bluuebunny/crossref_metadata_2025 huggingface dataset:
Efficient Signature Based Malware Detection on Mobile Devices
Authors: Venugopal Deepak , Hu Guoning
Published: January 2015

The threat of malware on mobile devices is gaining attention recently. It is important to provide security solutions to these devices before these threats cause widespread damage. However, mobile devices have severe resource constraints in terms of memory and power. Hence, even though there are well developed techniques for malware detection on the PC domain, it requires considerable effort to adapt these techniques for mobile devices. In this paper, we outline the considerations for malware detection on mobile devices and propose a signature based malware detection method. Specifically, we detail a signature matching algorithm that is well suited for use in mobile device scanning due to its low memory requirements. Additionally, the matching algorithm is shown to have high scanning speed which makes it unobtrusive to users. Our evaluation and comparison study with the well known Clam‐AV scanner shows that our solution consumes less than 50% of the memory used by Clam‐AV while maintaining a fast scanning rate.
Open | SpeedShop: An Open Source Infrastructure for Parallel Performance Analysis
Authors: Schulz Martin , Galarowicz Jim , Maghrak Don , Hachfeld William , Montoya David , Cranford Scott
Published: January 2015

Over the last decades a large number of performance tools has been developed to analyze and optimize high performance applications. Their acceptance by end users, however, has been slow: each tool alone is often limited in scope and comes with widely varying interfaces and workflow constraints, requiring different changes in the often complex build and execution infrastructure of the target application. We started the Open | SpeedShop project about 3 years ago to overcome these limitations and provide efficient, easy to apply, and integrated performance analysis for parallel systems. Open | SpeedShop has two different faces: it provides an interoperable tool set covering the most common analysis steps as well as a comprehensive plugin infrastructure for building new tools. In both cases, the tools can be deployed to large scale parallel applications using DPCL/Dyninst for distributed binary instrumentation. Further, all tools developed within or on top of Open | SpeedShop are accessible through multiple fully equivalent interfaces including an easy-to-use GUI as well as an interactive command line interface reducing the usage threshold for those tools.
A Speed‐Aware Handover System for Wireless Cellular Networks Based on Fuzzy Logic
Authors: Barolli Leonard
Published: January 2015

Presently, the wireless mobile networks and devices are becoming increasingly popular to provide users the access anytime and anywhere. The mobile systems are based on cellular approach and the area is covered by cells that overlap each other. In mobile cellular systems the handover is a very important process, which refers to a mechanism that transfers an ongoing call from one Base Station (BS) to another. The performance of the handover mechanism is very important to maintain the desired Quality of Service (QoS). Many handover algorithms are proposed in the literature. However, to make a better handover and keep the QoS in wireless networks is very difficult. In this paper, we propose a speed‐aware handover system based on fuzzy logic. The proposed system has 3 subsystems. The performance evaluation via simulations shows that proposed system has a good handover decision.
Design and Evaluation of Reliable Data Transmission Protocol in Wireless Sensor Networks
Authors: Aikebaier Ailixier , Enokido Tomoya , Takizawa Makoto
Published: January 2015

A wireless sensor‐actuator network (WSAN) is composed of sensor modes and actuator modes which are interconnected in wireless networks. A sensor node collects information on the physical world and sends a sensed value in a wireless network. Another sensor node forwards the sensed value to deliver to an actuator node. A sensor node can deliver messages with sensed values to only nearby nodes due to weak radio. Messages are forwarded by sensor nodes to an actuator node by a type of flooding protocol. A sensor mode senses an event and sends a message with the sensed value. In addition, on receipt of a message with a sensed value from another sensor mode, a sensor node forwards the sensed value. Messages transmitted by sensor nodes might be lost due to noise and collisions. In this paper, we discuss a redundant data transmission (RT) protocol to reliably and efficiently deliver sensed values sensed by sensor nodes to an actuator node. Here, a sensor node sends a message with not only its sensed value but also sensed values received from other sensor nodes. The more number of sensed values are included in a message, the more frequently the message is lost. Each message carries so many number of sensed values that the message loss ratio is not increased. Even if a message with a sensed value v is lost in the wireless network, an actuator node can receive the sensed value v from a message sent by another sensor node. Thus, each sensed value is redundantly carried in multiple messages. The redundancy of a sensed value is in nature increased since the sensed value is broadcast. In order to reduce the redundancy of sensed value, we take a strategy that the farther sensor nodes from an actuator node forward the fewer number of sensed values. We evaluate the RT protocol in terms of loss ratio, redundancy, and delay time of a sensed value. We show that about 80% of sensed values can be delivered to an actuator node even if 95% of messages are lost due to noise and collision.
Fractional Factorial Design for Parameter Sweep Experiments Using Nimrod/E
Authors: Peachey T.C. , Diamond N.T. , Abramson D.A. , Sudholt W. , Michailova A. , Amirriazi S.
Published: January 2015

The techniques of formal experimental design and analysis are powerful tools for scientists and engineers. However, these techniques are currently underused for experiments conducted with computer models. This has motivated the incorporation of experimental design functionality into the Nimrod tool chain. Nimrod has been extensively used for exploration of the response of models to their input parameters; the addition of experimental design tools will combine the efficiency of carefully designed experiments with the power of distributed execution. This paper describes the incorporation of one type of design, the fractional factorial design, and associated analysis tools, into the Nimrod framework. The result provides a convenient environment that automates the design of an experiment, the execution of the jobs on a computational grid and the return of results, and which assists in the interpretation of those results. Several case studies are included which demonstrate various aspects of this approach.
A Low‐Cost Hybrid Coordinated Checkpointing Protocol for Mobile Distributed Systems
Authors: Kumar Parveen
Published: January 2015

Mobile distributed systems raise new issues such as mobility, low bandwidth of wireless channels, disconnections, limited battery power and lack of reliable stable storage on mobile nodes. In minimum‐process coordinated checkpointing, some processes may not checkpoint for several checkpoint initiations. In the case of a recovery after a fault, such processes may rollback to far earlier checkpointed state and thus may cause greater loss of computation. In all‐process coordinated checkpointing, the recovery line is advanced for all processes but the checkpointing overhead may be exceedingly high. To optimize both matrices, the checkpointing overhead and the loss of computation on recovery, we propose a hybrid checkpointing algorithm, wherein an all‐process coordinated checkpoint is taken after the execution of minimum‐process coordinated checkpointing algorithm for a fixed number of times. Thus, the Mobile nodes with low activity or in doze mode operation may not be disturbed in the case of minimum‐process checkpointing and the recovery line is advanced for each process after an all‐process checkpoint. Additionally, we try to minimize the information piggybacked onto each computation message. For minimum‐process checkpointing, we design a blocking algorithm, where no useless checkpoints are taken and an effort has been made to optimize the blocking of processes. We propose to delay selective messages at the receiver end. By doing so, processes are allowed to perform their normal computation, send messages and partially receive them during their blocking period. The proposed minimum‐process blocking algorithm forces zero useless checkpoints at the cost of very small blocking.
From Data to Knowledge to Discoveries: Artificial Intelligence and Scientific Workflows
Authors: Gil Yolanda
Published: January 2015

Scientific computing has entered a new era of scale and sharing with the arrival of cyberinfrastructure facilities for computational experimentation. A key emerging concept is scientific workflows, which provide a declarative representation of complex scientific applications that can be automatically managed and executed in distributed shared resources. In the coming decades, computational experimentation will push the boundaries of current cyberinfrastructure in terms of inter-disciplinary scope and integrative models of scientific phenomena under study. This paper argues that knowledge-rich workflow environments will provide necessary capabilities for that vision by assisting scientists to validate and vet complex analysis processes and by automating important aspects of scientific exploration and discovery.
Maximization of Energy Efficiency in Wireless ad hoc and Sensor Networks With SERENA
Authors: Mahfoudh Saoucene , Minet Pascale
Published: January 2015

In wireless ad hoc and sensor networks, an analysis of the node energy consumption distribution shows that the largest part is due to the time spent in the idle state. This result is at the origin of SERENA, an algorithm to SchEdule RoutEr Nodes Activity. SERENA allows router nodes to sleep, while ensuring end-to-end communication in the wireless network. It is a localized and decentralized algorithm assigning time slots to nodes. Any node stays awake only during its slot and the slots assigned to its neighbors, it sleeps the remaining time. Simulation results show that SERENA enables us to maximize network lifetime while increasing the number of user messages delivered. SERENA is based on a two-hop coloring algorithm, whose complexity in terms of colors and rounds is evaluated. We then quantify the slot reuse. Finally, we show how SERENA improves the node energy consumption distribution and maximizes the energy efficiency of wireless ad hoc and sensor networks. We compare SERENA with classical TDMA and optimized variants such as USAP in wireless ad hoc and sensor networks.
QR Factorization for the Cell Broadband Engine
Authors: Kurzak Jakub , Dongarra Jack
Published: January 2015

The QR factorization is one of the most important operations in dense linear algebra, offering a numerically stable method for solving linear systems of equations including overdetermined and underdetermined systems. Modern implementations of the QR factorization, such as the one in the LAPACK library, suffer from performance limitations due to the use of matrix–vector type operations in the phase of panel factorization. These limitations can be remedied by using the idea of updating of QR factorization, rendering an algorithm, which is much more scalable and much more suitable for implementation on a multi-core processor. It is demonstrated how the potential of the cell broadband engine can be utilized to the fullest by employing the new algorithmic approach and successfully exploiting the capabilities of the chip in terms of single instruction multiple data parallelism, instruction level parallelism and thread-level parallelism.
Streaming Model Based Volume Ray Casting Implementation for Cell Broadband Engine
Authors: Kim Jusub , JaJa Joseph
Published: January 2015

Interactive high quality volume rendering is becoming increasingly more important as the amount of more complex volumetric data steadily grows. While a number of volumetric rendering techniques have been widely used, ray casting has been recognized as an effective approach for generating high quality visualization. However, for most users, the use of ray casting has been limited to datasets that are very small because of its high demands on computational power and memory bandwidth. However the recent introduction of the Cell Broadband Engine (Cell B.E.) processor, which consists of 9 heterogeneous cores designed to handle extremely demanding computations with large streams of data, provides an opportunity to put the ray casting into practical use. In this paper, we introduce an efficient parallel implementation of volume ray casting on the Cell B.E. The implementation is designed to take full advantage of the computational power and memory bandwidth of the Cell B.E. using an intricate orchestration of the ray casting computation on the available heterogeneous resources. Specifically, we introduce streaming model based schemes and techniques to efficiently implement acceleration techniques for ray casting on Cell B.E. In addition to ensuring effective SIMD utilization, our method provides two key benefits: there is no cost for empty space skipping and there is no memory bottleneck on moving volumetric data for processing. Our experimental results show that we can interactively render practical datasets on a single Cell B.E. processor.
A Simulation Based Analysis of The Impact of IEEE 802.15.4 MAC Parameters on the Performance Under Different Traffic Loads
Authors: Rohm D. , Goyal M. , Hosseini H. , Divjak A. , Bashir Y.
Published: January 2015

IEEE 802.15.4, a MAC/PHY protocol for low power and low data rate wireless networks, is emerging as the popular choice for various monitoring and control applications. Depending on the application, the traffic load on an IEEE 802.15.4 network may vary over a wide range. The performance of the protocol, measured in terms of the packet loss probability and the packet latency, depends upon the prevailing traffic load among the nodes competing for channel access, the level of interference from the hidden nodes and the configuration of IEEE 802.15.4 MAC parameters. In this paper, we analyze via simulations the impact of different configurable MAC parameters on the performance of beaconless IEEE 802.15.4 networks under different traffic loads and under different levels of interference from the hidden nodes. Based on this analysis, we suggest the values of IEEE 802.15.4 MAC parameters that results in a good tradeoff between the packet loss probability and the packet latency under different conditions.
A Multimodal Technique for an Embedded Fingerprint Recognizer in Mobile Payment Systems
Authors: Conti V. , Militello C. , Sorbello F. , Vitabile S.
Published: January 2015

The development and the diffusion of distributed systems, directly connected to recent communication technologies, move people towards the era of mobile and ubiquitous systems. Distributed systems make merchant-customer relationships closer and more flexible, using reliable e-commerce technologies. These systems and environments need many distributed access points, for the creation and management of secure identities and for the secure recognition of users. Traditionally, these access points can be made possible by a software system with a main central server. This work proposes the study and implementation of a multimodal technique, based on biometric information, for identity management and personal ubiquitous authentication. The multimodal technique uses both fingerprint micro features (minutiae) and fingerprint macro features (singularity points) for robust user authentication. To strengthen the security level of electronic payment systems, an embedded hardware prototype has been also created: acting as self-contained sensors, it performs the entire authentication process on the same device, so that all critical information (e.g. biometric data, account transactions and cryptographic keys), are managed and stored inside the sensor, without any data transmission. The sensor has been prototyped using the Celoxica RC203E board, achieving fast execution time, low working frequency, and good recognition performance.
Strong Scaling Analysis of a Parallel, Unstructured, Implicit Solver and the Influence of the Operating System Interference
Authors: Sahni Onkar , Carothers Christopher D. , Shephard Mark S. , Jansen Kenneth E.
Published: January 2015

PHASTA falls under the category of high-performance scientific computation codes designed for solving partial differential equations (PDEs). Its a massively parallel unstructured, implicit solver with particular emphasis on fluid dynamics (CFD) applications. More specifically, PHASTA is a parallel, hierarchic, adaptive, stabilized, transient analysis code that effectively employs advanced anisotropic adaptive algorithms and numerical models of flow physics. In this paper, we first describe the parallelization of PHASTA's core algorithms for an implicit solve, where one of our key assumptions is that on a properly balanced supercomputer with appropriate attributes, PHASTA should continue to strongly scale on high core counts until the computational workload per core becomes insufficient and inter-processor communications start to dominate. We then present and analyze PHASTA's parallel performance across a variety of current near petascale systems, including IBM BG/L, IBM BG/P, Cray XT3, and custom Opteron based supercluster; this selection of systems with inherently different attributes covers a majority of potential candidates for upcoming petascale systems. On one hand, we achieve near perfect (linear) strong scaling out to 32,768 cores of IBM BG/L; showing that a system with desirable attributes will allow implicit solvers to strongly scale on high core counts (including petascale systems). On the contrary, we find that the relative tipping point for strong scaling fundamentally differs among current supercomputer systems. To understand the loss of scaling observed on a particular system (Opteron based supercluster) we analyze the performance and demonstrate that such a loss can be associated to an unbalance in a system attribute; specifically compute-node operating system (OS). In particular, PHASTA scales well to high core counts (up to 32,768 cores) during an implicit solve on systems with compute nodes using lightweight kernels (for example, IBM BG/L); however, we show that on a system where the compute node OS is more heavy weight (e.g., one with background processes) a loss in strong scaling is observed relatively at much fewer number of cores (4,096 cores).
XPL the Extensible Presentation Language
Authors: Santangelo A. , Gentile A. , Vella G. , Ingraffia N. , Liotta M.
Published: January 2015

The last decade has witnessed a growing interest in the development of web interfaces enabling both multiple ways to access contents and, at the same time, fruition by multiple modalities of interaction (point-and-click, contents reading, voice commands, gestures, etc.). In this paper we describe a framework aimed at streamlining the design process of multi-channel, multimodal interfaces enabling full reuse of software components. This framework is called the eXtensible Presentation architecture and Language (XPL), a presentation language based on design pattern paradigm that keeps separated the presentation layer from the underlying programming logic. The language supplies a methodology to expedite multimodal interface development and to reduce the effort to implement interfaces for multiple access devices, by means of using the same code. This paper describes a methodology approach based on Visual Design Pattern (ViDP) and Verbal Design Pattern (VeDP), offering examples of multimodal and multichannel interfaces created with the XPL Editor.
A new MAC Protocol for Reducing Effect of Needless Transmission Deferment Induced by Missed RTS/CTS Handshake
Authors: Shigeyasu Tetsuya , Inoue Daishi , Matsuno Hiroshi , Morinaga Norihiko
Published: January 2015

IEEE802.11DCF employs RTS/CTS (Request To Send/Clear To Send) mechanism for mitigating effect of hidden terminals. The RTS/CTS mechanism sets transmission deferral timer to neighbor terminals by exchanging RTS and CTS between transmitter and receiver. Then, in the case that RTS/CTS exchange succeeds, effect of hidden terminals could be suppressed, otherwise, any neighbor which received RTS and/or CTS defers its new transmission needlessly although DATA packet corresponding to the previous RTS/CTS exchange will not be transmitted. In this paper, we propose Cancel CTS, procedure in order to cope with the unnecessarily transmission deferment. Results of computer simulation confirms that our method well improves the throughput performance of IEEE802.11DCF.
Multiagent Based Information Dissemination in Vehicular Ad Hoc Networks
Authors: Manvi S.S. , Kakkasageri M. S. , Pitt Jeremy
Published: January 2015

Vehicular Ad hoc Networks (VANETs) are a compelling application of ad hoc networks, because of the potential to access specific context information (e.g. traffic conditions, service updates, route planning) and deliver multimedia services (Voice over IP, in-car entertainment, instant messaging, etc.). This paper proposes an agent based information dissemination model for VANETs. A two-tier agent architecture is employed comprising of the following: 1) 'lightweight', network-facing, mobile agents; 2) 'heavyweight', application-facing, norm-aware agents. The limitations of VANETs lead us to consider a hybrid wireless network architecture that includes Wireless LAN/Cellular and ad hoc networking for analyzing the proposed model. The proposed model provides flexibility, adaptability and maintainability for traffic information dissemination in VANETs as well as supports robust and agile network management. The proposed model has been simulated in various network scenarios to evaluate the effectiveness of the approach.
Evaluating Multicore Algorithms on the Unified Memory Model
Authors: Savage John E. , Zubair Mohammad
Published: January 2015

One of the challenges to achieving good performance on multicore architectures is the effective utilization of the underlying memory hierarchy. While this is an issue for single-core architectures, it is a critical problem for multicore chips. In this paper, we formulate the unified multicore model (UMM) to help understand the fundamental limits on cache performance on these architectures. The UMM seamlessly handles different types of multiple-core processors with varying degrees of cache sharing at different levels. We demonstrate that our model can be used to study a variety of multicore architectures on a variety of applications. In particular, we use it to analyze an option pricing problem using the trinomial model and develop an algorithm for it that has near-optimal memory traffic between cache levels. We have implemented the algorithm on a two Quad-Core Intel Xeon 5310 1.6 GHz processors (8 cores). It achieves a peak performance of 19.5 GFLOPs, which is 38% of the theoretical peak of the multicore system. We demonstrate that our algorithm outperforms compiler-optimized and auto-parallelized code by a factor of up to 7.5.
Tools for Performance Assessment of OLSR Protocol
Authors: Ikeda Makoto , Barolli Leonard , De Marco Giuseppe , Yang Tao , Durresi Arjan , Xhafa Fatos
Published: January 2015

In this paper, we evaluate the performance of Optimized Link State Routing (OLSR) protocol by experimental and simulation results. The experiments are carried out by using our implemented testbed and the simulations by using ns-2 simulator. We also designed and implemented a new interface for the ad-hoc network testbed in order to make more easier the experiments. The comparison between experimental and simulation results shows that for the same parameters set, in the simulation we did not notice any packet loss. On the other hand, in the experiments we experienced packet loss because of the environment effects and traffic interference.
Implementation and Performance Modeling of Deterministic Particle Transport (Sweep3D) on the IBM Cell/B.E.
Authors: Lubeck Olaf , Lang Michael , Srinivasan Ram , Johnson Greg
Published: January 2015

The IBM Cell Broadband Engine (BE) is a novel multi-core chip with the potential for the demanding floating point performance that is required for high-fidelity scientific simulations. However, data movement within the chip can be a major challenge to realizing the benefits of the peak floating point rates. In this paper, we present the results of implementing Sweep3D on the Cell/B.E. using an intra-chip message passing model that minimizes data movement. We compare the advantages/disadvantages of this programming model with a previous implementation using a master–worker threading strategy. We apply a previously validated micro-architecture performance model for the application executing on the Cell/B.E. (based on our previous work in Monte Carlo performance models), that predicts overall CPI (cycles per instruction), and gives a detailed breakdown of processor stalls. Finally, we use the micro-architecture model to assess the performance of future design parameters for the Cell/B.E. micro-architecture. The methodologies and results have broader implications that extend to multi-core architectures.
ePRO-MP: A Tool for Profiling and Optimizing Energy and Performance of Mobile Multiprocessor Applications
Authors: Choi Wonil , Kim Hyunhee , Song Wook , Song Jiseok , Kim Jihong
Published: January 2015

For mobile multiprocessor applications, achieving high performance with low energy consumption is a challenging task. In order to help programmers to meet these design requirements, system development tools play an important role. In this paper, we describe one such development tool, ePRO-MP, which profiles and optimizes both performance and energy consumption of multi-threaded applications running on top of Linux for ARM11 MPCore-based embedded systems. One of the key features of ePRO-MP is that it can accurately estimate the energy consumption of multi-threaded applications without requiring a power measurement equipment, using a regression-based energy model. We also describe another key benefit of ePRO-MP, an automatic optimization function, using two example problems. Using the automatic optimization function, ePRO-MP can achieve high performance and low power consumption without programmer intervention. Our experimental results show that ePRO-MP can improve the performance and energy consumption by 6.1% and 4.1%, respectively, over a baseline version for the co-running applications optimization example. For the producer-consumer application optimization example, ePRO-MP improves the performance and energy consumption by 60.5% and 43.3%, respectively over a baseline version.
Mobility Management Algorithms for the Client-Driven Mobility Frame System–Mobility from a Brand New Point of View
Authors: Fülöp Péter , Kovács Benedek , Imre Sándor
Published: January 2015

In this paper a new mobility management is introduced. The main idea in this approach is that the mobil node should manage the mobility for itself not the network. The network nodes provide only basic services for mobile entities: connectivity and administration. We construct a framework called the Client-based Mobility Frame System (CMFS) for this mobility environment. We developed the CMFS protocol as a solution over IPv4 and we show how to use Mobile IPv6 to realize our concept. We propose some basic mobility management solutions that can be implemented into the mobile clients and give details about a working simulation of a complete Mobility Management System. Example mobility management approaches such as the centralized- and hierarchical- or cellular-like ones are also defined and hints are given what kind of algorithms might be implemented upon the Client-based Mobility Frame System over IPv4 and IPv6 as well. We introduce some example algorithms that can work with the CMFS making mobility management efficient by minimizing signalling load on the network. In the present work modeling and detailed discussion on the parameters of the algorithms is given and comparison to existing mobility approaches and protocols is done. We prepared a simulation to test our protocol and to back up the proposals we provide the reader with simulation results. We stress that still one the most important benefit of our findings is that all the MNs can run different management strategies and can optimize mobility for themselves.
Performance Evaluation with Different Mobility Models for Dynamic Probabilistic Flooding in MANETs
Authors: Hanashi Abdalla M. , Awan Irfan , Woodward Mike
Published: January 2015

Broadcasting is an essential and effective data propagation mechanism, with several of important applications such as route discovery, address resolution, as well as many other network services. As data broadcasting has many advantages, also causing a lot of contention, collision, and congestion, which induces what is known as "broadcast storm problems". Broadcasting has traditionally been based on the flooding protocol, which simply overflows the network with high number of rebroadcast messages until the messages reach to all network nodes. A good probabilistic broadcasting protocol can achieve higher saved rebroadcast, low collisions and less number of relays. In this paper, we propose a dynamic probabilistic approach that dynamically fine-tunes the rebroadcasting probability according to the number of neighbour's nodes distributed in the ad hoc network for routing request packets (RREQs). The performance of the proposed approach is investigated and compared with the simple AODVand fixed probabilistic schemes using the GloMoSim network simulator under different mobility models. The performance results reveal that the improved approach is able to achieve higher saved rebroadcast and low collision as well as low number of relays than the fixed probabilistic scheme and simple AODV.
EXtending Mobility to Publish/Subscribe Systems Using a Pro-Active Caching Approach
Authors: Gaddah Abdulbaset , Kunz Thomas
Published: January 2015

The publish/subscribe communication paradigm has many characteristics that lend themselves well to mobile wireless networks. Our research investigates the extension of current publish/subscribe systems to support subscriber mobility in such networks. We present a novel mobility management scheme based on a pro-active caching approach to overcome the challenges and the performance concerns of disconnected operations in publish/subscribe systems. We discuss the mechanism of our proposed scheme and present a comprehensive experimental evaluation of our approach and alternative state-of-the-art solutions based on reactive approaches and durable subscriptions. The obtained results illustrate significant performance benefits of our proposed scheme across a range of scenarios. We conclude our work by discussing a modeling approach that can be used to extrapolate the performance of our approach in a near-size environment (in terms of broker network and/or subscriber population) to our experimental testbed.
Automated Analysis of Protein Expression and Gene Amplification within the Same Cells of Paraffin-Embedded Tumour Tissue
Authors: Gaiser Timo , Berroa-Garcia Lissa , Kemmerling Ralf , Dutta Aparajita , Ried Thomas , Heselmeyer-Haddad Kerstin
Published: January 2015

Background: The simultaneous detection of protein expression and gene copy number changes in patient samples, like paraffin-embedded tissue sections, is challenging since the procedures of immunohistochemistry (IHC) and Fluorescence in situ Hybridization (FISH) negatively influence each other which often results in suboptimal staining. Therefore, we developed a novel automated algorithm based on relocation which allows subsequent detection of protein content and gene copy number changes within the same cell.

Methods: Paraffin-embedded tissue sections of colorectal cancers were stained for CD133 expression. IHC images were acquired and image coordinates recorded. Slides were subsequently hybridized with fluorescently labeled DNA probes. FISH images were taken at the previously recorded positions allowing for direct comparison of protein expression and gene copy number signals within the same cells/tissue areas. Relocation, acquisition of the IHC and FISH images, and enumeration of FISH signals in the immunophenotyped tumour areas were done in an automated fashion.

Results: Automated FISH analysis was performed on 13 different colon cancer samples that had been stained for CD133; each sample was scored for MYC, ZNF217 and Chromosome 6 in CD133 positive and negative glands. From the 13 cases four (31%) showed amplification for the MYC oncogene and seven of 13 (54%) cases were amplified for ZNF217. There was no significant difference between CD133 positive tumour and CD133 negative tumour cells.

Conclusion: The technique and algorithm presented here enables an easy and reproducible combination of IHC and FISH based on a novel automated algorithm using relocation and automated spot counting.
Adjacency-Based Data Reordering Algorithm for Acceleration of Finite Element Computations
Authors: Zhou Min , Sahni Onkar , Shephard Mark S. , Carothers Christopher D. , Jansen Kenneth E.
Published: January 2015

Effective use of the processor memory hierarchy is an important issue in high performance computing. In this work, a part level mesh topological traversal algorithm is used to define a reordering of both mesh vertices and regions that increases the spatial locality of data and improves overall cache utilization during on processor finite element calculations. Examples based on adaptively created unstructured meshes are considered to demonstrate the effectiveness of the procedure in cases where the load per processing core is varied but balanced (e.g., elements are equally distributed across cores for a given partition). In one example, the effect of the current ajacency-based data reordering is studied for different phases of an implicit analysis including element-data blocking, element-level computations, sparse-matrix filling and equation solution. These results are compared to a case where reordering is applied to mesh vertices only. The computations are performed on various supercomputers including IBM Blue Gene (BG/L and BG/P), Cray XT (XT3 and XT5) and Sun Constellation Cluster. It is observed that reordering improves the per-core performance by up to 24% on Blue Gene/L and up to 40% on Cray XT5. The CrayPat hardware performance tool is used to measure the number of cache misses across each level of the memory hierarchy. It is determined that the measured decrease in L1, L2 and L3 cache misses when data reordering is used, closely accounts for the observed decrease in the overall execution time.
Glioblastomas with Oligodendroglial Component – Common Origin of the Different Histological Parts and Genetic Subclassification
Authors: Klink Barbara , Schlingelhof Ben , Klink Martin , Stout-Weider Karen , Patt Stephan , Schrock Evelin
Published: January 2015

Background: Glioblastomas are the most common and most malignant brain tumors in adults. A small subgroup of glioblastomas contains areas with histological features of oligodendroglial differentiation (GBMO). Our objective was to genetically characterize the oligodendroglial and the astrocytic parts of GBMOs and correlate morphologic and genetic features with clinical data.

Methods: The oligodendroglial and the “classic” glioblastoma parts of 13 GBMO were analyzed separately by interphase fluorescence in situ hybridization (FISH) on paraffin sections using a custom probe set (regions 1p, 1q, 7q, 10q, 17p, 19q, cen18, 21q) and by comparative genomic hybridization (CGH) of microdissected paraffin embedded tumor tissue.

Results: We identified four distinct genetic subtypes in 13 GBMOs: an “astrocytic” subtype (9/13) characterized by +7/−10; an “oligodendroglial” subtype with −1p/−19q (1/13); an “intermediate” subtype showing +7/−1p (1/13), and an “other” subtype having none of the former aberrations typical for gliomas (2/13). The different histological tumor parts of GBMO revealed common genetic changes in all tumors and showed additional aberrations specific for each part.

Conclusion: Our findings demonstrate the monoclonal origin of GBMO followed by the development of the astrocytic and oligodendroglial components. The diagnostic determination of the genetic signatures may allow for a better prognostication of the patients.
Implementation of CAVENET and Its Usage for Performance Evaluation of AODV, OLSR and DYMO Protocols in Vehicular Networks
Authors: Spaho Evjola , Barolli Leonard , Mino Gjergji , Xhafa Fatos , Kolici Vladi , Miho Rozeta
Published: January 2015

Vehicle Ad-hoc Network (VANET) is a kind of Mobile Ad-hoc Network (MANET) that establishes wireless connection between cars. In VANETs and MANETs, the topology of the network changes very often, therefore implementation of efficient routing protocols is very important problem. In MANETs, the Random Waypoint (RW) model is used as a simulation model for generating node mobility pattern. On the other hand, in VANETs, the mobility patterns of nodes is restricted along the roads, and is affected by the movement of neighbour nodes. In this paper, we present a simulation system for VANET called CAVENET (Cellular Automaton based VEhicular NETwork). In CAVENET, the mobility patterns of nodes are generated by an 1-dimensional cellular automata. We improved CAVENET and implemented some routing protocols. We investigated the performance of the implemented routing protocols by CAVENET. The simulation results have shown that DYMO protocol has better performance than AODV and OLSR protocols.
Supporting Fault-Tolerance for Time-Critical Events in Distributed Environments
Authors: Zhu Qian , Agrawal Gagan
Published: January 2015

In this paper, we consider the problem of supporting fault tolerance foradaptiveandtime-criticalapplications in heterogeneous and unreliable grid computing environments. Our goal for this class of applications is to optimize a user-specifiedbenefit functionwhile meeting the time deadline. Our first contribution in this paper is a multi-objective optimization algorithm for scheduling the application onto the most efficient and reliable resources. In this way, the processing can achieve the maximum benefit while also maximizing thesuccess-rate, which is the probability of finishing execution without failures. However, for the cases where failures do occur, we have developed ahybrid failure recoveryscheme to ensure that the application can complete within the pre-specified time interval. Our experimental results show that our scheduling algorithm can achieve better benefit when compared to several heuristics-based greedy scheduling algorithms, while still having a negligible overhead. Benefit is further improved when we apply the hybrid failure recovery scheme, and the success-rate becomes 100%.
High Frequency Microsatellite Instability Has a Prognostic Value in Endometrial Endometrioid Adenocarcinoma, But Only in FIGO Stage 1 Cases
Authors: Steinbakk Anita , Malpica Anais , Slewa Aida , Gudlaugsson Einar , Janssen Emiel A. M. , Arends Mark , Kruse Arnold Jan , Yinhua Yu , Feng Weiwei , Baak Jan P.
Published: January 2015

Objectives: To analyze the prognostic value of microsatellite instability (MSI) in a population-based study of FIGO stage 1–4 endometrial endometrioid adenocarcinomas.

Study Design: Survival analysis in 273 patients of MSI status and clinico-pathologic features. Using a highly sensitive pentaplex polymerase chain reaction to establish MSI status, cases were divided into microsatellite stable (MSS), MSI-low (MSI-L, 1 marker positive) and MSI-high (MSI-H, 2–5 markers positive).

Results: After 61 months median follow-up (1-209), 34 (12.5%) of the patients developed metastases but only 6.4% of the FIGO 1. MSI (especially as MSI-H vs. MSS/MSI-Lcombined) was prognostic in FIGO 1 but not in FIGO 2–4. The 5 and 10 year recurrence-free survival rates were 98% and 95% in the MSS/MSI-L vs. 85% and 73% in the MSI-H patients (p=0.005).

Conclusions: MSI-H status assessed by pentaplex polymerase chain reaction is an indicator of poor prognosis in FIGO 1, but not in FIGO 2–4 endometrial endometrioid adenocarcinomas.
RFID-Based Human Behavior Modeling and Anomaly Detection for Elderly Care
Authors: Hsu Hui-Huang , Chen Chien-Chen
Published: January 2015

This research aimed at building an intelligent system that can detect abnormal behavior for the elderly at home. Active RFID tags can be deployed at home to help collect daily movement data of the elderly who carries an RFID reader. When the reader detects the signals from the tags, RSSI values that represent signal strength are obtained. The RSSI values are reversely related to the distance between the tags and the reader and they are recorded following the movement of the user. The movement patterns, not the exact locations, of the user are the major concern. With the movement data (RSSI values), the clustering technique is then used to build a personalized model of normal behavior. After the model is built, any incoming datum outside the model can be viewed as abnormal and an alarm can be raised by the system. In this paper, we present the system architecture for RFID data collection and preprocessing, clustering for anomaly detection, and experimental results. The results show that this novel approach is promising.
Role of Pituitary Tumour Transforming Gene 1 in Medullary Thyroid Carcinoma
Authors: Zatelli Maria Chiara , Tagliati Federico , Amodio Vincenzo , Buratto Mattia , Pelizzo Mariarosa , Pansini Giancarlo , Bondanelli Marta , Ambrosio Maria Rosaria , Uberti Ettore C. degli
Published: January 2015

Background: Pituitary tumour transforming gene 1 (PTTG1) is over-expressed in a variety of endocrine-related tumours. We aimed at evaluatingPTTG1expression and function in human neoplastic parafollicular C-cells, represented by medullary thyroid carcinoma (MTC) and C-cell hyperplasia (CCH) samples and by the TT cell line.

Methods: TT cells and tissues derived from human CCH (8 samples) and MTC (12 samples) were analyzed by northern blot, furthermore TT cells were subjected to PTTG gene silencing and cells were analyzed for DNA synthesis.

Results:PTTG1expression was significantly higher (p< 0.01) in CCH (3-fold), in papillary thyroid cancer and in MTC (5-fold) than in normal thyroid, and in MTC lymph-node metastases as compared to primary lesions (~2-fold; p < 0.05).PTTG1mRNA and protein correlated with tumour diameter and TNM status (p < 0.05). In TT cells,PTTG1silencing did not completely block DNA synthesis, but significantly reduced [3H]Thymidine incorporation (~50%; p < 0.01) for up to 3 days.

Conclusion:PTTG1levels correlate with tumour aggressiveness.PTTG1silencing causes reduced MTC cell proliferation, supporting the hypothesis thatPTTG1might have an important role in C-cell neoplastic proliferation.
Concurrent Collections
Authors: Budimlić Zoran , Burke Michael , Cavé Vincent , Knobe Kathleen , Lowney Geoff , Newton Ryan , Palsberg Jens , Peixotto David , Sarkar Vivek , Schlimbach Frank , Taşırlar Sağnak
Published: January 2015

We introduce the Concurrent Collections (CnC) programming model. CnC supports flexible combinations of task and data parallelism while retaining determinism. CnC is implicitly parallel, with the user providing high-level operations along with semantic ordering constraints that together form a CnC graph. We formally describe the execution semantics of CnC and prove that the model guarantees deterministic computation. We evaluate the performance of CnC implementations on several applications and show that CnC offers performance and scalability equivalent to or better than that offered by lower-level parallel programming models.
Immunohistochemical Expression and Localization of Somatostatin Receptor Subtypes in Androgen Ablated Prostate Cancer
Authors: Mazzucchelli Roberta , Morichetti Doriana , Santinelli Alfredo , Scarpelli Marina , Bono Aldo V. , Lopez-Beltran Antonio , Cheng Liang , Montironi Rodolfo
Published: January 2015

Objective: The aim was to examine the expression and localization of the five somatostatin receptors (termed SSTR1–5) in radical prostatectomies (RPs) from patients with prostatic adenocarcinoma (PCa) under complete androgen ablation (CAA) before operation.

Material: The five SSTRs were evaluated in the epithelial, smooth muscle and endothelial cells of normal-looking epithelium (Nep), high-grade prostatic intraepithelial neoplasia (HGPIN) and PCa in 20 RPs with clinically detected PCa from patients under CAA. 20 RPs with clinically detected PCa from hormonally untreated patients were used as control group.

Results: Concerning the secretory cells (i) membrane staining was seen for SSTR3 and SSTR4; the mean percentages of positive cells, higher in SSTR3 than in SSTR4, decreased sharply in HGPIN and PCa compared with Nep; the mean percentages in the androgen ablated group were 30–90% lower than in the untreated; (ii) cytoplasmic staining was seen for all 5 SSTRs; the mean percentages of positive cells in Nep, HGPIN and PCa of the untreated group were similar, and in general as high as 80% or more; in the treated group, the Nep values were similar to those in the untreated, whereas the values in HGPIN and PCa were lower for SSTR1, 3 and 5, with a decrease of 30% for SSTR1; (iii) nuclear staining was seen with SSTR4 and SSTR5, the mean percentages for the former being much lower than for the latter; treatment affected both HGPIN and PCa, whose proportions of stained cells were 30–55% lower than in the untreated group. Cytoplasmic staining in the basal cells was seen for all 5 SSTRs, both in Nep and HGPIN. The values in the treated group were lower than in the other, the difference between the two group being in general comprised between 10 and 40%. Treatment did not affect SSTR staining in the smooth muscle and endothelial cells.

Conclusions: The present study expands our knowledge on the expression and localization of the five SSTRs in the prostate following CAA.
Acceleration of a CFD Code with a GPU
Authors: Jespersen Dennis C.
Published: January 2015

The Computational Fluid Dynamics code OVERFLOW includes as one of its solver options an algorithm which is a fairly small piece of code but which accounts for a significant portion of the total computational time. This paper studies some of the issues in accelerating this piece of code by using a Graphics Processing Unit (GPU). The algorithm needs to be modified to be suitable for a GPU and attention needs to be given to 64-bit and 32-bit arithmetic. Interestingly, the work done for the GPU produced ideas for accelerating the CPU code and led to significant speedup on the CPU.