bluuebunny/crossref_metadata_2025 huggingface dataset:
A Problem Solving Environment Based on CORBA
Authors: Lancaster David
Published: January 2015

We have investigated aspects of the design of Problem Solving Environments (PSE) by constructing a prototype using CORBA as middleware. The two issues we are mainly concerned with are the use of non‐trivial (containing more than just a start method) CORBA interfaces for the computational components, and the provision of interactivity using the same mechanisms used for flow control. After describing the design decisions that allow us to investigate these issues, and contrasting them with alternatives, we describe the architecture of the prototype and its use in the context of a study of photonic materials. We argue that having several methods on a component interface can be used to mitigate performance problems that may arise when trying to solve problems in PSE′s based on small components. We describe how our mechanism allows a high degree of computational steering over all components.
Fourth Updated ESACP Consensus Report on Diagnostic DNA Image Cytometry
Authors: Haroske G. , Baak J. P. A. , Danielsen H. , Giroud F. , Gschwendtner A. , Oberholzer M. , Reith A. , Spieler P. , Böcking A.
Published: January 2015

A task force of experts in the field of diagnostic DNA image cytometry, invited by the ESACP, and further scientists or physicians revealing experience in that diagnostic procedure (names are given in Addendum A), agreed upon the following 4th updated Consensus Report on Standardised Diagnostic DNA Image Cytometry during the 7th International Congress of that society in Caen, 2001. This report is based on the three preceding ones [6,14,17]. It deals with the following items: – Critical review and update of the definitions given in the 1997 Consensus Update; – Review and detailed description of basic terms, principles and algorithms for diagnostic interpretation; – Recommendations concerning diagnostic or prognostic applications in specific fields of tumour pathology. This update is not aimed to substitute the 1997 consensus, but to make necessary addenda and give more detailed descriptions of those items not unequivocally to interpret by potential users of the methodology.
Prognostic Classification of Early Ovarian Cancer Based on very Low Dimensionality Adaptive Texture Feature Vectors from Cell Nuclei from Monolayers and Histological Sections
Authors: Nielsen Birgitte , Albregtsen Fritz , Kildal Wanja , Danielsen Håvard E.
Published: January 2015

In order to study the prognostic value of quantifying the chromatin structure of cell nuclei from patients with early ovarian cancer, low dimensionality adaptive fractal and Gray Level Cooccurrence Matrix texture feature vectors were extracted from nuclei images of monolayers and histological sections. Each light microscopy nucleus image was divided into a peripheral and a central part, representing 30% and 70% of the total area of the nucleus, respectively. Textural features were then extracted from the peripheral and central parts of the nuclei images. The adaptive feature extraction was based on Class Difference Matrices and Class Distance Matrices. These matrices were useful to illustrate the difference in chromatin texture between the good and bad prognosis classes of ovarian samples. Class Difference and Distance Matrices also clearly illustrated the difference in texture between the peripheral and central parts of cell nuclei. Both when working with nuclei images from monolayers and from histological sections it seems useful to extract separate features from the peripheral and central parts of the nuclei images.
Spectral Imaging of Multi‐Color Chromogenic Dyes in Pathological Specimens
Authors: Macville Merryn V. E. , Van der Laak Jeroen A. W. M. , Speel Ernst J. M. , Katzir Nir , Garini Yuval , Soenksen Dirk , McNamara George , de Wilde Peter C. M. , Hanselaar Antonius G. J. M. , Hopman Anton H.N. , Ried Thomas
Published: January 2015

We have investigated the use of spectral imaging for multi‐color analysis of permanent cytochemical dyes and enzyme precipitates on cytopathological specimens. Spectral imaging is based on Fourier‐transform spectroscopy and digital imaging. A pixel‐by‐pixel spectrum‐based color classification is presented of single‐, double‐, and triple‐color in situ hybridization for centromeric probes in T24 bladder cancer cells, and immunocytochemical staining of nuclear antigens Ki‐67 and TP53 in paraffin‐embedded cervical brush material (AgarCyto). The results demonstrate that spectral imaging unambiguously identifies three chromogenic dyes in a single bright‐field microscopic specimen. Serial microscopic fields from the same specimen can be analyzed using a spectral reference library. We conclude that spectral imaging of multi‐color chromogenic dyes is a reliable and robust method for pixel color recognition and classification. Our data further indicate that the use of spectral imaging (a) may increase the number of parameters studied simultaneously in pathological diagnosis, (b) may provide quantitative data (such as positive labeling indices) more accurately, and (c) may solve segmentation problems currently faced in automated screening of cell‐ and tissue specimens. Figures on http://www.esacp.org/acp/2001/22‐3/macville.htm.
Cytologic and DNA‐Cytometric Early Diagnosis of Oral Cancer
Authors: Remmerbach Torsten W. , Weidenbach Horst , Pomjanski Natalja , Knops Kristiane , Mathes Stefanie , Hemprich Alexander , Böcking Alfred
Published: January 2015

Objective. The aim of this prospective study was to report on the diagnostic accuracy of conventional oral exfoliative cytology taken from white‐spotted, ulcerated or other suspicious oral lesions in our clinic. In addition we checked DNA‐image cytometry as an adjuvant diagnostic tool. Our hypothesis is that DNA‐aneuploidy is a sensitive and specific marker for the early identification of tumor cells in oral brushings. Study design. 251 cytological diagnoses obtained from exfoliative smears of 181 patients from macroscopically suspicious lesions of the oral mucosa and from clinically seemingly benign oral lesions which were exisiced for establishing histological diagnoses were compared with histological and/or clinical follow‐ups of the respective patients. Additionally nuclear DNA‐contents were measured after Feulgen restaining using a TV image analysis system. Results. Sensitivity of our cytological diagnosis on oral smears for the detection of cancer cells was 94.6%, specificity 99.5%, positive predictive value 98.1% and negative predictive value 98.5%. DNA‐aneuploidy was assumed if abnormal DNA‐stemlines or cells with DNA‐content greater 9c were observed. On this basis the prevalence of DNA‐aneuploidy in smears of oral squamous cell carcinomas in situ or invasive carcinomas was 96.4%. Sensitivity of DNA‐aneuploidy in oral smears for the detection of cancer cells was 96.4%, specificity 100%, positive predictive value 100% and negative 99.0%. The combination of both techniques increased the sensivity to 98.2%, specificity to 100%, positive predictive value to 100% and negative to 99.5%. Conclusions. Brush cytology of all visible oral lesions, if they are clinically considered as suspicious for cancer, are an easily practicable, cheap, non‐invasive, painless, safe and accurate screening method for detection of oral precancerous lesions, carcinoma in situ or invasive squamous cell carcinoma in all stages. We conclude that DNA‐image cytometry is a very sensitive, highly specific and objective adjuvant tool for the early identification of neoplastic epithelial cells in oral smears.
Topical Mitomycin C and Radiation Induce Conjunctival DNA‐Polyploidy
Authors: Cartsburg Olaf , Kallen Christopher , Hillenkamp Jost , Sundmacher Rainer , Pomjanski Natalia , Böcking Alfred
Published: January 2015

Introduction: Atypical cell changes often occur following treatment of premalignant or malignant conjunctival neoplasias with topical mitomycin C (MMC) and/or radiation. These reactive, non‐neoplastic alterations of the conjunctival epithelium can be a differential diagnostic problem. Our aim was to investigate changes in the nuclear DNA‐distribution of conjunctival epithelial cells after MMC‐ and radiation therapy by DNA‐image‐cytometry. Methods: Conjunctival brush smears were obtained from 13 patients (13 eyes) with squamous cell carcinomas and six patients (6 eyes) with conjunctival malignant melanomas in situ before, during and after treatment. The patients were treated with MMC‐drops (0.02% or 0.04%) alone (n=12), with radiation therapy (n=3) or both (n=4). At first, the obtained brush smears were evaluated by cytology. Secondly, after Feulgen restaining, the DNA content of reactively changed cells was determined using the AutoCyte‐QUIC‐DNA® workstation. Results: We observed euploid DNA‐polyploidy and cytomorphological changes in all patients (19/19). We considered these alterations as reactive to treatment. Four patients showed their greatest DNA‐stemline at 4c and 15 patients at 8c. This effect was observed during and following MMC‐drops and/or radiation and remained stable in 94% of all patients after a mean follow‐up of 22.5 months (SD 15.4). In five cases image cytometry additionally demonstrated DNA‐stemline aneuploidy as an evidence of tumor recurrence. Conclusion: Measurements of DNA‐content revealed euploid polyploidisation of morphological suspicious but benign squamous cells which is the biologic correlate of well known secondary morphologic changes following topical chemotherapy and/or radiation. DNA‐image‐cytometry is a useful tool in the differention of euploid polyploidization as a sign of reactive cell changes following treatment and tumor recurrences.
Scientific Computing on the Itanium® Processor
Authors: Greer Bruce , Harrison John , Henry Greg , Li Wei , Tang Peter
Published: January 2015

The 64‐bit Intel® Itanium® architecture is designed for high‐performance scientific and enterprise computing, and the Itanium processor is its first silicon implementation. Features such as extensive arithmetic support, predication, speculation, and explicit parallelism can be used to provide a sound infrastructure for supercomputing. A large number of high‐performance computer companies are offering Itanium® ‐based systems, some capable of peak performance exceeding 50 GFLOPS. In this paper we give an overview of the most relevant architectural features and provide illustrations of how these features are used in both low‐level and high‐level support for scientific and engineering computing, including transcendental functions and linear algebra kernels.
NINJA: Java for High Performance Numerical Computing
Authors: Moreira José E. , Midkiff Samuel P. , Gupta Manish , Wu Peng , Almasi George , Artigas Pedro
Published: January 2015

When Java was first introduced, there was a perception that its many benefits came at a significant performance cost. In the particularly performance‐sensitive field of numerical computing, initial measurements indicated a hundred‐fold performance disadvantage between Java and more established languages such as Fortran and C. Although much progress has been made, and Java now can be competitive with C/C++ in many important situations, significant performance challenges remain. Existing Java virtual machines are not yet capable of performing the advanced loop transformations and automatic parallelization that are now common in state‐of‐the‐art Fortran compilers. Java also has difficulties in implementing complex arithmetic efficiently. These performance deficiencies can be attacked with a combination of class libraries (packages, in Java) that implement truly multidimensional arrays and complex numbers, and new compiler techniques that exploit the properties of these class libraries to enable other, more conventional, optimizations. Two compiler techniques, versioning and semantic expansion, can be leveraged to allow fully automatic optimization and parallelization of Java code. Our measurements with the NINJA prototype Java environment show that Java can be competitive in performance with highly optimized and tuned Fortran code.
Performance Engineering, PSEs and the GRID
Authors: Hey Tony , Papay Juri
Published: January 2015

Performance Engineering is concerned with the reliable prediction and estimation of the performance of scientific and engineering applications on a variety of parallel and distributed hardware. This paper reviews the present state of the art in ′Performance Engineering′ for both parallel computing and meta‐computing environments and attempts to look forward to the application of these techniques in the wider context of Problem Solving Environments and the Grid. The paper compares various techniques such as benchmarking, performance measurements, analytical modelling and simulation, and highlights the lessons learned in the related projects. The paper concludes with a discussion of the challenges of extending such methodologies to computational Grid environments.
Genetic Alterations in Presumptive Precursor Lesions of Breast Carcinomas
Authors: Aubele Michaela , Werner Martin , Höfler Heinz
Published: January 2015

The hypothetical multistep model of breast carcinogenesis suggests a transition from normal epithelium to invasive carcinoma via intraductal hyperplasia (without and with atypia) and in situcarcinoma. These presumptive precursor lesions are currently defined by their histological features, and their prognosis is imprecisely estimated from indirect epidemiological evidence. Cytogenetic and molecular‐genetic analysis of these lesions give evidence for an accumulation of various genetic alterations during breast tumorigenesis. Using immuno‐histochemistry overexpression of the c‐erbB‐2 oncogene was found in ductal carcinoma in situ(DCIS), but not in atypical intraductal hyperplasia (AIDH) and intraductal hyperplasia (IDH). An expression of mutant p53 tumor suppressor gene as well as expression of cyclin D1 was identified in DCIS. In IDH lesions loss of heterozygosity (LOH) at various loci could be identified, and comparative genomic hybridization (CGH) and fluorescence in situhybridization (FISH) studies delivered evidence for DNA amplification on chromosomal region 20q13 in the early stage of IDH. However, little is currently known about genetic alterations in those premalignant lesions, and the chronology of genetic alterations and histopathological changes during carcinogenesis is mainly undiscovered. Figure 1 can be viewed in colour on http://www.esacp.org/acp/2002/24‐23/aubele.htm
Grid Data Mirroring Package (GDMP)
Authors: Stockinger Heinz , Samar Asad , Muzaffar Shahzad , Donno Flavia
Published: January 2015

The GDMP client‐server software system is a generic file replication tool that replicates files securely and efficiently from one site to another in a Data Grid environment using Globus Grid tools. In addition, it manages replica catalogue entries for file replicas and thus maintains a consistent view on names and locations of replicated files. Files to be transferred can be of any particular file format and GDMP treats them all in the same way. However, for Objectivity database files a particular plug‐in exists. All files are assumed to be read‐only.
Dynamic Performance Tuning Supported by Program Specification
Authors: César Eduardo , Morajko Anna , Margalef Tomàs , Sorribes Joan , Espinosa Antonio , Luque Emilio
Published: January 2015

Performance analysis and tuning of parallel/distributed applications are very difficult tasks for non‐expert programmers. It is necessary to provide tools that automatically carry out these tasks. These can be static tools that carry out the analysis on a post‐mortem phase or can tune the application on the fly. Both kind of tools have their target applications. Static automatic analysis tools are suitable for stable application while dynamic tuning tools are more appropriate to applications with dynamic behaviour. In this paper, we describe KappaPi as an example of a static automatic performance analysis tool, and also a general environment based on parallel patterns for developing and dynamically tuning parallel/distributed applications.
VLAM‐G: A Grid‐Based Virtual Laboratory
Authors: Afsarmanesh H. , Belleman R.G. , Belloum A.S.Z. , Benabdelkader A. , van den Brand J.F.J. , Eijkel G.B. , Frenkel A. , Garita C. , Groep D.L. , Heeren R.M.A. , Hendrikse Z.W. , Hertzberger L.O. , Kaandorp J.A. , Kaletas E.C. , Korkhov V. , de Laat C.T.A.M. , Sloot P.M.A. , Vasunin D. , Visser A. , Yakali H.H.
Published: January 2015

The Grid‐based Virtual Laboratory AMsterdam (VLAM‐G), provides a science portal for distributed analysis in applied scientific research. It offers scientists remote experiment control, data management facilities and access to distributed resources by providing cross‐institutional integration of information and resources in a familiar environment. The main goal is to provide a unique integration of existing standards and software packages. This paper describes the design and prototype implementation of the VLAM‐G platform. In this testbed we applied several recent technologies such as the Globus toolkit, enhanced federated database systems, and visualization and simulation techniques. Several domain specific case studies are described in some detail. Information management will be discussed separately in a forthcoming paper.
A Bayesian Approach for Structural Learning with Hidden Markov Models
Authors: Li Cen , Biswas Gautam
Published: January 2015

Hidden Markov Models(HMM) have proved to be a successful modeling paradigm for dynamic and spatial processes in many domains, such as speech recognition, genomics, and general sequence alignment. Typically, in these applications, the model structures are predefined by domain experts. Therefore, the HMM learning problem focuses on the learning of the parameter values of the model to fit the given data sequences. However, when one considers other domains, such as, economics and physiology, model structure capturing the system dynamic behavior is not available. In order to successfully apply the HMM methodology in these domains, it is important that a mechanism is available for automatically deriving the model structure from the data. This paper presents a HMM learning procedure that simultaneously learns the model structure and the maximum likelihood parameter values of a HMM from data. The HMM model structures are derived based on the Bayesian model selection methodology. In addition, we introduce a new initialization procedure for HMM parameter value estimation based on the K‐means clustering method. Experimental results with artificially generated data show the effectiveness of the approach.
Memory Access Behavior Analysis of NUMA‐Based Shared Memory Programs
Authors: Tao Jie , Karl Wolfgang , Schulz Martin
Published: January 2015

Shared memory applications running transparently on top of NUMA architectures often face severe performance problems due to bad data locality and excessive remote memory accesses. Optimizations with respect to data locality are therefore necessary, but require a fundamental understanding of an application′s memory access behavior. The information necessary for this cannot be obtained using simple code instrumentation due to the implicit nature of the communication handled by the NUMA hardware, the large amount of traffic produced at runtime, and the fine access granularity in shared memory codes. In this paper an approach to overcome these problems and thereby to enable an easy and efficient optimization process is presented. Based on a low‐level hardware monitoring facility in coordination with a comprehensive visualization tool, it enables the generation of memory access histograms capable of showing all memory accesses across the complete address space of an application′s working set. This information can be used to identify access hot spots, to understand the dynamic behavior of shared memory applications, and to optimize applications using an application specific data layout resulting in significant performance improvements.
Mobile Objects in Java
Authors: Moreau Luc , Ribbens Daniel
Published: January 2015

Mobile Objects in Java provides support for object mobility in Java. Similarly to the RMI technique, a notion of client‐side stub, called startpoint, is used to communicate transparently with a server‐side stub, called endpoint. Objects and associated endpoints are allowed to migrate. Our approach takes care of routing method calls using an algorithm that we studied in. The purpose of this paper is to present and evaluate the implementation of this algorithm in Java. In particular, two different strategies for routing method invocations are investigated, namely call forwarding and referrals. The result of our experimentation shows that the latter can be more efficient by up to 19%.
Architecting Web Sites for High Performance
Authors: Iyengar Arun , Rosu Daniela
Published: January 2015

Web site applications are some of the most challenging high‐performance applications currently being developed and deployed. The challenges emerge from the specific combination of high variability in workload characteristics and of high performance demands regarding the service level, scalability, availability, and costs. In recent years, a large body of research has addressed the Web site application domain, and a host of innovative software and hardware solutions have been proposed and deployed. This paper is an overview of recent solutions concerning the architectures and the software infrastructures used in building Web site applications. The presentation emphasizes three of the main functions in a complex Web site: the processing of client requests, the control of service levels, and the interaction with remote network caches.
The XCAT Science Portal
Authors: Krishnan Sriram , Bramley Randall , Gannon Dennis , Ananthakrishnan Rachana , Govindaraju Madhusudhan , Slominski Aleksander , Simmhan Yogesh , Alameda Jay , Alkire Richard , Drews Timothy , Webb Eric
Published: January 2015

This paper describes the design and prototype implementation of the XCAT Grid Science Portal. The portal lets grid application programmers script complex distributed computations and package these applications with simple interfaces for others to use. Each application is packaged as a notebook which consists of web pages and editable parameterized scripts. The portal is a workstation‐based specialized personal web server, capable of executing the application scripts and launching remote grid applications for the user. The portal server can receive event streams published by the application and grid resource information published by Network Weather Service (NWS) [35] or Autopilot [16] sensors. Notebooks can be published and stored in web based archives for others to retrieve and modify. The XCAT Grid Science Portal has been tested with various applications, including the distributed simulation of chemical processes in semiconductor manufacturing and collaboratory support for X‐ray crystallographers.
Variable Precision Arithmetic: A Fortran 95 Module
Authors: Schonfelder J.L.
Published: January 2015

This paper describes the design and development of a software package supporting variable precision arithmetic as a semantic extension to the Fortran 95 language. The working precision of the arithmetic supported by this package can be dynamically and arbitrarily varied. The facility exploits the data‐abstraction capabilities of Fortran 95 and allows the operations to be used elementally with array operands as well as with scalars. The number system is defined in such a way as to be closed under all of the basic operations of normal arithmetic; no program‐terminating numerical exceptions can occur. Precision loss situations like underflow and overflow are handled by defining special value representations that preserve as much of the numeric information as is practical and the operation semantics are defined so that these exceptional values propagate as appropriate to reflect this loss of information. The number system uses an essentially conventional variable precision floating‐point representation. When operations can be performed exactly within the currently‐set working precision limit, the excess trailing zero digits are not stored, nor do they take part in future operations. This is both economical in storage and improves efficiency.
Cytogenetic Evolution of Human Ovarian Cell Lines Associated with Chemoresistance and Loss of Tumorigenicity
Authors: Struski Stéphanie , Doco‐Fenzy Martine , Koehler Michael , Chudoba Ilse , Levy Francis , Masson Linda , Michel Nicole , Ulrich Evelyne , Gruson Nadine , Bénard Jean , Potron Gérard , Cornillet‐Lefebvre Pascale
Published: January 2015

In order to identify genomic changes associated with a resistant phenotype acquisition, we used comparative genomic hybridization (CGH) to compare a human ovarian cell line, Igrov1, and four derived subcell lines, resistant to vincristine and presenting a reversion of malignant properties. Multicolor FISH (Multiplex‐FISH and Spectral Karyotype) and conventional FISH are also used to elucidate the karyotype of parental cell line. The drug‐resistant subcell lines displayed many chromosomal abnormalities suggesting the implication of different pathways leading to a multidrug resistance phenotype. However, these cell lines shared two common rearrangements: an unbalanced translocation der(8)t(8;13)(p22;q?) and a deletion of the 11p. These chromosomal imbalances could reflected the acquisition of the chemoresistance (der(8)) or the loss of tumorigenicity properties (del(11p)). Colour figure can be viewed on http://www.esacp.org/acp/2003/25‐3/struski.htm.
Risk Biomarker Assessment for Breast Cancer Progression: Replication Precision of Nuclear Morphometry
Authors: Poulin N. , Frost A. , Carraro A. , Mommers E. , Guillaud M. , van Diest P.J. , Grizzle W. , Beenken S.
Published: January 2015

Nuclear morphometry is a method for quantitative measurement of histopathologic changes in the appearance of stained cell nuclei. Numerous studies have indicated that these assessments may provide clinically relevant information related to the degree of progression and malignant potential of breast neoplasia. Nuclear features are derived from computerized analysis of digitized microscope images, and a quantitative Feulgen stain for DNA was used. Features analyzed included: (1) DNA content; (2) nuclear size and shape; and (3) texture features, describing spatial features of chromatin distribution. In this study replicated measurements are described on a series of 54 breast carcinoma specimens of differing pathologic grades. Duplicate measurements were performed using two serial sections, which were processed and analyzed separately. The value of a single feature measurement, the nuclear area profile, was shown to be the strongest indicator of progression. A quantitative nuclear grade was derived and shown to be strongly correlated with not only the pathologic nuclear grade, but also with tubule formation, mitotic grade, and with the overall histopathologic grade. Analysis of replication precision showed that the standard methods of the histopathology laboratory, if practiced in a uniform manner, are sufficient to ensure reproducibility of these assessments. We argue that nuclear morphometry provides a standardized and reproducible framework for quantitative pathologic assessments.
An OpenMP Compiler Benchmark
Authors: Müller Matthias S.
Published: January 2015

The purpose of this benchmark is to propose several optimization techniques and to test their existence in current OpenMP compilers. Examples are the removal of redundant synchronization constructs, effective constructs for alternative code and orphaned directives. The effectiveness of the compiler generated code is measured by comparing different OpenMP constructs and compilers. If possible, we also compare with the hand coded "equivalent" solution. Six out of seven proposed optimization techniques are already implemented in different compilers. However, most compilers implement only one or two of them.
Dynamic Compilation of C++ Template Code
Authors: Cole Martin J. , Parker Steven G.
Published: January 2015

Generic programming using the C++ template facility has been a successful method for creating high‐performance, yet general algorithms for scientific computing and visualization. However, adding template code tends to require more template code in surrounding structures and algorithms to maintain generality. Compiling all possible expansions of these templates can lead to massive template bloat. Furthermore, compile‐time binding of templates requires that all possible permutations be known at compile time, limiting the runtime extensibility of the generic code. We present a method for deferring the compilation of these templates until an exact type is needed. This dynamic compilation mechanism will produce the minimum amount of compiled code needed for a particular application, while maintaining the generality and performance that templates innately provide. Through a small amount of supporting code within each templated class, the proper templated code can be generated at runtime without modifying the compiler. We describe the implementation of this goal within the SCIRun dataflow system. SCIRun is freely available online for research purposes.
BSML: A Binding Schema Markup Language for Data Interchange in Problem Solving Environments
Authors: Verstak Alex , Ramakrishnan Naren , Watson Layne T. , He Jian , Shaffer Clifford A. , Bae Kyung Kyoon , Jiang Jing , Tranter William H. , Rappaport Theodore S.
Published: January 2015

We describe a binding schema markup language (BSML) for describing data interchange between scientific codes. Such a facility is an important constituent of scientific problem solving environments (PSEs). BSML is designed to integrate with a PSE or application composition system that views model specification and execution as a problem of managing semistructured data. The data interchange problem is addressed by three techniques for processing semistructured data: validation, binding, and conversion. We present BSML and describe its application to a PSE for wireless communications system design.
Design Patterns for Library Optimization
Authors: Gregor Douglas , Schupp Sibylle , Musser David R.
Published: January 2015

We apply the notion of design patterns to optimizations performed by designers of software libraries, focusing especially on object‐oriented numerical libraries. We formalize three design patterns that we have abstracted from many existing libraries and discuss the role of these formalizations as a tool for guiding compiler optimizers. These optimizers operate at a very high level that would otherwise be left unoptimized by traditional optimizers. Finally, we discuss the implementation of a design pattern‐based compiler optimizer for C++ abstract data types.
Correlation of Grade of Urothelial Cell Carcinomas and DNA Histogram Features Assessed by Flow Cytometry and Automated Image Cytometry
Authors: Bol Marco G. W. , Baak Jan P. A. , Diermen Bianca v. , Janssen E. A. M. , Buhr-Wildhagen Susanne B. K. , Kjellevold Kjell-Henning
Published: January 2015

Objective: To analyse how DNA ploidy and S‐phase fraction (SPF) by flow cytometry (FCM) and an optimised fully
automatic DNA image cytometer (ICM) correlate with grade in TaT1 urothelial cell carcinomas (UC) of the urinary bladder.
Materials and methods: Two‐hundred‐and twenty‐eight consensus cases were analysed. Single cell suspensions were stained
(DAPI for FCM, Feulgen for ICM). There was enough material for both FCMand ICMin 202 of these cases. FCMand optimised
ICM measurements were performed on the 202 UCs. To discriminate between different grades, single‐ and multivariate analyses
was performed on DNA histogram features obtained with the MultiCycle program (using DNA index (DI) and SPF). Results:
Overall measurement time of the adapted ICM method was 10.7 minutes per case (range 5.9–29.8 min.) and required little
additional interactive object rejection (average 152 objects (84–298) on 3000 objects per case measured, which took 9.9 minutes
on average, range 8.3–15.5 minutes). The ICM histograms looked much “cleaner” with less noise than the FCM graphs. The
coefficient of variation (CV) of the diploid peak for ICM(5.4%) was significantly lower than for FCM(5.9%) (p < 0.0001). ICM
features were more strongly correlated to grade than FCMfeatures. In multivariate analysis, the best discriminating set of features
was DNA ploidy and SPF (both by ICM). Conclusions: The adapted fully automated DNA ICM works very well for UCs. Low
CV DNA ICM histograms are obtained in a time comparable to FCM. The DNA ICM results have stronger discriminative power
than DNA FCM for grade in TaT1 UCs. Colour figures can be viewed on http://www.esacp.org/acp/2003/25-3/bol.htm.
DNA Amplifications and Aneuploidy, High Proliferative Activity and Impaired Cell Cycle Control Characterize Breast Carcinomas with Poor Prognosis
Authors: Blegen Harald , Will John S. , Ghadimi B. Michael , Nash Hesed‐Padilla , Zetterberg Anders , Auer Gert , Ried Thomas
Published: January 2015

In order to explore whether specific cytogenetic abnormalities can be used to stratify tumors with a distinctly different clinical course, we performed comparative genomic hybridization (CGH) of tumors from patients who were diagnosed with metastatic disease after an interval of less than 2 years or who remained free from distant metastases for more than 10 years. All patients presented with distant metastases after mastectomy indicating that none of the patients in this study was cured and free of remaining tumor cells. Tumors in the group of short‐term survivors showed a higher average number of chromosomal copy alterations compared to the long‐term survivors. Of note, the number of sub‐chromosomal high‐level copy number increases (amplifications) was significantly increased in the group of short‐term survivors. In both short‐ and long‐term survivors recurrent chromosomal gains were mapped to chromosomes 1q, 4q, 8q, and 5p. Copy number changes that were more frequent in the group of short‐term survivors included gains of chromosome 3q, 9p, 11p and 11q and loss of 17p. Our results indicate that low‐ and high grade malignant breast adenocarcinomas are characterized by a specific pattern of chromosomal copy number changes. Furthermore, immunohistochemical evaluation of the expression levels of Ki‐67, p27KIP1, p21WAF1, p53, cyclin A and cyclin E revealed a correlation between increased proliferative activity and poor outcome.
A Performance‐Prediction Model for PIC Applications on Clusters of Symmetric MultiProcessors: Validation with Hierarchical HPF+OpenMP Implementation
Authors: Briguglio Sergio , Martino Beniamino Di , Vlad Gregorio
Published: January 2015

A performance‐prediction model is presented, which describes different hierarchical workload decomposition strategies for particle in cell (PIC) codes on Clusters of Symmetric MultiProcessors. The devised workload decomposition is hierarchically structured: a higher‐level decomposition among the computational nodes, and a lower‐level one among the processors of each computational node. Several decomposition strategies are evaluated by means of the prediction model, with respect to the memory occupancy, the parallelization efficiency and the required programming effort. Such strategies have been implemented by integrating the high‐level languages High Performance Fortran (at the inter‐node stage) and OpenMP (at the intra‐node one). The details of these implementations are presented, and the experimental values of parallelization efficiency are compared with the predicted results.
A General Symbolic PDE Solver Generator: Beyond Explicit Schemes
Authors: Sheshadri K. , Fritzson Peter
Published: January 2015

This paper presents an extension of our Mathematica‐ and MathCode‐based symbolic‐numeric framework for solving a variety of partial differential equation (PDE) problems. The main features of our earlier work, which implemented explicit finite‐difference schemes, include the ability to handle (1) arbitrary number of dependent variables, (2) arbitrary dimensionality, and (3) arbitrary geometry, as well as (4) developing finite‐difference schemes to any desired order of approximation. In the present paper, extensions of this framework to implicit schemes and the method of lines are discussed. While C++ code is generated, using the MathCode system for the implicit method, Modelica code is generated for the method of lines. The latter provides a preliminary PDE support for the Modelica language. Examples illustrating the various aspects of the solver generator are presented.
A General Symbolic PDE Solver Generator: Explicit Schemes
Authors: Sheshadri K. , Fritzson Peter
Published: January 2015

A symbolic solver generator to deal with a system of partial differential equations (PDEs) in functions of an arbitrary number of variables is presented; it can also handle arbitrary domains (geometries) of the independent variables. Given a system of PDEs, the solver generates a set of explicit finite‐difference methods to any specified order, and a Fourier stability criterion for each method. For a method that is stable, an iteration function is generated symbolically using the PDE and its initial and boundary conditions. This iteration function is dynamically generated for every PDE problem, and its evaluation provides a solution to the PDE problem. A C++/Fortran 90 code for the iteration function is generated using the MathCode system, which results in a performance gain of the order of a thousand over Mathematica, the language that has been used to code the solver generator. Examples of stability criteria are presented that agree with known criteria; examples that demonstrate the generality of the solver and the speed enhancement of the generated C++ and Fortran 90 codes are also presented.
Lifting a Butterfly – A Component‐Based FFT
Authors: Schupp Sibylle
Published: January 2015

While modern software engineering, with good reason, tries to establish the idea of reusability and the principles of parameterization and loosely coupled components even for the design of performance‐critical software, Fast Fourier Transforms (FFTs) tend to be monolithic and of a very low degree of parameterization. The data structures to hold the input and output data, the element type of these data, the algorithm for computing the so‐called twiddle factors, the storage model for a given set of twiddle factors, all are unchangeably defined in the so‐called butterfly, restricting its reuse almost entirely. This paper shows a way to a component‐based FFT by designing a parameterized butterfly. Based on the technique of lifting, this parameterization includes algorithmic and implementation issues without violating the complexity guarantees of an FFT. The paper demonstrates the lifting process for the Gentleman‐Sande butterfly, i.e., the butterfly that underlies the large class of decimation‐in‐frequency (DIF) FFTs, shows the resulting components and summarizes the implementation of a component‐based, generic DIF library in C++.
Graph Transformation and Designing Parallel Sparse Matrix Algorithms beyond Data Dependence Analysis
Authors: Lin H.X.
Published: January 2015

Algorithms are often parallelized based on data dependence analysis manually or by means of parallel compilers. Some vector/matrix computations such as the matrix‐vector products with simple data dependence structures (data parallelism) can be easily parallelized. For problems with more complicated data dependence structures, parallelization is less straightforward. The data dependence graph is a powerful means for designing and analyzing parallel algorithms. However, for sparse matrix computations, parallelization based on solely exploiting the existing parallelism in an algorithm does not always give satisfactory results. For example, the conventional Gaussian elimination algorithm for the solution of a tri‐diagonal system is inherently sequential, so algorithms specially for parallel computation has to be designed. After briefly reviewing different parallelization approaches, a powerful graph formalism for designing parallel algorithms is introduced. This formalism will be discussed using a tri‐diagonal system as an example. Its application to general matrix computations is also discussed. Its power in designing parallel algorithms beyond the ability of data dependence analysis is shown by means of a new algorithm called ACER (Alternating Cyclic Elimination and Reduction algorithm).
Improving Locality for ODE Solvers by Program Transformations
Authors: Rauber Thomas , Rünger Gudula
Published: January 2015

Runge‐Kutta methods are popular methods for the solution of ordinary differential equations and implementations are provided by many scientific libraries. The performance of Runge‐Kutta methods depends on the specific application problem to be solved, but also on the characteristics of the target machine. For processors with a memory hierarchy, the locality of data referencing pattern has a large impact on the efficiency of a program. In this paper, we describe program transformations for Runge‐Kutta methods resulting in implementations with improved locality behavior for systems of ODEs. The transformations are based on properties of the solution method but are independent from the specific application problem or the specific target machine so that the resulting implementation is suitable as library function. We show that the locality improvement leads to performance gains on different recent microprocessors.
A Peer‐to‐Peer Distributed Collaborative Optimization System
Authors: Xue Caijun , Nie Hong , Qiu Qingying , Feng Peien
Published: January 2015

It is difficult to solve design optimization problems of complex systems by using a traditional computing method because complex simulation processes usually lead to large‐scale computation. Therefore the distributed computing technology based on decomposition‐coordination theory has received much attention by design engineers. This paper studies a peer‐to‐peer collaborative optimization method based on distributed computing technology in order to examine flexible optimization. A new distributed collaborative optimization framework is proposed, and a coordination method is developed and used to deal with the conflict of related variables among sub‐optimization problems. A multi‐agent based distributed computing environment is implemented. The implementation of an optimization agent, in which CORBA technology is used to implement communication between the components of the optimization agent, is discussed in detail. Two examples are used to demonstrate the efficiency of the computing method and the reliability and flexibility of the multi‐agent system.
Parallel Computing Applications and Financial Modelling
Authors: Liddell Heather M. , Parkinson D. , Hodgson G.S. , Dzwig P.
Published: January 2015

At Queen Mary, University of London, we have over twenty years of experience in Parallel Computing Applications, mostly on "massively parallel systems", such as the Distributed Array Processors (DAPs). The applications in which we were involved included design of numerical subroutine libraries, Finite Element software, graphics tools, the physics of organic materials, medical imaging, computer vision and more recently, Financial modelling. Two of the projects related to the latter are described in this paper, namely Portfolio Optimisation and Financial Risk Assessment.
Resource Bartering in Data Grids
Authors: Özturan Can
Published: January 2015

We present models for bartering of resources on grids. Bartering models can be useful for making resource allocation decisions in grids and perhaps even for building a so called barter grid whereby distributed resources such as electronic media can be bartered. Grids allow various resources to be shared among many users. This sharing however definitely does not mean that everyone will have unrestricted use of the resources. Some mechanism such as pricing or quotas can be employed in order to enforce controlled sharing of resources. A barter model for resource sharing can enable people or computer centers to directly get something in return for letting their resources to be used by others. We utilize directed hypergraphs to develop a barter model in which multiple resources can be traded. We prove that the decision version of the multi‐resource bartering problem is NP‐complete. We present an integer programming formulation for the bartering problem. We also present a linear time algorithm to compute components that may contain feasible bartering solutions. We generalize our multi‐resource bartering formulation to the case where multiple instances of resources are present. Finally, we present various computational results from our software that makes use of LP_SOLVE and CPLEX mixed integer programming libraries to solve example bartering problems.
Grid Environment for On‐line Application Monitoring and Performance Analysis
Authors: Baliś Bartosz , Bubak Marian , Funika Włodzimierz , Wismüller Roland , Radecki Marcin , Szepieniec Tomasz , Arodź Tomasz , Kurdziel Marcin
Published: January 2015

This paper presents an application monitoring infrastructure developed within the CrossGrid project. The software is aimed at enabling performance measurements for the application developer and in this way facilitating the development of applications in the Grid environment. The application monitoring infrastructure is composed of a distributed monitoring system, the OCM‐G, and a performance analysis tool called G‐PM. The OCM‐G is an on‐line, grid‐enabled, monitoring system, while G‐PM is an advanced graphical tool which allows to evaluate and present the results of performance monitoring, to support optimization of the application execution. G‐PM supports build‐in standard metrics and user‐defined metrics expressed in the Performance Measurement Specification Language (PMSL). Communication between the G‐PM and the OCM‐G is performed according to a well‐defined protocol, OMIS (On‐line Monitoring Interface Specification). In this paper, the architecture and features of the OCM‐G and G‐PM are described as well as an example of use of the monitoring infrastructure to visualize the status and communication in the application, to evaluate the performance, including discovering the reason of the performance flaw.
Design Metrics in Quantum Turbulence Simulations: How Physics Influences Software Architecture
Authors: Rouson Damian W.I. , Xiong Yi
Published: January 2015

The information hiding philosophy of object‐oriented programming encourages localizing data structures within objects rather than sharing data globally across different classes of objects. This emphasis on local data leads naturally to fine‐grained data abstractions, particularly in scientific simulations involving large collections of small, discrete physical or mathematical objects. This paper focuses on a subset of such simulations where dynamically reconfigurable links bind the objects together. It is demonstrated that fine‐grained data structures reduce the complexity of local operations on the data at the potential expense of increased global operation complexity. Two metrics are used to describe data structures: granularity is the number of instantiations required to cover the data space, whereas extent is the continuously traversable length of the data along a given direction. These definitions are applied to two abstractions for simulating the turbulent motion of quantum vortices in superfluid liquid helium. Several local and global operations on a fine‐grained linked list are compared with those on a coarse‐grained array. It is demonstrated that fine‐grained data structures recover the simplicity of more coarse‐grained structures if maximal extent is maintained as the granularity increases.