bluuebunny/crossref_metadata_2025 huggingface dataset:
Creating Java to Native Code Interfaces with Janet
Authors: Bubak Marian , Kurzyniec Dawid , Łuszczek Piotr , Sunderam Vaidy
Published: January 2015

Java is growing in appropriateness and usability for high performance computing. With this increasing adoption, issues relating to combining Java with existing codes in other languages become more important. The Java Native Interface (JNI) API is portable but too inconvenient to be used directly owing to its low‐level API. This paper presents Janet — a highly expressive Java language extension and preprocessing tool that enables convenient integration of native code with Java programs. The Janet methodology overcomes some of the limitations of JNI and generates Java programs that execute with little or no degradation despite the flexibility and generality of the interface.
Cluster‐Enabled OpenMP: An OpenMP Compiler for the SCASH Software Distributed Shared Memory System
Authors: Sato Mitsuhisa , Harada Hiroshi , Hasegawa Atsushi , Ishikawa Yutaka
Published: January 2015

OpenMP is attracting wide‐spread interest because of its easy‐to‐use parallel programming model for shared memory multiprocessors. We have implemented a "cluster‐enabled" OpenMP compiler for a page‐based software distributed shared memory system, SCASH, which works on a cluster of PCs. It allows OpenMP programs to run transparently in a distributed memory environment. The compiler transforms OpenMP programs into parallel programs using SCASH so that shared global variables are allocated at run time in the shared address space of SCASH. A set of directives is added to specify data mapping and loop scheduling method which schedules iterations onto threads associated with the data mapping. Our experimental results show that the data mapping may greatly impact on the performance of OpenMP programs in the software distributed shared memory system. The performance of some NAS parallel benchmark programs in OpenMP is improved by using our extended directives.
RNA Relocation and Persistence of Nucleolus‐Like Bodies at Mitosis in Benzo[a]Pyrene‐Transformed Human Breast Epithelial Cells after Microcell‐Mediated Transfer of Chromosomes 11 and 17
Authors: Mello Maria Luiza S. , Lareef Mohamed H. , Vidal Benedicto C. , Russo Jose
Published: January 2015

RNA relocation and the incidence of nucleolus‐like bodies accumulated during mitosis were studied cytochemically in benzo[a]pyrene (BP)‐transformed human breast epithelial MCF‐10F cells after microcell‐mediated transfer of normal chromosomes 11 and 17. The changes resulting from the transfer of these two chromosomes in tumorigenic MCF‐10F cells (BP1‐E cell line) were examined, since alterations in these chromosomes are involved in the expression of the transformed and tumorigenic phenotypes in the MCF‐10F cell series. In addition, the frequency of nucleolus‐like bodies decreases drastically with transformation and tumorigenicity in MCF‐10F cells, thus being conceivable that it would be affected in presence of normal chromosomes 11 or 17. The pattern of RNA relocation associated with the mitotic spindle did not vary in the cell lines analyzed. The introduction of chromosome 17 in BP1‐E cells either decreased or did not affect the frequency of persistent nucleolus‐like bodies. In contrast, in cells which received a normal chromosome 11, the frequency of nucleolus‐like bodies was closer to that of non‐transformed MCF‐10F cells. These results suggest that a normal chromosome 11 but not chromosome 17 contributes to the maintenance of an RNA surplus which accumulates in nucleolus‐like bodies during cell division of the human breast epithelial cells, at least in vitro. Some loci which were retained in the BP1‐E cells which received a normal chromosome 11 are probably involved with the control of RNA transcript production.
Application of Neural Networks to the Classification of Pancreatic Intraductal Proliferative Lesions
Authors: Okoń Krzysztof , Tomaszewska Romana , Nowak Krystyna , Stachura Jerzy
Published: January 2015

The aim of the study was to test applycability of neural networks to classification of pancreatic intraductal proliferative lesions basing on nuclear features, especially chromatin texture. Material for the study was obtained from patients operated on for pancreatic cancer, chronic pancreatitis and other tumours requiring pancreatic resection. Intraductal lesions were classified as low and high grade as previously described. The image analysis system consisted of a microscope, CCD camera combined with a PC and AnalySIS v. 2.11 software. The following texture characteristics were measured: variance of grey levels, features extracted from the grey levels correlation matrix and mean values, variance and standard deviation of the energy obtained from Laws matrices. Furthermore we used moments derived invariants and basic geometric data such as surface area, the minimum and maximum diameter and shape factor. The sets of data were randomly divided into training and testing groups. The training of the network using the back‐propagation algorithm, and the final classification of data was carried out with a neural network simulator SNNS v. 4.1. We studied the efficacy of networks containing from one to three hidden layers. Using the best network, containing three hidden layers, the rate of correct classification of nuclei was 73%, and the rate of misdiagnosis was 3%; in 24% the network response was ambiguous. The present findings may serve as a starting point in search for methods facilitating early diagnosis of ductal pancreatic carcinoma.
Investigation on Cell Proliferation with a New Antibody against Thymidine Kinase 1
Authors: Wang Naining , He Qimin , Skog Sven , Eriksson Staffan , Tribukait Bernhard
Published: January 2015

The cytosolic thymidine kinase 1 (TK1) is one of the enzymes involved in DNA replication. Based on biochemical studies, TK1 is activated at late G1 of cell cycle, and its activity correlates with the cell proliferation. We have developed a polyclonal anti‐TK1 antibody against a synthetic peptide from the C‐terminus of human TK1. Using this antibody, here we demonstrate the exclusive location of TK1 in the cytoplasm of cells. Cell cycle dependent TK1 expression was studied by simultaneous fluorescence staining for TK1 and bromodeoxyuridine, by using elutriated cells, and by quantitation of the amount TK1 in relation to the cellular DNA content. TK1, which was strongly expressed in the cells in S+G2 period, raised at late G1 and decreased during mitosis. The amount of TK1 increased three folds from late G1 to G2. TK1 positive cells were demonstrated in areas of proliferation activity of various normal and malignant tissues. The new anti‐TK1 antibody works in archival specimens and is a specific marker of cell proliferation.
Comparison of Message‐Passing and Shared Memory Implementations of the GMRES Method on MIMD Computers
Authors: Płażek Joanna , Banaś Krzysztof , Kitowski Jacek
Published: January 2015

In this paper we compare different parallel implementations of the same algorithm for solving nonlinear simulation problems on unstructured meshes. In the first implementation, making use of the message‐passing programming model and the PVM system, the domain decomposition of unstructured mesh is implemented, while the second implementation takes advantage of the inherent parallelism of the algorithm by adopting the shared‐memory programming model. Both implementations are applied to the preconditioned GMRES method that solves iteratively the system of linear equations. A combined approach, the hybrid programming model suitable for multicomputers with SMP nodes, is introduced. For performance measurements we use compressible fluid flow simulation in which sequences of finite element solutions form time approximations to the Euler equations. The tests are performed on HP SPP1600, HP S2000 and SGI Origin2000 multiprocessors and report wall‐clock execution time and speedup for different number of processing nodes and for different meshes. Experimentally, the explicit programming model proves to be more efficient than the implicit model by 20—70%, depends on the mesh and the machine.
Diagnosis of Bladder Cancer with Urinary Cytology, Immunocytology and DNA‐Image‐Cytometry1
Authors: Planz Bernhard , Synek Christian , Deix Thomas , Böcking Alfred , Marberger Michael
Published: January 2015

DNA‐image‐cytometry and antibodies directed against the Lewis X‐ and the 486p 3/12 antigen were applied to improve diagnostic accuracy of urinary cytology for the detection of bladder cancer. Cytology, immunocytology and DNA‐image‐cytometry were performed in spontaneously voided urine samples and barbotage bladder washings from 71 patients. The DNA content was determined using the CM‐1 Cytometer according to the recommendation of the ESCAP Consensus Report on Standardization of DNA‐image‐cytometry (1995). For immunocytological examination we used the monoclonal anti Lewis X antibody P‐12 and antibody 486p 3/12. All patients underwent subsequent cystoscopy and for any suspicious lesion biopsy or transurethral resection was done. Histological findings revealed 31 patients with transitional cell carcinomas of different stages and grades of malignancy. 40 patients had various benign diseases of the urinary bladder. Cytology yielded a sensitivity of 68% and a specificity of 100%. DNA aneuploidy was detected in 81% of cancer patients with a specificity of 100%. By combination of these two methods the overall sensitivity increased to 87%. Immunocytology with Lewis X and 486p 3/12 antibodies showed reactivity in 84% and 87% in combination with a specificity of 80% and 70%, respectively. By combining urinary cytology, immunocytology and/or DNA‐image‐cytometry the overall sensitivity increased to 94% with no change in specificity. DNA‐image‐cytometry should be used to evaluate particularly urothelial cells suspicious for malignancy in urinary specimens. Because of low specificity the monoclonal antibodies against Lewis X‐ and 486p 3/12 antigens are not helpful in screening for bladder cancer. Nevertheless, their high sensitivity may justify their use in case DNA image cytometry is not available and in the follow up of patients with transitional cell carcinoma.
Variations in Cell Surfaces of Estrogen Treated Breast Cancer Cells Detected by A Combined Instrument for Far‐Field and Near‐Field Microscopy
Authors: Perner P. , Rapp A. , Dressler C. , Wollweber L. , Beuthan J. , Greulich K. O. , Hausmann M.
Published: January 2015

The response of single breast cancer cells (cell line T‐47D) to 17β‐estradiol (E2) under different concentrations was studied by using an instrument that allows to combine far‐field light microscopy with high resolution scanning near‐field (AFM/SNOM) microscopy on the same cell. Different concentrations of E2 induce clearly different effects as well on cellular shape (in classical bright‐field imaging) as on surface topography (atomic force imaging) and absorbance (near‐field light transmission imaging). The differences range from a polygonal shape at zero via a roughly spherical shape at physiological up to a spindle‐like shape at un‐physiologically high concentrations. The surface topography of untreated control cells was found to be regular and smooth with small overall height modulations. At physiological E2 concentrations the surfaces became increasingly jagged as detected by an increase in membrane height. After application of the un‐physiological high E2 concentration the cell surface structures appeared to be smoother again with an irregular fine structure. The general behaviour of dose dependent differences was also found in the near‐field light transmission images. In order to quantify the treatment effects, line scans through the normalised topography images were drawn and a rate of co‐localisation between high topography and high transmission areas was calculated. The cell biological aspects of these observations are, so far, not studied in detail but measurements on single cells offer new perspectives to be empirically used in diagnosis and therapy control of breast cancers.
Scalable Atomistic Simulation Algorithms for Materials Research
Authors: Nakano Aiichiro , Kalia Rajiv K. , Vashishta Priya , Campbell Timothy J. , Ogata Shuji , Shimojo Fuyuki , Saini Subhash
Published: January 2015

A suite of scalable atomistic simulation programs has been developed for materials research based on space‐time multiresolution algorithms. Design and analysis of parallel algorithms are presented for molecular dynamics (MD) simulations and quantum‐mechanical (QM) calculations based on the density functional theory. Performance tests have been carried out on 1,088‐processor Cray T3E and 1,280‐processor IBM SP3 computers. The linear‐scaling algorithms have enabled 6.44‐billion‐atom MD and 111,000‐atom QM calculations on 1,024 SP3 processors with parallel efficiency well over 90%. production‐quality programs also feature wavelet‐based computational‐space decomposition for adaptive load balancing, spacefilling‐curve‐based adaptive data compression with user‐defined error bound for scalable I/O, and octree‐based fast visibility culling for immersive and interactive visualization of massive simulation data.
Applying Scheduling and Tuning to On‐line Parallel Tomography
Authors: Smallen Shava , Casanova Henri , Berman Francine
Published: January 2015

Tomography is a popular technique to reconstruct the three‐dimensional structure of an object from a series of two‐dimensional projections. Tomography is resource‐intensive and deployment of a parallel implementation onto Grid platforms has been studied in previous work. In this work, we address on-line execution of the application where computation is performed as data is collected from an on‐line instrument. The goal is to compute incremental 3‐D reconstructions that provide quasi‐real‐time feedback to the user. We model on‐line parallel tomography as a tunable application: trade‐offs between resolution of the reconstruction and frequency of feedback can be used to accommodate various resource availabilities. We demonstrate that application scheduling/tuning can be framed as multiple constrained optimization problems and evaluate our methodology in simulation. Our results show that prediction of dynamic network performance is key to efficient scheduling and that tunability allows for production runs of on‐line parallel tomography in Computational Grid environments.
Additional Techniques in Serous Effusions
Authors: Hanselaar A. G. J. M.
Published: January 2015

Cytological examination is a valuable diagnostic tool in case of a serous effusion. The firstmanifestation of malignancy may be an effusion of the pleural, pericardial, or peritoneal cavity, especially in carcinoma of the ovary, or lung, and malignant mesothelioma. In other malignancies effusions may occur in the course of the disease. The contribution by Motherby et al. in this issue of ACP focuses on the contribution of image and flow cytometry to establish the presence or absence of malignancy in serous effusions [16]. They point out that the sensitivity of DNA image cytometry in equivocal effusions may be as high as 87.5%, and that for the detection of malignancy, DNA image cytometry is superior to flow cytometry.
Achieving Extreme Resolution in Numerical Cosmology Using Adaptive Mesh Refinement: Resolving Primordial Star Formation
Authors: Bryan Greg L. , Abel Tom , Norman Michael L.
Published: January 2015

As an entry for the 2001 Gordon Bell Award in the "special" category, we describe our 3‐d, hybrid, adaptive mesh refinement (AMR) code Enzo designed for high‐resolution, multiphysics, cosmological structure formation simulations. Our parallel implementation places no limit on the depth or complexity of the adaptive grid hierarchy, allowing us to achieve unprecedented spatial and temporal dynamic range. We report on a simulation of primordial star formation which develops over 8000 subgrids at 34 levels of refinement to achieve a local refinement of a factor of 1012 in space and time. This allows us to resolve the properties of the first stars which form in the universe assuming standard physics and a standard cosmological model. Achieving extreme resolution requires the use of 128‐bit extended precision arithmetic (EPA) to accurately specify the subgrid positions. We describe our EPA AMR implementation on the IBM SP2 Blue Horizon system at the San Diego Supercomputer Center.
CX: A Scalable, Robust Network for Parallel Computing
Authors: Cappello Peter , Mourloukos Dimitrios
Published: January 2015

CX, a network‐based computational exchange, is presented. The system′s design integrates variations of ideas from other researchers, such as work stealing, non‐blocking tasks, eager scheduling, and space‐based coordination. The object‐oriented API is simple, compact, and cleanly separates application logic from the logic that supports interprocess communication and fault tolerance. Computations, of course, run to completion in the presence of computational hosts that join and leave the ongoing computation. Such hosts, or producers, use task caching and prefetching to overlap computation with interprocessor communication. To break a potential task server bottleneck, a network of task servers is presented. Even though task servers are envisioned as reliable, the self‐organizing, scalable network of n‐ servers, described as a sibling-connected height-balanced fat tree, tolerates a sequence of n‐1 server failures. Tasks are distributed throughout the server network via a simple "diffusion" process. CX is intended as a test bed for research on automated silent auctions, reputation services, authentication services, and bonding services. CX also provides a test bed for algorithm research into network‐based parallel computation.
Evaluation of Prognostic Factors Following Flow‐Cytometric DNA Analysis after Cytokeratin Labelling: I. Breast Cancer
Authors: Wimberger Pauline , Hillemanns Peter , Kapsner Thomas , Hepp Hermann , Kimmig Rainer
Published: January 2015

In gynecologic oncology valid prognostic factors are necessary to estimate the course of disease and to define biologically similar subgroups for analysis of therapeutic efficacy. The presented study is a prospective study concerning prognostic significance of DNA ploidy and S‐phase fraction in breast cancer following enrichment of tumor cells by cytokeratin labelling. Epithelial cells were labeled by FITC‐conjugated cytokeratin antibody (CK 5, 6, 8, and CK 17) prior to flow cytometric cell cycle analysis in 327 fresh specimens of primary breast cancer. Univariate analysis in breast cancer detected the prognostic significance of DNA‐ploidy, S‐phase fraction and CV (coefficient of variation) of G0G1‐peak of tumor cells for clinical outcome, especially for nodal‐negative patients. Multivariate analysis could not confirm prognostic evidence of DNA‐ploidy and S‐phase fraction. In conclusion, in breast cancer no clinical significance for determination of DNA‐parameters was found.
HMM‐Based Techniques for Speech Segments Extraction
Authors: Abdulla Waleed H.
Published: January 2015

The goal of the speech segments extraction process is to separate acoustic events of interest (the speech segment to be recognised) in a continuously recorded signal from other parts of the signal (background). The recognition rate of many voice command systems is very much dependent on speech segment extraction accuracy. This paper discusses two novel HMM based techniques that segregate a speech segment from its concurrent background. The first method can be reliably used in clean environments while the second method, which makes use of the wavelets denoising technique, is effective in noisy environments. These methods have been implemented and shown superiority over other popular techniques, thus, indicating that they have the potential to achieve greater levels of accuracy in speech recognition rates.
Algorithms for Cytoplasm Segmentation of Fluorescence Labelled Cells
Authors: Wählby Carolina , Lindblad Joakim , Vondrus Mikael , Bengtsson Ewert , Björkesten Lennart
Published: January 2015

Automatic cell segmentation has various applications in cytometry, and while the nucleus is often very distinct and easy to identify, the cytoplasm provides a lot more challenge. A new combination of image analysis algorithms for segmentation of cells imaged by fluorescence microscopy is presented. The algorithm consists of an image pre‐processing step, a general segmentation and merging step followed by a segmentation quality measurement. The quality measurement consists of a statistical analysis of a number of shape descriptive features. Objects that have features that differ to that of correctly segmented single cells can be further processed by a splitting step. By statistical analysis we therefore get a feedback system for separation of clustered cells. After the segmentation is completed, the quality of the final segmentation is evaluated. By training the algorithm on a representative set of training images, the algorithm is made fully automatic for subsequent images created under similar conditions. Automatic cytoplasm segmentation was tested on CHO‐cells stained with calcein. The fully automatic method showed between 89% and 97% correct segmentation as compared to manual segmentation.
Diagnostic DNA‐Flow‐ vs. ‐Image‐Cytometry in Effusion Cytology
Authors: Motherby Helma , Pomjanski Natalia , Kube Mary , Boros Alexandra , Heiden Thomas , Tribukait Bernhard , Böcking Alfred
Published: January 2015

Aims: To determine the sensitivity and specificity of flow‐ and image‐cytometry for the detection of DNA‐aneuploidy as a marker for malignant cells in effusions. Methods: 200 effusions (80 tumor cell‐positive, 74 negative and 46 cytologically equivocal) were stained with DAPI‐SR for DNA‐flow‐ and with Feulgen‐Pararosaniline for ‐image‐cytometry. They were measured using a PAS‐flow‐cytometer and an AutoCyte‐QUIC‐DNA‐workstation according to the ESACP consensus reports for DNA‐flow‐ and ‐image‐cytometry, respectively [7,23,29,49]. Results: Sensitivity of DNA‐aneuploidy for the identification of malignant cells was 32.1% for DNA‐flow‐ and 75.0% for ‐image‐cytometry, specificity of ‐euploidy in benign cells was 100.0% for both methods. Positive predictive value of DNA‐aneuploidy for the identification of malignant cells was 100.0% for both techniques, negative predictive value of DNA‐euploidy was 48.6% for DNA‐flow‐ and 72.0% for ‐image‐cytometry. Conclusions: Searching for DNA‐aneuploidy as a diagnostic marker for neoplastic cells in serous effusions image‐cytometry revealed superior sensitivity as compared with monoparametric flow cytometry.
The Grid Resource Broker, A Ubiquitous Grid Computing Framework
Authors: Aloisio Giovanni , Cafaro Massimo , Blasi Euro , Epicoco Italo
Published: January 2015

Portals to computational/data grids provide the scientific community with a friendly environment in order to solve large‐scale computational problems. The Grid Resource Broker (GRB) is a grid portal that allows trusted users to create and handle computational/data grids on the fly exploiting a simple and friendly web‐based GUI. GRB provides location‐transparent secure access to Globus services, automatic discovery of resources matching the user′s criteria, selection and scheduling on behalf of the user. Moreover, users are not required to learn Globus and they do not need to write specialized code or to rewrite their existing legacy codes. We describe GRB architecture, its components and current GRB features addressing the main differences between our approach and related work in the area.
Microdissection and Molecular Analysis of Single Cells or Small Cell Clusters in Pathology and Diagnosis – Significance and Challenges
Authors: Heinmöller E. , Schlake G. , Renke B. , Liu Q. , Hill K. A. , Sommer S. S. , Rüschoff J.
Published: January 2015

Colour figures can be viewed on http://www.esacp.org/acp/2002/24‐4_5/heinmoeller.htm
Use of Nuclear Morphometry Characteristics to Distinguish between Normal and Abnormal Cervical Glandular Histologies
Authors: Swartz Richard , West Loyd , Boiko Iouri , Malpica Anais , MacAulay Calum , Carraro Anita , Guillaud Martial , Cox Dennis , Follen Michele
Published: January 2015

This is a methodological study exploring the use of quantitative histopathology applied to the cervix to discriminate between normal and cancerous (consisting of adenocarcinoma and adenocarcinoma in situ) tissue samples. The goal is classifying tissue samples, which are populations of cells, from measurements on the cells. Our method uses one particular feature, the IODs‐Index, to create a tissue level feature. The specific goal of this study is to find a threshold for the IODs‐Index that is used to create the tissue level feature. The main statistical tool is Receiver Operating Characteristic (ROC) curve analysis. When applied to the data, our method achieved promising results with good estimated sensitivity and specificity for our data set. The optimal threshold for the IODs‐Index was found to be 2.12.
Scaling Non‐Regular Shared‐Memory Codes by Reusing Custom Loop Schedules
Authors: Nikolopoulos Dimitrios S. , Artiaga Ernest , Ayguadé Eduard , Labarta Jesús
Published: January 2015

In this paper we explore the idea of customizing and reusing loop schedules to improve the scalability of non‐regular numerical codes in shared‐memory architectures with non‐uniform memory access latency. The main objective is to implicitly setup affinity links between threads and data, by devising loop schedules that achieve balanced work distribution within irregular data spaces and reusing them as much as possible along the execution of the program for better memory access locality. This transformation provides a great deal of flexibility in optimizing locality, without compromising the simplicity of the shared‐memory programming paradigm. In particular, the programmer does not need to explicitly distribute data between processors. The paper presents practical examples from real applications and experiments showing the efficiency of the approach.
Quantitative Performance Analysis of the SPEC OMPM2001 Benchmarks
Authors: Aslot Vishal , Eigenmann Rudolf
Published: January 2015

The state of modern computer systems has evolved to allow easy access to multiprocessor systems by supporting multiple processors on a single physical package. As the multiprocessor hardware evolves, new ways of programming it are also developed. Some inventions may merely be adopting and standardizing the older paradigms. One such evolving standard for programming shared‐memory parallel computers is the OpenMP API. The Standard Performance Evaluation Corporation (SPEC) has created a suite of parallel programs called SPEC OMP to compare and evaluate modern shared‐memory multiprocessor systems using the OpenMP standard. We have studied these benchmarks in detail to understand their performance on a modern architecture. In this paper, we present detailed measurements of the benchmarks. We organize, summarize, and display our measurements using a Quantitative Model. We present a detailed discussion and derivation of the model. Also, we discuss the important loops in the SPEC OMPM2001 benchmarks and the reasons for less than ideal speedup on our platform.
Application of Multilevel Models to Morphometric Data. Part 2. Correlations
Authors: Tsybrovskyy O. , Berghold A.
Published: January 2015

Multilevel organization of morphometric data (cells are “nested” within patients) requires special methods for studying correlations between karyometric features. The most distinct feature of these methods is that separate correlation (covariance) matrices are produced for every level in the hierarchy. In karyometric research, the cell‐level (i.e., within‐tumor) correlations seem to be of major interest. Beside their biological importance, these correlation coefficients (CC) are compulsory when dimensionality reduction is required. Using MLwiN, a dedicated program for multilevel modeling, we show how to use multivariate multilevel models (MMM) to obtain and interpret CC in each of the levels. A comparison with two usual, “single‐level” statistics shows that MMM represent the only way to obtain correct cell‐level correlation coefficients. The summary statistics method (take average values across each patient) produces patient‐level CC only, and the “pooling” method (merge all cells together and ignore patients as units of analysis) yields incorrect CC at all. We conclude that multilevel modeling is an indispensable tool for studying correlations between morphometric variables.
Automatic Multilevel Parallelization Using OpenMP
Authors: Jin Haoqiang , Jost Gabriele , Yan Jerry , Ayguade Eduard , Gonzalez Marc , Martorell Xavier
Published: January 2015

In this paper we describe the extension of the CAPO parallelization support tool to support multilevel parallelism based on OpenMP directives. CAPO generates OpenMP directives with extensions supported by the NanosCompiler to allow for directive nesting and definition of thread groups. We report some results for several benchmark codes and one full application that have been parallelized using our system.
Efficient Active Contour and K‐Means Algorithms in Image Segmentation
Authors: Rommelse J.R. , Lin H.X. , Chan T.F.
Published: January 2015

In this paper we discuss a classic clustering algorithm that can be used to segment images and a recently developed active contour image segmentation model. We propose integrating aspects of the classic algorithm to improve the active contour model. For the resulting CVK and B‐means segmentation algorithms we examine methods to decrease the size of the image domain. The CVK method has been implemented to run on parallel and distributed computers. By changing the order of updating the pixels, it was possible to replace synchronous communication with asynchronous communication and subsequently the parallel efficiency is improved.
Adaptive Load Balancing of Parallel Applications with Multi‐Agent Reinforcement Learning on Heterogeneous Systems
Authors: Parent Johan , Verbeeck Katja , Lemeire Jan , Nowe Ann , Steenhaut Kris , Dirkx Erik
Published: January 2015

We report on the improvements that can be achieved by applying machine learning techniques, in particular reinforcement learning, for the dynamic load balancing of parallel applications. The applications being considered in this paper are coarse grain data intensive applications. Such applications put high pressure on the interconnect of the hardware. Synchronization and load balancing in complex, heterogeneous networks need fast, flexible, adaptive load balancing algorithms. Viewing a parallel application as a one‐state coordination game in the framework of multi‐agent reinforcement learning, and by using a recently introduced multi‐agent exploration technique, we are able to improve upon the classic job farming approach. The improvements are achieved with limited computation and communication overhead.
Dynamic Location and Forwarding Pointers for Mobility Management
Authors: Abondo Charles , Pierre Samuel
Published: January 2015

GSM and IS‐41 are two mobility management standards widely used in second generation networks. These two standards lean on a centralized architecture made up of home location registers (HLRs) and visitor location registers (VLRs). From these standards, the location update and search procedures always imply interrogation of the HLR, even if the two mobile terminals that want to communicate are in the same location area. Given the limited bandwidth of the radio operator channel and the new time sensitive applications of third‐generation systems, such an approach of mobility management is not convenient for the next generation mobile networks. This paper proposes a method for reducing the processing load and the signalization traffic generated by update and search location procedures compared to IS‐41 standard. Taking into account the specific characteristics of the traffic in the mobile networks, it introduces a semi‐dynamic approach based on a hybrid architecture using forwarding pointers without the load related to the dynamic models. Numerical results show that such a method significantly improves the efficiency of location procedures.
Vector Nonlinear Time‐Series Analysis of Gamma‐Ray Burst Datasets on Heterogeneous Clusters
Authors: Banicescu Ioana , Cariño Ricolindo L. , Harvill Jane L. , Lestrade John Patrick
Published: January 2015

The simultaneous analysis of a number of related datasets using a single statistical model is an important problem in statistical computing. A parameterized statistical model is to be fitted on multiple datasets and tested for goodness of fit within a fixed analytical framework. Definitive conclusions are hopefully achieved by analyzing the datasets together. This paper proposes a strategy for the efficient execution of this type of analysis on heterogeneous clusters. Based on partitioning processors into groups for efficient communications and a dynamic loop scheduling approach for load balancing, the strategy addresses the variability of the computational loads of the datasets, as well as the unpredictable irregularities of the cluster environment. Results from preliminary tests of using this strategy to fit gamma‐ray burst time profiles with vector functional coefficient autoregressive models on 64 processors of a general purpose Linux cluster demonstrate the effectiveness of the strategy.
Large Atmospheric Computation on the Earth Simulator: The LACES Project
Authors: Desgagné Michel , McTaggart-Cowan Ron , Ohfuchi Wataru , Brunet Gilbert , Yau Peter , Gyakum John , Furukawa Yuki , Valin Michel
Published: January 2015

The Large Atmospheric Computation on the Earth Simulator (LACES) project is a joint initiative between Canadian and Japanese meteorological services and academic institutions that focuses on the high resolution simulation of Hurricane Earl (1998). The unique aspect of this effort is the extent of the computational domain, which covers all of North America and Europe with a grid spacing of 1 km. The Canadian Mesoscale Compressible Community (MC2) model is shown to parallelize effectively on the Japanese Earth Simulator (ES) supercomputer; however, even using the extensive computing resources of the ES Center (ESC), the full simulation for the majority of Hurricane Earl′s lifecycle takes over eight days to perform and produces over 5.2 TB of raw data. Preliminary diagnostics show that the results of the LACES simulation for the tropical stage of Hurricane Earl′s lifecycle compare well with available observations for the storm. Further studies involving advanced diagnostics have commenced, taking advantage of the uniquely large spatial extent of the high resolution LACES simulation to investigate multiscale interactions in the hurricane and its environment. It is hoped that these studies will enhance our understanding of processes occurring within the hurricane and between the hurricane and its planetary‐scale environment.
Formal Constraints on Memory Management for Composite Overloaded Operations
Authors: Rouson Damian W.I. , Xu Xiaofeng , Morris Karla
Published: January 2015

The memory management rules for abstract data type calculus presented by Rouson, Morris & Xu [15] are recast as formal statements in the Object Constraint Language (OCL) and applied to the design of a thermal energy equation solver. One set of constraints eliminates memory leaks observed in composite overloaded expressions with three current Fortran 95/2003 compilers. A second set of constraints ensures economical memory recycling. The constraints are preconditions, postconditions and invariants on overloaded operators and the objects they receive and return. It is demonstrated that systematic run‐time assertion checking inspired by the formal constraints facilitated the pinpointing of an exceptionally hard‐to‐reproduce compiler bug. It is further demonstrated that the interplay between OCL′s modeling capabilities and Fortran′s programming capabilities led to a conceptual breakthrough that greatly improved the readability of our code by facilitating operator overloading. The advantages and disadvantages of our memory management rules are discussed in light of other published solutions [11,19]. Finally, it is demonstrated that the run‐time assertion checking has a negligible impact on performance.
The Transition and Adoption to Modern Programming Concepts for Scientific Computing in Fortran
Authors: Norton Charles D. , Decyk Viktor K. , Szymanski Boleslaw K. , Gardner Henry
Published: January 2015

This paper describes our experiences in the early exploration of modern concepts introduced in Fortran90 for large‐scale scientific programming. We review our early work in expressing object‐oriented concepts based on the new Fortran90 constructs – foreign to most programmers at the time – our experimental work in applying them to various applications, the impact on the WG5/J3 standards committees to consider formalizing object‐oriented constructs for later versions of Fortran, and work in exploring how other modern programming techniques such as Design Patterns can and have impacted our software development. Applications will be drawn from plasma particle simulation and finite element adaptive mesh refinement for solid earth crustal deformation modeling.
Cooperative Proxy Caching for Wireless Base Stations
Authors: Wang James Z. , Du Zhidian , Srimani Pradip K.
Published: January 2015

This paper proposes a mobile cache model to facilitate the cooperative proxy caching in wireless base stations. This mobile cache model uses a network cache line to record the caching state information about a web document for effective data search and cache space management. Based on the proposed mobile cache model, a P2P cooperative proxy caching scheme is proposed to use a self‐configured and self‐managed virtual proxy graph (VPG), independent of the underlying wireless network structure and adaptive to the network and geographic environment changes, to achieve efficient data search, data cache and date replication. Based on demand, the aggregate effect of data caching, searching and replicating actions by individual proxy servers automatically migrates the cached web documents closer to the interested clients. In addition, a cache line migration (CLM) strategy is proposed to flow and replicate the heads of network cache lines of web documents associated with a moving mobile host to the new base station during the mobile host handoff. These replicated cache line heads provide direct links to the cached web documents accessed by the moving mobile hosts in the previous base station, thus improving the mobile web caching performance. Performance studies have shown that the proposed P2P cooperative proxy caching schemes significantly outperform existing caching schemes.
Performance Characterization of a Rover Navigation Algorithm Using Large‐Scale Simulation
Authors: Madison Richard , Jain Abhinandan , Lim Christopher , Maimone Mark
Published: January 2015

Autonomous rover navigation is a critical technology for robotic exploration of Mars. Simulation allows more extensive testing of such technologies than would be possible with hardware test beds alone. A large number of simulations, running in parallel, can test an algorithm under many different operating conditions to quickly identify the operational envelope of the technology and identify failure modes that were not discovered in more limited testing. GESTALT is the autonomous navigation algorithm developed for NASA′s Mars rovers. ROAMS is a rover simulator developed to support the Mars program. We have integrated GESTALT into ROAMS to test closed‐loop, autonomous navigation in simulation. We have developed a prototype capability to run many copies of ROAMS in parallel on a supercomputer, varying input parameters to rapidly explore GESTALT′s performance across a parameter space. Using these tools, we have demonstrated that large scale simulation can identify performance limits and unexpected behaviors in an algorithm. Such parallel simulation was able to test approximately 500 parameter combinations in the time required for a single test on a hardware test bed.
Vectorized Matlab Codes for Linear Two‐Dimensional Elasticity
Authors: Koko Jonas
Published: January 2015

A vectorized Matlab implementation for the linear finite element is provided for the two‐dimensional linear elasticity with mixed boundary conditions. Vectorization means that there is no loop over triangles. Numerical experiments show that our implementation is more efficient than the standard implementation with a loop over all triangles.
Hybrid Training with Binary Search Protocol for Wireless Sensor Networks
Authors: Ishak Ruzana , Xu Qingwen , Olariu Stephan , Salleh Shaharuddin
Published: January 2015

Locationing problem in Wireless Sensor Networks(WSNs) can be viewed as a general distributed sensor problem. It is with sensors that can discover other nodes or estimate ranges between nodes, that serve as position references. In this paper, we show that sensors acquire coarse‐grain location awareness by the training protocol. The training protocol which hybrids the synchronization and training procedure. In this protocol, synchronization and training are combined into one scheme. The sink node sends two beacons in each slot instead of one. In the training, sensor searching for its location using a binary search scheme. Our simulation results shown less number of cycles needed for training.
Co‐arrays in the Next Fortran Standard
Authors: Reid John , Numrich Robert W.
Published: January 2015

The WG5 committee, at its meeting in Delft, May 2005, decided to include co‐arrays in the next Fortran Standard. A Fortran program containing co‐arrays is interpreted as if it were replicated a fixed number of times and all copies were executed asynchronously. Each copy has its own set of data objects and is called an image. The array syntax of Fortran is extended with additional trailing subscripts in square brackets to give a clear and straightforward representation of access to data on other images. References without square brackets are to local data, so code that can run independently is uncluttered. Any occurrence of
square brackets is a warning about communication between images.
The additional syntax requires support in the compiler, but it has been designed to be easy to implement and to give the
compiler scope both to apply its optimizations within each image and to optimize the communication between images.
The extension includes execution control statements for synchronizing images and intrinsic procedures to return the number
of images, to return the index of the current image, and to perform collective operations.
The paper does not attempt to describe the full details of the feature as it now appears in the draft of the new standard. Instead,
we describe a subset and demonstrate the use of this subset with examples.
Architecture for the Development of Context‐Sensitive Mobile Applications
Authors: Aleksy Markus , Butter Thomas , Schader Martin
Published: January 2015

Recent advances in the development of mobile terminals and the appropriate communication infrastructures have the consequence that new kinds of applications arise. This trend leads to more and more complex mobile client applications as well. In this paper, we present a generic architecture, which can be used for the development of context‐sensitive mobile applications.
Discover Gene Specific Local Co-Regulations from Time-Course Gene Expression Data
Authors: Zhang Ji , Gao Qigang , Wang Hai
Published: January 2015

Discovering gene co-regulatory relationships is one of most important research in DNA microarray data analysis. The problem of gene specific co-regulation discovery is to, for a particular gene of interest (called target gene), identify the condition subsets where strong gene co-regulations of the target gene are observed and its co-regulated genes in these condition subsets. The co-regulations are local in the sense that they occur in some subsets of full experimental conditions. The study on this problem can contribute to better understanding and characterizing the target gene during the biological activity involved. In this paper, we propose an innovative method for finding gene specific co-regulations using genetic algorithm (GA). A sliding window is used to delimit the allowed length of conditions in which gene co-regulations occur and anad hocGA, called the progressive GA, is performed in each window position to find those condition subsets having high fitness. It is called progressive because the initial population for the GA in a window position inherits the top-ranked individuals obtained in its preceding window position, enabling the GA to achieve a better accuracy than the non-progressive algorithm.kNN Lookup Table is utilized to substantially speed up fitness evaluation in the GA. Experimental results with a real-life gene expression data demonstrate the efficiency and effectiveness of our technique in discovering gene specific co-regulations.
Novel Directory Service and Message Delivery Mechanism Enabling Scalable Mobile Agent Communication
Authors: Ahn Jinho
Published: January 2015

Mobile agent technology has emerged as a promising programming paradigm for developing highly dynamic and large‐scale service‐oriented computing middlewares due to its desirable features. For this purpose, first of all, scalable location‐transparent agent communication issue should be addressed in mobile agent systems despite agent mobility. Although there were proposed several directory service and message delivery mechanisms, their disadvantages force them not to be appropriate to both low‐overhead location management and fast delivery of messages to agents migrating frequently. To mitigate their limitations, this paper presents a scalable distributed directory service and message delivery mechanism. The proposed mechanism enables each mobile agent to autonomously leave tails of forwarding pointers on some few of its visiting nodes depending on its preferences. This feature results in low message forwarding overhead and low storage and maintenance cost of increasing chains of pointers per host. Also, keeping mobile agent location information in the effective binding cache of each sending agent, the sending agent can communicate with mobile agents much faster compared with the existing ones.
Home‐Explorer: Ontology‐Based Physical Artifact Search and Hidden Object Detection System
Authors: Guo Bin , Satake Satoru , Imai Michita
Published: January 2015

A new system named Home‐Explorer that searches and finds physical artifacts in a smart indoor environment is proposed. The view on which it is based is artifact‐centered and uses sensors attached to the everyday artifacts (called smart objects) in the real world. This paper makes two main contributions: First, it addresses, the robustness of the embedded sensors, which is seldom discussed in previous smart artifact research. Because sensors may sometimes be broken or fail to work under certain conditions, smart objects become hidden ones. However, current systems provide no mechanism to detect and manage objects when this problem occurs. Second, there is no common context infrastructure for building smart artifact systems, which makes it difficult for separately developed applications to interact with each other and uneasy for them to share and reuse knowledge. Unlike previous systems, Home‐Explorer builds on an ontology‐based knowledge infrastructure named Sixth‐Sense, which makes it easy for the system to interact with other applications or agents also based on this ontology. The hidden object problem is also reflected in our ontology, which enables Home‐Explorer to deal with both smart objects and hidden objects. A set of rules for deducing an object′s status or location information and for locating hidden objects are described and evaluated.