor ribbon synapses, to which it has been localized. Here we show that the loss of Cav1.4 leads to the aberrant outgrowth of rod bipolar cell dendrites and horizontal cell processes into the outer nuclear layer (ONL) of the nob2 retina and to the formation of ectopic synaptic contacts with rod photoreceptors in the ONL. Ectopic contacts are predominantly between rods and rod bipolar cells, with horizontal cell processes also present at some sites. Ectopic contacts contain apposed pre‐ and postsynaptic specializations, albeit with malformed synaptic ribbons. Cone photoreceptor terminals do not participate in ectopic contacts in the ONL. During retinal development, ectopic contacts appear in the days after eye opening, appearing progressively farther into the ONL at later postnatal stages. Ectopic contacts develop at the tips of rod bipolar cell dendrites and are less frequently associated with the tips of horizontal cell processes, consistent with the adult phenotype. The relative occurrence of pre‐ and postsynaptic markers in the ONL during development suggests a mechanism for the formation of ectopic synaptic contacts that is driven by the retraction of rod photoreceptor terminals and neurite outgrowth by rod bipolar cell dendrites. J. Comp. Neurol. 500:286–298, 2007. © 2006 Wiley‐Liss, Inc.
Strategic expression of ion transport peptide gene products in central and peripheral neurons of insects
Authors: Dai Li , Zitnan Dusan , Adams Michael E.
Published: November 2006

Structurally related ion transport peptides (ITP) and crustacean hyperglycemic hormones (CHH) are increasingly implicated in diverse metabolic and developmental functions in arthropods. We identified a conserved ITP gene encoding two peptides by alternative splicing in Manduca sexta, Bombyx mori, and Aedes aegypti: A C‐terminally amidated ITP and a C‐terminally unblocked ITP‐like peptide (ITPL), which share common N‐terminal sequences but have divergent C‐termini. In the moth M. sexta, these peptides are expressed in two, regionally distinct neuronal populations in the central and peripheral nervous systems (CNS, PNS). MasITP expression is confined to the brain in five pairs of lateral neurosecretory cells (type Ia2) projecting ipsilateral axons into the retrocerebral complex and three to five pairs of adjacent small neurons that arborize extensively within the brain. Expression of MasITPL is comparatively weak in the brain but strong in the ventral ganglia and the PNS, where MasITP is absent. MasITPL occurs in bilaterally paired neurons of all thoracic and abdominal ganglia. In the PNS, MasITPL is coexpressed with crustacean cardioactive peptide in type II link nerve neurons (L1) of abdominal segments 2–7, which project axons into neurohemal transverse nerves. During metamorphosis, additional expression of MasITPL is observed in two pairs of small lateral neurons in the brain and one pair of ventromedial neurons in each of AG2–6. A similar pattern of differential ITP and ITPL expression was observed in the CNS and PNS of B. mori and Schistocerca americana. These distinctive cellular expression patterns suggest that ITP and ITPL have evolved specialized physiological functions in arthropods. J. Comp. Neurol. 500:353–367, 2007. © 2006 Wiley‐Liss, Inc.
A locally discontinuous enriched finite element formulation for acoustics
Authors: Rochinha F. A. , Alvarez G. B. , do Carmo E. G. D. , Loula A. F. D.
Published: November 2006

In (Comput. Methods Appl. Mech. Eng. 2006, in press) we introduced a discontinuous Galerkin finite element method for Helmholtz equation in which continuity is relaxed locally in the interior of the element. The shape functions associated with interior nodes of the element are bilinear discontinuous bubbles, and the corresponding degrees of freedom can be eliminated at element level by static condensation yielding a global finite element method with the same connectivity of classical C0 Galerkin finite element approximations. Stability is provided by the discontinuous bubbles with appropriate choice of the stabilization parameters related to the weak enforcement of continuity inside each element. In the present work, departing from the stencil obtained by condensation of the bubble degrees of freedom, we build a new strategy for determining the optimal values of these parameters aiming at matching the exact wave number in two different directions. Stability and accuracy of the proposed formulation are demonstrated in several numerical examples. Copyright © 2006 John Wiley & Sons, Ltd.
Extension of weakly compressible approximations to incompressible thermal flows
Authors: El‐Amrani Mofdi , Seaïd Mohammed
Published: November 2006

Weakly compressible and advection approximations of incompressible isothermal flows were developed and tested in (Commun. Numer. Methods Eng. 2006; 22:831–847). In this paper, we extend the method to solve equations governing incompressible thermal flows. The emphasis is again on the reconstruction of unconditionally stable numerical scheme such that, restriction on time steps, projection procedures, solution of linear system of algebraic equations and staggered grids are completely avoided in its implementation. These features are achieved by combining a low‐Mach asymptotic in compressible flow equations with a semi‐Lagrangian method for the weakly compressible approach. The time integration is carried out using an explicit Runge–Kutta with variable stages. The method is applied to the natural convection flows in a squared cavity for both steady and transient computations. The numerical results demonstrate high resolution of the proposed method and confirm its capability to provide accurate and efficient simulations for thermal flow problems. Copyright © 2006 John Wiley & Sons, Ltd.
Erratum: Yan Guo. Boltzmann diffusive limit beyond the Navier‐Stokes approximation, Communications on Pure and Applied Mathematics (2006) 59(5) 626‐687
Authors: Guo Yan
Published: November 2006

The original article to which this erratum refers was published in Communications on Pure and Applied MathematicsComm Pure Appl Math(2006)59(5) 626.
Multiprogramming a distributed‐memory multiprocessor
Authors: Leuze Michael R. , Dowdy Lawrence W. , Park Kee Hyun
Published: November 2006

The development of computing systems with large numbers of processors has been motivated primarily by the need to solve large, complex problems more quickly than is possible with uniprocessor systems. Traditionally, multiprocessor systems have been uniprogrammed, i.e., dedicated to the execution of a single set of related processes, since this approach provides the fastest response for an individual program once it begins execution. However, if the goal of a multiprocessor system is to minimize average response time or to maximize throughput, then multiprogramming must be considered.

In this paper, a model of a simple multiprocessor system with a two‐program workload is reviewed; the model is then applied to an Intel iPSC/2 hypercube multiprocessor with a workload consisting of parallel wavefront algorithms for solving triangular systems of linear equations. Throughputs predicted by the model are compared with throughputs obtained experimentally from an actual system. The results provide validation for the model and indicate that significant performance improvements for multiprocessor systems are possible through multiprogramming.
Supersonic fluid flow in parallel with an unstructured mesh
Authors: Williams Roy D.
Published: November 2006

An algorithm has been implemented for time‐accurate solutions of the two‐dimensional compressible Euler equations using an irregular triangular mesh. The code runs on distributed or shared memory or sequential machines, and is written using the Distributed Irregular Mesh Environment (DIME). DIME is a programming environment for calculations with such meshes, with adaptive mesh refinement and dynamic load balancing. Results are presented for an example of a Mach 3 flow over a step, computed with a 32‐processor NCUBE hypercube.
A Parallel sorting algorithm for tightly coupled multiprocessors
Authors: Wheat Mitchell
Published: November 2006

In this paper we present a new parallel sorting algorithm suitable for implementation on a tightly coupled multiprocessor. The algorithm utilizes P processors to sort a set of N data items subdivided into M subsets. The performance of the algorithm is investigated, and the results of experiments carried out on the Balance 8000 multiprocessor are presented.
A step‐wise‐overlapped parallel annealing algorithm on a message‐passing multiprocessor system
Authors: Kim Youngtak , Kim Myunghwan
Published: November 2006

This paper proposes a parallel annealing algorithm, called step‐wise‐overlapped parallel annealing, that can provide a massive speed‐up utilizing a multiprocessor system with a large number of processors. We improve the parallel annealing scheme of the systolic algorithm that was proposed by Aart et al. Instead of the temperature decrement at each subchain, it decides the decrement ratio at the start of each Markov chain using the standard deviation of the cost distribution in the previous Markov chain of the full length. Thus the improved annealing schedule keeps a good temperature profile even with a large number of processors. We also enhance the communication pattern.

The new parallel annealing algorithm has a simple communication pattern and thus less communication overheads. The decomposition strategy of this parallel annealing algorithm is independent of application problems. Experimental results of the step‐wise‐overlapped parallel annealing algorthm for the travelling salesman problems show high efficiencies even when a large number of processors are used; it produces near optimal solutions with a speedup of 70.8 by using 128 processors. It can be implemented efficiently on a message‐passing multiprocessor system with a large number of processors, such as a hypercube computer.
Benchmarking advanced architecture computers
Authors: Messina P. , Felten E. , Hipes P. , Williams R. , Alagar A. , Kamrath A. , Leary R. , Pfeiffer W. , Rogers J. , Walker D.
Published: November 2006

Recently, a number of advanced architecture machines have become commercially available. These new machines promise better cost performance than traditional computers, and some of them have the potential of competing with current supercomputers, such as the CRAY X‐MP, in terms of maximum performance. This paper describes the methodology and results of a pilot study of the performance of a broad range of advanced architecture computers using a number of complete scientific application programs. The computers evaluated include:

shared‐memory bus architecture machines such as the Alliant FX/8, the Encore Multimax, and the Sequent Balance and Symmetry

shared‐memory network‐connected machines such as the Butterfly

distributed‐memory machines such as the NCUBE, Intel and Jet Propulsion Laboratory (JPL)/Caltech hypercubes

very long instruction word machines such as the Cydrome Cydra‐5

SIMD machines such as the Connection Machine

‘traditional’ supercomputers such as the CRAY X‐MP, CRAY‐2 and SCS‐40.

Seven application codes from a number of scientific disciplines have been used in the study, although not all the codes were run on every machine. The methodology and guidelines for establishing a standard set of benchmark programs for advanced architecture computers are discussed. The CRAYs offer the best performance on the benchmark suite; the shared memory multiprocessor machines generally permitted some parallelism, and when coupled with substantial floating point capabilities (as in the Alliant FX/8 and Sequent Symmetry), provided an order of magnitude less speed than the CRAYs. Likewise, the early generation hypercubes studied here generally ran slower than the CRAYs, but permitted substantial parallelism from each of the application codes.
Performance of a benchmark parallel implementation of the Van Slyke and Wets algorithm for two‐stage stochastic programs on the Sequent/Balance
Authors: Ariyawansa K. A. , Hudson D. D.
Published: November 2006

We describe a benchmark parallel version of the Van Slyke and Wets (1969) algorithm for two‐stage stochastic programs and an implementation of that algorithm on the Sequent/Balance. We also report results of a numerical experiment using random test problems and our implementation. These performance results, to the best of our knowledge, are the first available for the Van Slyke and Wets (1969) algorithm on a parallel processor. They indicate that the benchmark implementation parallelizes well.
Cluster Identification Algorithms for Spin Models — Sequential and Parallel
Authors: Baillie Clive F. , Coddington Paul D.
Published: November 2006

Monte Carlo cluster update algorithms are extremely efficient for simulating spin models near their phase transitions, where local update algorithms suffer severe critical slowing down. Unfortunately, as the cluster algorithms are highly irregular as well as nonlocal, they are much more difficult to parallelize efficiently. The main difficulty lies in identifying which spins belong to which cluster. In this paper we investigate a number of cluster identification algorithms, both sequential and parallel, which we have implemented on serial, SIMD and MIMD computers.
‘Blade Runner’: A real‐time speech recognizer
Authors: Chong Mike , Fallside Frank , Marsland Tim , Prager Richard
Published: November 2006

A real‐time prototype speech recognizer has been implemented on a 66‐processor distributed‐memory parallel computer. Simple phrases are recognized in approximately 4 to 10 seconds. Scalability, performance and flexibility are the three main aims of this implementation, the ultimate goal being to construct a large vocabulary speech recognizer which responds quickly. A set of three techniques is investigated in this implementation: asynchronous methodology to minimize synchronization overheads, distributed control to avoid a central communications bottleneck, and dynamic load balancing to provide a flexible response to an unpredictable computational load. The effect on memory, processor time allocation and communications is observed in real‐time using hardware monitoring aids.
Parallel processing architectures used in a realtime display application
Authors: Vaughan J. R. , Brookes G. R. , Fletcher M. A. , Wills D. P. M.
Published: November 2006

Data which is stored as a terrain data base is to be displayed graphically in a real‐time application. Various parallel configurations of processing elements have been used to achieve the required performance. The results which have been achieved using transputers as the processing elements are presented in this report.
Performance of dynamic load balancing algorithms for unstructured mesh calculations
Authors: Williams Roy D.
Published: November 2006

If a finite element mesh has a sufficiently regular structure, it is easy to decide in advance how to distribute the mesh among the processors of a distributed‐memory parallel processor, but if the mesh is unstructured the problem becomes much more difficult. The distribution should be made so that each processor has approximately equal work to do, and such that communication overhead is minimized.

If the mesh is solution‐adaptive, i.e. the mesh and hence the load‐balancing problem change discretely during execution of the code, then it is most efficient to decide the optimal mesh distribution in parallel. In this paper three parallel algorithms, orthogonal recursive bisection (ORB), eigenvector recursive bisection (ERB) and a simple parallelization of simulated annealing (SA) have been implemented for load balancing a dynamic unstructured triangular mesh on 16 processors of an NCUBE machine.

The test problem is a solution‐adaptive Laplace solver, with an initial mesh of 280 elements, refined in seven stages to 5772 elements. We present execution times for the solver resulting from the mesh distributions using the three algorithms, as well as results on imbalance, communication traffic and element migration.

The load‐balancing itself is fastest with ORB, but a very long run of SA produces a saving of 21% in the execution time of the Laplace solver. ERB is only a little slower than ORB, and yet produces a mesh distribution whose execution time is 15% faster than ORB.
Performance of a particle‐in‐cell plasma simulation code on the BBN TC2000
Authors: Sturtevant Judy E. , Campbell Phil M. , Maccabe Arthur B.
Published: November 2006

The BBN TC2000 is a multiple instruction, multiple data (MIMD) machine that combines a physically distributed memory with a logically shared memory programming environment using the unique Butterfly switch. Particle‐in‐cell (PIC) plasma simulations model the interaction of charged particles with electric and magnetic fields. This paper describes the implementation of both a 1‐D electrostatic and a 2 1/2‐D electromagnetic PIC (particle‐in‐cell) plasma simulation code on a BBN TC2000. Performance is compared to implementation of the same code on the shared memory Sequent Balance 21000.
Numerical simulation of three‐dimensional thermal convection on the array processor DAP 510
Authors: Erhard W. , Schäfer M.
Published: November 2006

In this paper we deal with the numerical simulation of time dependent three‐dimensional thermal convection on the array processor DAP 510. Applying finite differences in combination with a pressure correction method to the underlying non‐linear system of partial differential equations, we reduce the numerical solution of the problem to the solution of a sequence of sparse linear systems. Using polynomial preconditioned conjugate gradient methods for the solution of these systems results in a highly parallel algorithm for the simulation of the considered flows on the DAP 510. Using this parallel algorithm, data can be mapped in different ways onto the processor array. Depending on the number of grid points, several methods are shown. Numerical experiments illustrate the capabilities of the proposed algorithm.
Fault‐tolerant parallel programming in Argus
Authors: Bal Henri E.
Published: November 2006

Fault tolerance is an issue ignored in most parallel languages. The overhead of making parallel, high‐performance programs resilient to processor crashes is often too high, given the low probability of such events. If parallel systems become more large‐scaled, however, processor failures will become likely, so they should be dealt with. Two approaches to this problem are feasible. First, the system can make programs fault‐tolerant transparently. It can log messages, make checkpoints, and so on. Second, the programmer can write explicit code for handling failures in an application‐specific way. The latter approach is potentially more efficient, but also requires more work from the programmer. In this paper, we intend to get some initial insight into how hard and efficient explicit fault‐tolerant parallel programming is. We do so by implementing four parallel applications in Argus, a language supporting parallelism as well as fault tolerance. Our experiences indicate that the extra effort needed for fault tolerance varies much between different applications. Also, trade‐offs can frequently be made between programming effort and efficiency. One lesson we learned is that fault tolerance should not be added as an afterthought, but is best taken into account from the start. As another result, the ability to integrate transparent and explicit mechanisms for fault tolerance would sometimes be highly useful.
Computation and data movement on RP3
Authors: Brochard Luigi , Freau Alex
Published: November 2006

We present in this paper a study of the computation and communication costs on RP3 and on some issues about algorithm designs on a three‐level memory hierarchy multi‐processor. Using very simple algorithms (vector‐add, vector‐sum, saxpy, … ), we compare different implementations which differ on data localization (global or local) and data cacheability (cacheable or non‐cacheable). This comparison is done using a performance monitoring system (VPMC) that records instructions, data movement, cache requests and misses. The output of the VPMC was then used as input to an analytical performance model which we used to compute the elemental computation and communication times of every basic algorithm. Regarding cacheability (marking the data cacheable instead of non‐cacheable), we found it worthwhile as long as data are blocked adequately. For our simple 1‐D data structures, a block size equal to a multiple of the cache line size gives the best results. However, considering possible load imbalance, a block size equal to the cache line seems optimal. Regarding localization (copying data from global to local, working on local data instead of global and copying data back), we found it ineffective, at least with the RP3 local and global communication speed ratios (1:10:15).
Designing Algorithms on RP3
Authors: Brochard Luigi , Freau Alex
Published: November 2006

We study here the behavior of two numerical algorithms (matrix multiplication and finite difference method) on a three‐level memory hierarchy multi‐processor RP3. Using different versions of these algorithms, which differ on data placement (global, local, global and cacheable, local and cacheable) and on data access (blocked or non‐blocked), we study the impact of these parameters on the performance of the program. This performance analysis is done using a very accurate monitoring system (VPMC) which records instructions, memory requests, cache requests and misses. We perform also a theoretical performance analysis of these programs using a model of computation and communication. Good agreement is found between theoretical and experimental results. As a conclusion we discuss the use of local memory on such a machine and show that it is ineffective with RP3 cache, local and global memory communication speed ratios. We also discuss optimal use of cache and show that the optima can only be realized under some cache properties (private store‐in cache with user control of write‐back) and show that blocked optimal algorithms are to be used to find it. Comparing programming of shared and distributed memory multi‐processors, we remark that optimized algorithms for shared memory systems utilize the same blocking techniques used for programming distributed memory systems, leading to a common programming paradigm.
Parallel‐processing applications for data analysis in the social sciences
Authors: Skvoretz John , Smith Shelley A. , Baldwin Chuck
Published: November 2006

We examine parallel‐processing applications to the analysis of large data sets typically used in social science research. Our research uses a parallel environment which makes it possible to have 1024 processors working simultaneously on a problem. The application is tested using various configurations of number of processors and block‐size of data reads on the estimation of a linear model of earnings for the California portion of the 15% sample of the 1970 Census. Performance factors assessed include total execution time, speed‐up and efficiency. Execution times are also compared with reference to execution times on an IBM 3081 using SPSS‐X. Results indicate that optimal configurations of number of processors and data block‐size can produce significantly faster execution times for linear model estimation on relatively large (80,000 cases) data sets. We also discuss other applications of parallel processing to statistical analyses commonly found in social science.
Data parallel sorting for particle simulation
Authors: Dagum Leonardo
Published: November 2006

Sorting on a parallel architecture is a communications intensive event which can incur a high penalty in applications where it is required. In the case of particle simulation, only integer sorting is necessary, and sequential implementations easily attain the minimum performance bound of O(N) for N particles. Parallel implementations, however, have to cope with the parallel sorting problem which, in addition to incurring a heavy communications cost, can make the minimum performance bound difficult to attain. This paper demonstrates how the sorting problem in a particle simulation can be reduced to a merging problem, and describes an efficient data parallel algorithm to solve this merging problem in a particle simulation. The new algorithm is shown to be optimal under conditions usual for particle simulation, and its fieldwise implementation on the Connection Machine is analysed in detail. The new algorithm is about four times faster than a fieldwise implementation of radix sort on the Connection Machine.
Hypercube clock synchronization
Authors: Dunigan Thomas H.
Published: November 2006

Algorithms for synchronizing the times and frequencies of the clocks of Intel and Ncube hypercube multiprocessors are presented. Bounds for the error in estimating clock offsets and frequencies are formulated in terms of the clock read error and message transmission time. Clock and communication performance of the Ncube and Intel hypercubes are analysed, and performance of the synchronization algorithms is presented.
Efficient communication primitives on hypercubes
Authors: Ho Ching‐Tien , Raghunath M. T.
Published: November 2006

We give practical algorithms, complexity analysis and implementation for one‐to‐all broadcasting, all‐to‐all personalized communication and matrix transpose (with two‐dimensional partitioning of the matrix) on hypercubes. We assume the following communication characteristics: circuit‐switched, e‐cube routing and one‐port communication model.

For one‐to‐all broadcasting, we give an algorithm that combines the well‐known recursive doubling algorithm[1] and the algorithm based on edgedisjoint spanning trees[2]. The measured times of the combined algorithm are always superior to those of the edge‐disjoint spanning tree algorithm and outperform the recursive doubling algorithm. For all‐to‐all personalized communication we propose a hybrid algorithm that combines the well‐known recursive doubling algorithm[3,4] and the recently proposed direct‐route algorithm[5,6] Our hybrid algorithm balances between data transfer time and start‐up time of these two algorithms, and its communication complexity is estimated to be better than the two previous algorithms for a range of machine parameters. For matrix transpose with two‐dimensional partitioning of the matrix, we relate a two‐phase algorithm to the previous result in Reference 7. The algorithm is predicted to be better than the recursive transpose algorithm[8] by n nearest‐neighbor communications[4]. It takes advantage of circuit‐switched routing and is congestion‐free within each phase. We also suggest a way of storing the matrix such that the transpose operation can be realized in one phase without congestion.
A fast poisson solver for distributed memory multiprocessors
Authors: Serafino D. Di , Murli A. , Perla F.
Published: November 2006

We present a parallel algorithm for distributed memory multiprocessors, which is based on generalized marching (GM), one of the fastest methods in the class of fast Poisson solvers.

The GM algorithm is not suited for any but very coarse‐grain parallel processing. The main difficulty with parallelization is that the number of independent processes and the amount of work in each process change exponentially and in inverse proportion of each other.

To improve parallelism, the matrices involved in GM are diagonalized performing multiple FFTs. In this way, independent processes extending across all the algorithm are obtained.

The parallel GM has been tested on an Ncube/10 and a Symult S2010, running the Express communication system. A performance evaluation has been carried out using a scaled efficiency model and some classical parameters.
Parallelizing the spectral transform method. Part II
Authors: Walker David W. , Worley Patrick H. , Drake John B.
Published: November 2006

The spectral transform method is a widely used numerical technique for solving partial differential equations on the sphere in global climate modeling. This paper describes the parallelization and performance of the spectral method for solving the non‐linear shallow water equations on the surface of a sphere using a 128‐node Intel iPSC/860 hypercube. Solving the shallow water equations represents a computational kernel of more complex climate models. This work is part of a research program to develop climate models that are capable of much longer simulations at a significantly finer resolution than current models. Such models are important in understanding the effects of the increasing atmospheric concentrations of greenhouse gases, and the computational requirements are so large that massively parallel multiprocessors will be necessary to run climate model simulations in a reasonable amount of time.

The spectral method involves the transformation of data between the physical, Fourier and spectral domains. Each of these domains is two‐dimensional. The spectral method performs Fourier transforms in the longitude direction followed by summation in the latitude direction to evaluate the discrete spectral transform. A simple way of parallelizing the spectral code is to decompose the physical problem domain in just the latitude direction. This allows an optimized sequential FFT algorithm to be used in the longitude direction. However, this approach limits the number of processors that can be brought to bear on the problem. Decomposing the problem over both directions allows the parallelism inherent in the problem to be exploited more effectively‐the grain size is reduced, so that more processors can be used.

Results are presented that show that decomposing over both directions does result in a more rapid solution of the problem. The results show that, for a given problem and number of processors, the optimum decomposition has approximately equal numbers of processors in each direction. Load imbalance also has an impact on the performance of the method. The importance of minimizing communication latency and overlapping communication with calculation is stressed. General methods for doing this, that may be applied to many other problems, are discussed.
Parallel program design using high‐level Petri nets
Authors: Gorton Ian
Published: November 2006

Petri nets are proposed as a general‐purpose design and modelling tool for parallel programs. The advantages of Petri nets for this purpose are discussed, and a solution to the Dining Philosophers problem is developed using simple Place‐Transition nets. The limitations of Place‐Transition nets are described, and the Dining Philosophers problem is used to illustrate how Coloured Petri nets can overcome these limitations. A more complex example of a Coloured Petri net is then given, and it is shown how a collection of processes in the Occam programming language can be developed directly from the properties of the net. Another Petri net model of a simple process farm is given, and a solution is developed in Parallel C: this further highlights the suitability of Petri nets as a design tool for parallel programs.
Massively parallel solution of quadratic programs via successive overrelaxation
Authors: De Leone R. , Roth M. A. Tork
Published: November 2006

Serial and parallel successive overrelaxation (SOR) solutions of specially structured large‐scale quadratic programs with simple bounds are discussed. By taking advantage of the sparsity structure of the problem, the SOR algorithm was successfully implemented on two massively parallel Single‐Instruction‐Multiple‐Data machines: a Connection Machine CM‐2 and a MasPar MP‐1. Computational results for the well known obstacle problems show the effectiveness of the algorithm. Problems with millions of variables have been solved in a few minutes on these massively parallel machines, and speed‐ups of 90% or more were achieved.