bluuebunny/crossref_metadata_2025 huggingface dataset:
Parallel Distributed FFT-Based Solvers for 3-D Poisson Problems in Meso-Scale Atmospheric Simulations
Authors: Giraud Luc , Guivarch Ronan , Stein Joël
Published: March 2005

Fast Poisson solvers based on fast Fourier transform (FFT) computations are among the fastest techniques to solve Poisson equation on uniform grids. In this paper, the authors present two parallel distributed implementations of a 3-D fast Poisson solver in the context of the atmospheric simulation code. The first approach consists of implementing data movement between each computational step so that no elementary computational routine involves communication. The second approach aims at reducing the global data movement and requires the parallelization of one step of the fast Poisson solver. Experimental results on a 128-node Cray T3E are presented to illustrate the advantages and drawbacks of each approach.
Parallel Implementation and Practical Use of Sparse Approximate Inverse Preconditioners with a Priori Sparsity Patterns
Authors: Chow Edmond
Published: March 2005

This paper describes and tests a parallel message-passing code for constructing sparse approximate inverse preconditioners using Frobenius norm minimization. The sparsity patterns of the preconditioners are chosen as patterns of powers of sparsified matrices. Sparsification is necessary when powers of a matrix have a large number of nonzeros, making the approximate inverse computation expensive. For our test problems, the minimum solution time is achieved with approximate inverses with less than twice the number of nonzeros of the original matrix. Additional accuracy is not compensated by the increased cost per iteration. The results lead to further understanding of how to use these methods and how well these methods work in practice. In addition, this paper describes programming techniques required for high performance, including one-sided communication, local coordinate numbering, and load repartitioning.
Using AMDAHL’s Law as a Metric to Drive Code Parallelization: Two Case Studies
Authors: Horoi Mihai , Enbody Richard J.
Published: March 2005

Using Amdahl’s law as a metric, the authors illustrate a technique for developing efficient code on massively parallel processor performance-class networks to solve nontrivial, high performance scientific problems. They also show the importance of collective communication within the message-passing interface paradigm for some applications. Given the popularity of Beowulf-like clusters of workstations, this work also indicates the necessity of a scalable high performance network for obtaining efficient performance in parallel code. Using this approach, the authors were able to obtain an effective speedup (comparison with the best sequential time) of 170 when using 256 of the Cray T3E 900 processing elements to solve a carbon, molecular-dynamic problem. The authors also examine the approach on a very different application: a Lanczos eigenvalue solver.
High Performance Computing Systems for Autonomous Spaceborne Missions
Authors: Sterling Thomas , Katz Daniel S. , Bergman Larry
Published: March 2005

Future-generation space missions across the solar system to the planets, moons, asteroids, and comets may someday incorporate supercomputers both to expand the range of missions being conducted and to significantly reduce their cost. By performing science computation directly on the spacecraft itself, the amount of data required to be downlinked may be reduced by many orders of magnitude, thus greatly reducing the mass of the resources needed for communication while increasing the quality and quantity of the science achieved. By performing the mission planning in real time directly on the spacecraft, complex and highly responsive missions can be conducted out of range of direct human intervention, and the cost of mission management can be reduced. Through highly replicated computing structures, continued operation can be maintained in the presence of faults by means of graceful degradation. Two classes of systems, reflecting very different strategies of computer system architecture, are actively being pursued by the NASA Jet Propulsion Laboratory (JPL) to take advantage of the opportunity of embedded high performance computing on spacecraft for deep-space missions. Commodity off-the-shelf (COTS) clusters may permit the direct application of commercial computing hardware in loosely coupled ensembles to benefit from the enormous investment of industry in mass-market components. New processor-in-memory (PIM) architectures combine multiple nodes on a single chip of processor-memory pairs exposing the full memory bandwidth. This paper examines the driving issues motivating the use of supercomputing for future deep-space missions and describes two active research projects at NASA JPL that are pursuing both the COTS and PIM strategies for next-generation spaceborne computing.
Numerical Libraries and the Grid
Authors: Petitet Antoine , Blackford Susan , Dongarra Jack , Ellis Brett , Fagg Graham , Roche Kenneth , Vadhiyar Sathish
Published: March 2005

This paper describes an overall framework for the design of numerical libraries on a computational grid of processors in which the processors may be geographically distributed and under the control of a grid-based scheduling system. Experiments are presented in the context of solving systems of linear equations using routines from the ScaLAPACK software collection along with various grid service components, such as Globus, NWS, and Autopilot.
Interactive Large-Scale Soil Modeling Using Distributed High Performance Computing Environments
Authors: Carrillo Alex R. , West John E. , Horner David A. , Peters John F.
Published: March 2005

The ability to visually interact with and guide a running simulation can greatly enhance understanding of both the nature of a numerical model and the characteristics of the underlying physical process. This article will discuss the development of a distributed, interactive modeling system capable of providing responsive visual feedback to user input. The system is built around a discrete element soil model being used to simulate the behavior of soil masses under large deformations. In designing this application to be interactively responsive to the user for soil masses of several hundred thousand particles, a range of technical problems were encountered, including the computational burden of the discrete element method (DEM), real-time visualization of large particle masses, and communication of data over large distances between heterogeneous resources using a variety of networks. This article will highlight how each of those obstacles was addressed and discuss the effectiveness of the final system.
Performance Enhancement on Microprocessors with Hierarchical Memory Systems for Solving Large Sparse Linear Systems
Authors: Wang G. , Tafti Danesh K.
Published: March 2005

In recent years, scientific computing is being driven by microprocessor-based architectures. Most architectural designs are characterized by fast processors, fast but small caches, and large but slow memories. As a result, problems of small sizes that fit in cache perform exceedingly well, whereas the performance of larger problems is limited by the speed of memory. In this paper, the authors study the performance characteristics of several iterative kernels for solving sparse linear systems on several popular microprocessors. Given the performance limitations posed by slow memory on large problem sizes, the authors show the effectiveness of using domain decomposition methods of the additive Schwarz type to enhance performance on single microprocessors.
Impact of Physical/Logical Network Topology on Parallel Matrix Computation
Authors: Chu Eleanor
Published: March 2005

In this work, the impact of physical/logical network topology on parallel matrix computation is studied on an Intel Touchstone DELTA mesh and three generations of hyper-cube multiprocessors. These machines are representative of the continued development of distributed-memory message-passing multiprocessors in the current decade. As the processor architecture and the network hardware continue to improve, it is important that the software being developed can easily take advantage of such improvement. The author shows that for a collection of mathematical software fundamental to parallel matrix computation, this objective is accomplished by basing the parallel algorithms and the software development on a logical subcube-grid network topology. Since a hypercube can be configured as a subcube-grid, a logical subcube-grid is naturally supported by an identical physical subcube-grid embedded in a hypercube network. However, a mesh network has fewer connections than a subcube-grid, and the aspect ratios of the available physical mesh or submeshes may not be altered. This analysis shows that the optimal aspect ratio of the physical mesh is independent from that of the desired logical subcube-grid. The author shows that to achieve the best performance on the DELTA mesh, the optimal aspect ratios for the physical mesh and the logical subcube-grid should be chosen independently at runtime. Numerical experiments were performed on the DELTA mesh and the hypercubes using the same software, and extensive timing results are provided to demonstrate this finding.
High Performance FFT Algorithms for Cache-Coherent Multiprocessors
Authors: Wadleigh Kevin R.
Published: March 2005

Computing one-dimensional fast Fourier transforms (FFTs) on microprocessors requires different algorithms, depending on whether the problem fits in the data cache. This paper describes efficient algorithms for both cases. Some implementations of out-of-cache one-dimensional FFTs use a six-step approach to reduce the number of cache misses. The six-step approach may be altered into a seven-step approach that allows increased data cache reuse. A natural parallelism is also developed. Performance results using these techniques are given for the Hewlett-Packard HP 9000 V-Class V2250 server.
Design and Evaluation of an HPVM-Based Windows NT Supercomputer
Authors: Chien A. , Lauria M. , Pennington R. , Showerman M. , Iannello G. , Buchanan M. , Connelly K. , Giannini L. , Koeni G. , Krishnamurthy S. , Liu Q. , Pakin S. , Sampemane G.
Published: March 2005

We describe the design and evaluation of a 192-processor Windows NT cluster for high performance computing based on the High Performance Virtual Machine (HPVM) communication suite. While other clusters have been described in the literature, building a 58 GFlop/s NT cluster to be used as a general-purpose production machine for NCSA required solving new problems. The HPVM software meets the challenges represented by the large number of processors, the peculiarities of the NT operating system, the need for a production-strength job submission facility, and the requirement for mainstream programming interfaces. First, HPVM provides users with a collection of standard APIs like MPI, Shmem, Global Arrays with supercomputer class performance (13 μs minimum latency, 84 MB/s peak bandwidth for MPI), efficiently delivering Myrinet’s hardware performance to application programs. Second, HPVM provides cluster management and scheduling (through integration with Platform Computing’s LSF). Finally, HPVM addresses Windows NT’s remote access problem, providing convenient remote access and job control (through a graphical Java-applet front-end). Given the production nature of the cluster, the performance characterization is largely based on a sample of the NCSA scientific applications the machine will be running. The side-by-side comparison with other present-generation NCSA supercomputers shows the cluster to be within a factor of 2 to 4 of the SGI Origin 2000 and Cray T3E performance at a fraction of the cost. The inherent scalability of the cluster design produces a comparable or better speedup than the Origin 2000 despite a limitation in the HPVM flow control mechanism.
Adaptive Scheduling for Task Farming with Grid Middleware
Authors: Casanova Henri , Kim MyungHo , Plank James S. , Dongarra Jack J.
Published: March 2005

Scheduling in metacomputing environments is an active field of research as the vision of a Computational Grid becomes more concrete. An important class of Grid applications are long-running parallel computations with large numbers of somewhat independent tasks (Monte Carlo simulations, parameter-space searches, etc.). A number of Grid middleware projects are available to implement such applications, but scheduling strategies are still open research issues. This is mainly due to the diversity of both Grid resource types and their availability patterns. The purpose of this work is to develop and validate a general adaptive scheduling algorithm for task farming applications along with a user interface that makes the algorithm accessible to domain scientists. The authors’ algorithm is general in that it is not tailored to a particular Grid middleware and it requires very few assumptions concerning the nature of the resources. Their first testbed is NetSolve as it allows quick and easy development of the algorithm by isolating the developer from issues such as process control, I/O, remote software access, or fault-tolerance.
Using Apples to Schedule Simple SARA on the Computational Grid
Authors: Su Alan , Berman Francine , Wolski Richard , Strout Michelle Mills
Published: March 2005

Computational Grids, composed of distributed and often heterogeneous computing resources, have become the platform of choice for many performance-challenged applications. Proof-of-concept implementations have demonstrated that both Grids and clustered environments have the potential to provide great performance benefits to distributed resource-intensive applications. However, at the present time, careful staging, scheduling, and/or reservation of resources is essential in order for applications to achieve performance in Grid environments. If Computational Grids and shared computational clusters are to achieve their full potential, it must be possible for users to achieve application performance at any given time, and when other users are present in the system. In this paper, we describe the initial development of an AppLeS (application-level scheduler) for the resource selection portion of the Synthetic Aperture Radar Atlas (SARA) application, developed at the Jet Propulsion Laboratory (JPL) and the San Diego Supercomputer Center (SDSC). We demonstrate the effectiveness of application scheduling for distributed data applications such as SARA by providing a performance-efficient strategy for retrieving SARA data files in everyday, multiple-user Grid environments.
Distributed Parallel Computing for Fluid-Structure Coupled Simulations on a Heterogeneous Parallel Computer Cluster
Authors: Kimura Toshiya , Takemiya Hiroshi
Published: March 2005

Distributed parallel computing for a fluid-structure coupled simulation has been performed on a heterogeneous parallel computer cluster. The fluid and the structure dynamics are simulated on different parallel computers connected by a high-speed local network. These dynamics are coupled by a loose coupling method exchanging the boundary data between the fluid and the structure domains through the network. The data communication among parallel computers is realized by using the new communication library, Stampi, which has been developed to enable communication in a heterogeneous environment. The performance evaluation on a heterogeneous parallel computer cluster has shown that the distributed parallel computing for fluid-structure coupled simulations has the advantage of increasing the performance compared with the parallel computing on a single parallel computer.
Economic Value of Conservation: The Case of the Asian Elephant
Authors: Bandara Ranjith
Published: March 2005

The survival of both Asian and African elephants has become increasingly critical. However, in many respects, the survival of the Asian elephant is more precarious than that of the African elephant. Throughout its range, the populations of Asian elephants have declined in recent decades while aggravating the conflict with human interests. This article examines the historical evidence about the abundance and geographical distribution of the Asian Elephant, and then discusses the economic, social and institutional dilemmas which are associated with conservation of elephants and mitigation of human-elephant conflict in Asia. The point is then highlighted and illustrated that new thinking about economic value strengthens the social case for the conserving the remaining populations of Asian elephants.
Globalization and South Asia: A Perspective
Authors: Murshed S. Mansoob
Published: March 2005

This article is about the contribution of increased international trade to the growth of international inequality and disparities between the developed and developing worlds. The central argument is that globalization in the nineteenth century created the present-day Third World, and contemporary globalization perpetuates this marginalization of the developing world. The difference lies in the fact that global disparities and inequities are far more transparent in our virtually uncensored information age. Throughout this article, I mainly refer to the ‘increased trade’ aspect of globalization, particularly the policy imperative to engineer increased trade, which is so keenly advocated by economic development specialists from both the North and the South. I also stress the hegemonistic and coercive aspect of globalization, which governs the asymmetric and unequal interaction between the North and the South. The processes of marginalization of the Third World during the two historical phases of globalization have certain striking historical similarities. I discuss mechanisms through which the growth of international trade may not promote convergence in incomes between North and South, utilizing in particular the new theories of international trade. I describe the nature of international inequality in our age of globalization. The article also traces the relative success of the South Asian region during the post-1980 period of rapid globalization. Finally, the article concludes by reviewing the backlash to globalization in our digital age, along with historical parallels.
Juvenile Transfers as Ritual Sacrifice
Authors: Titus Jordan J.
Published: March 2005

This article explores the dramaturgy of juvenile transfer provisions for the vestiges of ancient practices of child sacrifice that they reveal. Relying on theories by Girard, the social discord caused by young children who commit violent criminal acts is examined as a sacrificial crisis. The rhetorical demonization of the child criminal is described as their expurgation (as “Other”), the means by which their status is converted to scapegoat for the innocents their surrogacy benefits. Rather than deterrence or retribution functions, the legal response to children’s normative violations that involves transferring children to adult criminal court are presented here as an institutionalized and symbolic form of sacrifice to resolve a cultural crisis and ensure societal cohesion.
Using Snowball-Based Methods in Hidden Populations to Generate a Randomized Community Sample of Gang-Affiliated Adolescents
Authors: Petersen Rebecca D. , Valdez Avelardo
Published: March 2005

Snowball-based methods frequently have been used when working with hidden populations whose members are difficult to identify and locate. By the very nature of the processes of these methods, such samples usually are not random or representative, thereby, resulting in selection bias. This study provides a framework on how to generate a randomized community-based sample of Mexican American adolescent females involved with gangs whose understanding merits further examination given their apparent increase in number and degree. Research findings from a more robust sample can accentuate appropriate policy formation as well as prevention and intervention programs aimed at improving the lives of high-risk youth.
Local therapy with CpG motifs in a murine model of allergic airway inflammation in IFN-β knock-out mice
Authors: Matheu Victor , Treschow Alexandra , Teige Ingrid , Navikas Vaidrius , Issazadeh-Navikas Shohreh
Published: March 2005

Background

CpG oligodeoxynucleotides (CpG-ODN) are capable of inducing high amounts of type I IFNs with many immunomodulatory properties. Furthermore, type-I IFNs have been proposed to play a key role in mediating effects of CpG-ODN. The precise role of IFN-β in the immunomodulatory effects of CpG-ODN is not known.

Objective

Here, we aimed to elucidate the role of IFN-β in the anti-allergic effect of CpG motifs.

Methods

We assessed the immune response in OVA-primed/OVA-challenged IFN-β knockout (-/-) mice compared to wild type (WT) control, after intranasal and systemic treatment with synthetic CpG motifs.

Results

Vaccination with CpG-ODN reduced the number of cells in airways of OVA-sensitized WT but not IFN-β-/- mice. Although airway eosinophilia was reduced in both treated groups, they were significantly higher in IFN-β-/- mice. Other inflammatory cells, such as lymphocytes and macrophages were enhanced in airways by CpG treatment in IFN-β-/- mice. The ratio of IFN-γ/IL-4 cytokines in airways was significantly skewed to a Th1 response in WT compared to IFN-β-/- group. In contrast, IL-4 and IgE were reduced with no differences between groups. Ag-specific T-cell proliferation, Th1-cytokines such as IFN-γ, IL-2 and also IL-12 were significantly lower in IFN-β-/- mice. Surprisingly, we discovered that intranasal treatment of mice with CpG-ODN results in mild synovitis particularly in IFN-β-/- mice.

Conclusion

Our results indicate that induction of Th1 response by therapy with CpG-ODN is only slightly and partially dependent on IFN-β, while IFN-β is not an absolute requirement for suppression of airway eosinophilia and IgE. Furthermore, our finding of mild synovitis is a warning for possible negative effects of CpG-ODN vaccination.
wFleaBase: the Daphnia genome database
Authors: Colbourne John K , Singan Vasanth R , Gilbert Don G
Published: March 2005

Background

wFleaBase is a database with the necessary infrastructure to curate, archive and share genetic, molecular and functional genomic data and protocols for an emerging model organism, the microcrustacean Daphnia. Commonly known as the water-flea, Daphnia's ecological merit is unequaled among metazoans, largely because of its sentinel role within freshwater ecosystems and over 200 years of biological investigations. By consequence, the Daphnia Genomics Consortium (DGC) has launched an interdisciplinary research program to create the resources needed to study genes that affect ecological and evolutionary success in natural environments.

Discussion

These tools include the genome database wFleaBase, which currently contains functions to search and extract information from expressed sequenced tags, genome survey sequences and full genome sequencing projects. This new database is built primarily from core components of the Generic Model Organism Database project, and related bioinformatics tools.

Over the coming year, preliminary genetic maps and the nearly complete genomic sequence of Daphnia pulex will be integrated into wFleaBase, including gene predictions and ortholog assignments based on sequence similarities with eukaryote genes of known function. wFleaBase aims to serve a large ecological and evolutionary research community. Our challenge is to rapidly expand its content and to ultimately integrate genetic and functional genomic information with population-level responses to environmental challenges. URL: http://wfleabase.org/.
Promoter Hypermethylation Is Associated With Tumor Location, Stage, and Subsequent Progression in Transitional Cell Carcinoma
Authors: Catto James W.F. , Azzouzi Abdel-Rahmene , Rehman Ishtiaq , Feeley Kenneth M. , Cross Simon S. , Amira Najla , Fromont Gaelle , Sibony Mathilde , Cussenot Oliver , Meuth Mark , Hamdy Freddie C.
Published: March 2005

Purpose

Transitional cell carcinoma (TCC) is a pan-urothelial disease characterized by multiplicity. Although little is known about the molecular events in upper-tract TCC, similar carcinogenic mechanisms are thought to occur throughout the urinary tract. However, we have previously shown that distinct patterns of microsatellite instability occur in upper and lower urinary tract TCC, suggesting biologic differences between these tumors. Here we investigate the extent of promoter hypermethylation in TCC throughout the urinary tract.

Patients and Methods

Tissue was obtained from 280 patients (median follow-up, 56 months) whose tumors comprised 116 bladder and 164 upper-tract tumors (UTT). Analysis for hypermethylation at 11 CpG islands, using methylation-sensitive polymerase chain reaction and bisulfite sequencing, was performed for each sample and compared with the tumor's clinicopathologic details, microsatellite instability status, and subsequent behavior.

Results

Promoter methylation was present in 86% of TCC and occurred both more frequently and more extensively in UTT (94%) than in bladder tumors (76%; P < .0001). Methylation was associated with advanced tumor stage (P = .0001) and higher tumor progression (P = .03) and mortality rates (P = .04), when compared with tumors without methylation. Multivariate analysis revealed that methylation at the RASSF1A and DAPK loci, in addition to tumor stage and grade, were associated with disease progression (P < .04).

Conclusion

Despite morphologic similarities, there are genetic and epigenetic differences between TCC in the upper and lower urinary tracts. Methylation occurs commonly in urinary tract tumors, may affect carcinogenic mechanisms, and is a prognostic marker and a potential therapeutic target.
Fast-start muscle dynamics in the rainbow troutOncorhynchus mykiss: phase relationship of white muscle shortening and body curvature
Authors: Goldbogen Jeremy A. , Shadwick Robert E. , Fudge Douglas S. , Gosline John M.
Published: March 2005

Muscle length changes of the lateral myotomal fast fibers of rainbow trout(Oncorhynchus mykiss) were measured using sonomicrometry during induced fast-starts. Simultaneous high-speed videography allowed for the analysis of midline kinematics to estimate the degree of muscle strain that occurs during body deformation. Comparison of these data was used to examine the phase relationship between local muscle shortening and local body bending during unsteady, large amplitude maneuvers. Our analysis finds that muscle shortening is temporally decoupled from body bending, probably due to the influence of hydrodynamic forces. The phase shift was such that midline curvature lagged behind muscle shortening at both the anterior (0.4L,where L is fork length) and posterior (0.7L) axial positions. Stronger escape responses were correlated with high peak strains and rapid strain-wave velocities, but not faster curvature-wave velocities. Under these conditions of high strain, the phase shift at the posterior position is significantly increased, whereas the anterior position fails to be affected. Curvature lag was still observed at both axial locations under conditions of low strain, suggesting that hydrodynamic forces are still significant during weaker escape responses. These data support a previous model that suggests fast-start body bending is determined by the interaction between muscle torque and hydrodynamic resistance along the body.
How does the relative wall thickness of human femora follow the biomechanical optima? An experimental study on mummies
Authors: Évinger Sándor , Suhai Bence , Bernáth Balázs , Gerics Balázs , Pap Ildikó , Horváth Gábor
Published: March 2005

We studied how the ratio (K) of the internal:external diameter of human femora follows the biomechanical optima derived earlier by other researchers for marrow-filled tubular bones with circular cross section and minimum mass designed to withstand yield and fatigue, or stiffness, or bending fracture, or impact strengths. With evaluation of radiographs of 107 femora from 57 human mummies the values of K were measured. We found that Kposterior=0.498±0.085 for the posterior radiographic view, and Kmedial=0.589±0.070 for the medial view with Kmin=0.345 and Kmax=0.783. The theoretical optima for K depend on the ratio (Q) of the marrow:bone density. Accepting the assumption of earlier authors that Q=0.50, our data show that human femora are optimised to withstand bending fracture, or yield and fatigue strengths. There were no sex-, age- and length-specific differences in K, and the means of K of the right and left femora of individuals were statistically not significantly different. The biomechanical optimization for K of human femora is not finely tuned. Compared with fox femora, K of human femora follows the biomechanical optimum to a much lesser extent. Although the relative wall thickness W=1–K of human femora are optimised, the very low relative mass increment due to deviation of K from the optimum and the considerable intraspecific variance of K make it probable that an accurate optimization of the relative wall thickness is irrelevant in humans.
The outcome of surgery in 668 patients with acromegaly using current criteria of biochemical ‘cure’
Authors: Nomikos Panagiotis , Buchfelder Michael , Fahlbusch Rudolf
Published: March 2005

Background and aim: The aim of this study was to illustrate the present role of transsphenoidal surgery as primary therapy in GH-secreting adenomas, and to compare the results concerning control of disease with previous series using older criteria of cure.

Method: We report on a consecutive series of 688 acromegalic patients treated over a time period of 19 years. Biochemical cure was defined as normalisation of basal GH level, suppression of GH levels to below 1 ng/ml during an oral glucose load and normalisation of IGF-I levels. Of the 506 patients undergoing primary transsphenoidal surgery, a total of 57.3% postoperatively fulfilled the criteria used.

Results: The rate of biochemical ‘cure’ correlated with the magnitude of the initial GH levels, the tumour size and invasion. The overall complication rate was below 2%. Mortality in this series was 0.1% (1 of 688). During a follow-up period of 10.7 years only two recurrences (0.4%) occurred. However, in the patients treated by transcranial surgery and by repeat surgery the cure rate was found to be relatively low (5.2 and 21.3% respectively).

Conclusions: These data suggest that surgery remains with very few exceptions the primary treatment of acromegaly for (i) a high cure rate, (ii) low morbidity, (iii) low recurrence rate and (iv) immediate decline of GH. Based on current criteria of cure, recurrences are uncommon. However, cure by surgery alone is improbable in patients harbouring extended, invasive tumours with high secretory activity, in whom further adjuvant treatment is mandatory.
Relationship between inhibin A and B, estradiol and follicle growth dynamics during ovarian stimulation in normo-ovulatory women
Authors: Hohmann Femke P , Laven Joop S E , de Jong Frank H , Fauser Bart C J M
Published: March 2005

Objective: To investigate the relationship between serum concentrations of inhibin A, inhibin B and estradiol (E2) and the number of developing follicles during the administration of exogenous follicle-stimulating hormone (FSH) in various regimens in normo-ovulatory volunteers and to evaluate if inhibins act as suitable markers for the number of developing follicles during ovarian stimulation.

Design and methods: Serial hormone determinations and assessment of follicle numbers were carried out during unstimulated cycles and during various interventions with exogenous FSH. Subjects were randomized for FSH administration into the following groups: a single high dose (375 IU) during the early follicular phase (group A), 5 consecutive low doses (75 IU/day) starting in the mid follicular phase (group B) or daily low doses (75 IU/day) during the early to late follicular phase (starting on cycle days 3, 5 or 7; groups C, D and E respectively).

Results: Extending the FSH window increases the number of small antral follicles and hence inhibin B serum concentrations. If such an intervention results in multi-follicular growth, mid follicular phase inhibin B (P = 0.001) as well as late follicular phase inhibin B and inhibin A levels are significantly (P < 0.05 and P < 0.01 respectively) increased compared with mono-follicular cycles or the natural cycle. Although mid follicular inhibin B levels correlated well with the number of small antral (P < 0.05) and pre-ovulatory (P < 0.001) follicles in the late follicular phase, mid follicular inhibin A and estradiol serum concentrations only correlated with the number of pre-ovulatory follicles (P < 0.001 and P < 0.01 respectively).

Conclusions: The present data extend our understanding of the relationship between follicle dynamics, serum inhibins and FSH during ovarian hyperstimulation. However, although mid follicular inhibin B does correlate with the number of developing follicles, it does not facilitate the identification of women at risk for multiple follicle development.
The effects of exercise and adipose tissue lipolysis on plasma adiponectin concentration and adiponectin receptor expression in human skeletal muscle
Authors: Punyadeera Chamindie , Zorenc Antoine H G , Koopman René , McAinch Andrew J , Smit Egbert , Manders Ralph , Keizer Hans A , Cameron-Smith David , van Loon Luc J C
Published: March 2005

Objective: It has been suggested that adiponectin regulates plasma free fatty acid (FFA) clearance by stimulating FFA uptake and/or oxidation in muscle. We aimed to determine changes in plasma adiponectin concentration and adiponectin receptor 1 and 2 mRNA expression in skeletal muscle during and after prolonged exercise under normal, fasting conditions (high FFA trial; HFA) and following pharmacological inhibition of adipose tissue lipolysis (low FFA trial; LFA). Furthermore, we aimed to detect and locate adiponectin in skeletal muscle tissue.

Methods: Ten subjects performed two exercise trials (120 min at 50% VO2max). Indirect calorimetry was used to determine total fat oxidation rate. Plasma samples were collected at rest, during exercise and during post-exercise recovery to determine adiponectin, FFA and glycerol concentrations. Muscle biopsies were taken to determine adiponectin protein and adiponectin receptor 1 and 2 mRNA expression and to localise intramyocellular adiponectin.

Results: Basal plasma adiponectin concentrations averaged 6.57±0.7 and 6.63±0.8 mg/l in the HFA and LFA trials respectively, and did not change significantly during or after exercise. In the LFA trial, plasma FFA concentrations and total fat oxidation rates were substantially reduced. However, plasma adiponectin and muscle adiponectin receptor 1 and 2 mRNA expression did not differ between trials. Immunohistochemical staining of muscle cross-sections showed the presence of adiponectin in the sarcolemma of individual muscle fibres and within the interfibrillar arterioles.

Conclusion: Plasma adiponectin concentrations and adiponectin receptor 1 and 2 mRNA expression in muscle are not acutely regulated by changes in adipose tissue lipolysis and/or plasma FFA concentrations. Adiponectin is abundantly expressed in muscle, and, for the first time, it has been shown to be present in/on the sarcolemma of individual muscle fibres.
Separation Techniques for Carbon Nanotubes
Authors: Krupke R. , Hennrich F.
Published: March 2005

Single‐walled carbon nanotubes have considerable potential as building blocks in future nanoscale electronics. The tubes exist in two modifications, metallic and semiconducting, which might be used in a range of electronic applications. One of the grand challenges is to separate metallic from semiconducting tubes in substantial quantities. In this respect, this article gives a brief overview over the separation techniques in this new field of nanotube research.
Outstanding Ceramic Matrix Composites for High Temperature Applications
Authors: Vandenbulcke L. , Fantozzi G. , Goujard S. , Bourgeon M.
Published: March 2005

Accurate deposition of boron and silicon carbides and nitrides permits to improve the oxidation resistance of self‐healing matrices of multilayered composites. The uniformity and the microstructure of each layer and of their interfaces induce the final properties of these composites. Their mechanical behaviour in conditions very close to the applications in the energy, space and aeronautic domains, allows to demonstrate the breakthrough enabled by this new composite generation.
Di(p‐tert‐butylphenyl)‐N,N‐di‐(iso‐butyl)carbamoylmethylphosphine oxide and its organotin and uranyl adducts: structural and spectroscopic characterization
Authors: Kapoor Ramesh N. , Guillory Paulette , Schulte Louis , Cervantes‐Lee Francisco , Haiduc Ionel , Parkanyi Laszlo , Pannell Keith H.
Published: March 2005

The single‐crystal structure of the hydrophobic actinide extractant di(p‐tert‐butylphenyl)‐N,N‐di‐(iso‐butyl)carbamoylmethylphosphine oxide (CMPO, 1) has been determined, as has that of its 1:1 chelate complex with uranyl nitrate (2), its 1:1 monodentate complexes with Ph3SnCl (3) and Me2SnCl2 (4) bonding via the PO group. A 1:1 bidentate complex with Ph2SnCl2 bonding via both PO and CO functionalities (5) was obtained which in solution exhibits a CO → Sn bond dissociation to exist as the monodentate isomer coordinating only through the PO group. Copyright © 2005 John Wiley & Sons, Ltd.
Monoorganotin(IV) phosphonates
Authors: Chandrasekhar Vadapalli , Gopal Kandasamy
Published: March 2005

Recent progress in the assembly of monoorganotin(IV) phosphonates is reviewed. The molecular structures of these compounds and their dependence on the nature of the organotin precursor and that of the phosphonic acid are discussed. Copyright © 2005 John Wiley & Sons, Ltd.
Biochemical mode of action and differential activity of new ecdysone agonists against mosquitoes and moths
Authors: Palli S. R. , Tice C. M. , Margam V. M. , Clark A. M.
Published: March 2005

THQ (1‐aroyl‐4‐(arylamino)‐1,2,3,4‐tetrahydroquinoline) compounds were identified by FMC Corporation in cell‐based assays that used ecdysone receptors from Drosophila melanogaster, Heliothis virescens, or Plodia interpunctata. THQ compounds showed weak insecticidal activity against H. virescens and, therefore, were not developed further. Several ecdysone agonists based on THQ chemotype have been synthesized and tested for their activity against a number of EcRs in transactivation assays. The THQ compound, RG‐120768, activated AaEcR (EcR from A. aegypti) but did not activate EcRs cloned from other insects. In transactivation assays, all six THQ ligands tested functioned through AaEcR but not through CfEcR (EcR from Choristoneura fumiferana). Three THQ compounds that showed higher activity in transactivation assays were tested in tobacco bud moth, H. virescens, and yellow fever mosquito, A. aegypti. These compounds showed higher activity in A. aegypti when compared to their activity in H. virescens. These data show that the THQ ligands are a new class of non‐steroidal ecdysone agonists with preferential activity against mosquitoes. Arch. Insect Biochem. Physiol. 58:234–242, 2005. © 2005 Wiley‐Liss, Inc.
Differences in tumor core distribution between palpable and nonpalpable prostate tumors in patients diagnosed using extensive transperineal ultrasound‐guided template prostate biopsy
Authors: Demura Takayoshi , Hioka Takaya , Furuno Tsuyoshi , Kaneta Tatsuo , Gotoda Hiroko , Muraoka Shunji , Sato Toshihiro , Mochizuki Tsutomu , Nagamori Satoshi , Shinohara Nobuo
Published: March 2005

BACKGROUND

The authors performed extensive transperineal ultrasound‐guided template prostate biopsies to investigate carcinoma core distribution.

METHODS

Between August 2000 and May 2004, 371 men underwent template biopsies. Three hundred twelve patients had not undergone a previous biopsy (first group) and 59 had undergone previous transrectal sextant biopsies (repeat group). Of the 312 patients in the first group, 236 had normal digital rectal examination (DRE) findings (DRE– first group) and 76 patients had an abnormal DRE (DRE+ first group). A mean of 20.1 biopsy cores (range, 9–38 cores) was taken from the entire prostate. The region > 2.0 cm from the rectal face of the prostate was defined as the anterior region and the remaining area was defined as the posterior region.

RESULTS

In the DRE– first group, the carcinoma core rate (number of tumor cores/number of biopsy cores) in the anterior region (7.2%) did not differ from that of the posterior region (7.3%) (P = 0.9635). However, in the DRE+ first group, the carcinoma core rate in the posterior region (22.0%) was found to be higher than in the anterior region (13.2%) (P < 0.0001). In the repeat group, the carcinoma core rate in the posterior region (3.1%) was significantly (P = 0.0008) lower than that exhibited in the anterior region (7.2%).

CONCLUSIONS

The results of the current study suggest that nonpalpable prostate carcinoma is distributed equally within the entire prostate, although palpable carcinoma is distributed mainly in the posterior region and many of the tumor foci in the anterior region may be missed by a transrectal sextant biopsy. The examination of radical prostatectomy specimens is required to prove these results. Cancer 2005. © 2005 American Cancer Society.
Empirical force‐field assessment: The interplay between backbone torsions and noncovalent term scaling
Authors: Sorin Eric J. , Pande Vijay S.
Published: March 2005

The kinetic and thermodynamic aspects of the helix‐coil transition in polyalanine‐based peptides have been studied at the ensemble level using a distributed computing network. This study builds on a previous report, which critically assessed the performance of several contemporary force fields in reproducing experimental measurements and elucidated the complex nature of helix‐coil systems. Here we consider the effects of modifying backbone torsions and the scaling of noncovalent interactions. Although these elements determine the potential of mean force between atoms separated by three covalent bonds (and thus largely determine the local conformational distributions observed in simulation), we demonstrate that the interplay between these factors is both complex and force field dependent. We quantitatively assess the heliophilicity of several helix‐stabilizing potentials as well as the changes in heliophilicity resulting from such modifications, which can “make or break” the accuracy of a given force field, and our findings suggests that future force field development may need to better consider effect that vary with peptide length. This report also serves as an example of the utility of distributed computing in analyzing and improving upon contemporary force fields at the level of absolute ensemble equilibrium, the next step in force field development. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 682–690, 2005
Ultrastructural biologic effects of sonography with pulse inversion and microbubble contrast in rabbit liver
Authors: Caruso Giuseppe , Valentino Biagio , Salvaggio Giuseppe , Lipari Elvira Farina , Lipari Diego , Brancatelli Giuseppe , Lagalla Roberto , Cardinale Adelfio Elio
Published: March 2005

Purpose

This prospective study was conducted to evaluate the biologic effects of microbubble destruction with pulse‐inversion harmonic imaging on rabbit liver parenchyma.

Methods

The livers of 6 albino rabbits were examined sonographically by a single investigator. Three rabbits underwent contrast‐enhanced sonography, with scanning starting 5 seconds after injection by using pulse‐inversion harmonic imaging with a mechanical index of 1.2. Four time‐triggered images were recorded at a rate of 1 frame every 2 seconds. For comparison, 3 control rabbits had pulse‐inversion harmonic imaging with a mechanical index of 1.2 only, without contrast medium. Immediately after sonography, the animals were killed and uninterrupted, thin serial sections of the liver from both groups were analyzed by energy‐filtered transmission electron microscopy.

Results

The hepatic parenchyma of rabbits exposed to contrast agents had ultrastructural damage: mitochondria with fragmented crests; interrupted rough endoplasmic reticulum; enlarged intercellular spaces; highly vacuolized cytoplasmic areas; dilated sinusoids, sometimes with an irregular and interrupted endothelial wall; fragmented hepatocyte microvilli in dilated spaces of Disse; fragmented or missing microvilli in bile canaliculi; vacuolated and lysosome‐deprived hepatic cytoplasm around the bile canaliculi; markedly injured or fragmented endothelium in larger vessels; and damaged basal membrane. Control‐group results indicated that exposure to ultrasound alone did not cause ultrastructural damage to hepatic cells.

Conclusions

Simultaneous exposure to contrast administration and pulse‐inversion harmonic imaging with a high mechanical index causes ultrastructural damage in the rabbit liver. © 2005 Wiley Periodicals, Inc. J Clin Ultrasound 33:106–111, 2005
Differential diagnosis of hepatic cystic lesions with gray‐scale and color Doppler sonography
Authors: Liang Ping , Cao Bingsheng , Wang Yan , Yu Xiaoling , Yu Dejiang , Dong Baowei
Published: March 2005

Purpose

This study was conducted to evaluate the effectiveness of sonography, especially color Doppler sonography, in the differential diagnosis of cystic hepatic lesions.

Methods

Ninety‐two pathologically or clinically proven hepatic cystic lesions (20 cystic malignancies, 24 abscesses, and 48 simple cysts) were evaluated with gray‐scale and color Doppler sonography. The sonographic features were analyzed retrospectively. The percentage, sensitivity, specificity, and positive and negative predictive values of the sonographic features of each disease category were calculated.

Results

On gray‐scale sonography, the simple cysts were easily distinguished from cystic malignancies and abscesses. While no significant differences were found between hepatic cystic malignancies and hepatic abscesses with respect to the number, shape, margin status, and presence of thick wall of the lesion, the presence of septation and mural nodules was significantly higher in the cystic malignancies than in abscesses. The sensitivity and specificity of color Doppler sonography in differentiating cystic malignancies from abscesses and simple cysts were 85% and 96%, respectively.

Conclusions

Color Doppler sonography provides information about blood flow that supplements that gained on gray‐scale sonography, and the presence of color signals in the solid portion of the cystic lesions carries a high diagnostic value in differentiating hepatic cystic malignancies from abscesses and simple cysts. © 2005 Wiley Periodicals, Inc. J Clin Ultrasound 33:100–105, 2005
Extranodal primary B‐cell non‐Hodgkin lymphoma of the breast mimicking acute mastitis
Authors: Grubstein Ahuva , Givon‐Madhala Osnat , Morgenstern Sara , Cohen Maya
Published: March 2005

We report a case of primary, high‐grade non‐Hodgkin B‐cell lymphoma in the breast of a young woman. The clinical and sonographic presentation was not of a mass but of an infiltrating anechoic process mimicking mastitis. Primary breast lymphoma is a rare entity, especially in young females. Early detection and treatment are crucial because the results of salvage treatment are generally poor. In previous imaging reports of breast lymphoma, it has always been considered as a mass, though the presence of markedly hypoechoic regions that look like fluid collections is a well known sonographic characteristic of lymphoma. © 2005 Wiley Periodicals, Inc. J Clin Ultrasound 33:140–142, 2005