bluuebunny/crossref_metadata_2025 huggingface dataset:
Semantic Prefetching Strategy to Manage Location Dependent Data in Mobile Information Systems
Authors: Kang Sang-Won , Song MoonBae , Park KwangJin , Hwang Chong-Sun
Published: January 2015

In mobile computing environments, location plays an important role in determining user′s interests. If service providers can supply information reflecting users′ semantics, overall system performance can be improved. Users can avoid queries, resulting in unnecessary network usage. A query result can also be transferred to a local device. Through our proposed semantic prefetching scheme, we make it possible to send data to mobile clients in advance. Researchers have been, for a long time, trying to develop a method to overcome mobile information system issues. These issues consist mainly of low bandwidth, high delay and frequent disconnections. In this paper, we represent the semantic prefetching strategy, which utilizes users′ interests, relating to a users′ current location. Our performance results show that this method is superior when compared with traditional semantic cache schemes.
A Survey of Software Infrastructures and Frameworks for Ubiquitous Computing
Authors: Endres Christoph , Butz Andreas , MacWilliams Asa
Published: January 2015

In this survey, we discuss 29 software infrastructures and frameworks which support the construction of distributed interactive systems. They range from small projects with one implemented prototype to large scale research efforts, and they come from the fields of Augmented Reality (AR), Intelligent Environments, and Distributed Mobile Systems. In their own way, they can all be used to implement various aspects of the ubiquitous computing vision as described by Mark Weiser [60]. This survey is meant as a starting point for new projects, in order to choose an existing infrastructure for reuse, or to get an overview before designing a new one. It tries to provide a systematic, relatively broad (and necessarily not very deep) overview, while pointing to relevant literature for in‐depth study of the systems discussed.
Porting of Scientific Applications to Grid Computing on GridWay
Authors: Herrera J. , Huedo E. , Montero R.S. , Llorente I.M.
Published: January 2015

The expansion and adoption of Grid technologies is prevented by the lack of a standard programming paradigm to port existing applications among different environments. The Distributed Resource Management Application API has been proposed to aid the rapid development and distribution of these applications across different Distributed Resource Management Systems. In this paper we describe an implementation of the DRMAA standard on a Globus‐based testbed, and show its suitability to express typical scientific applications, like High‐Throughput and Master‐Worker applications. The DRMAA routines are supported by the functionality offered by the GridWay2 framework, which provides the runtime mechanisms needed for transparently executing jobs on a dynamic Grid environment based on Globus. As cases of study, we consider the implementation with DRMAA of a bioinformatics application, a genetic algorithm and the NAS Grid Benchmarks.
Dynamic Memory De‐allocation in Fortran 95/2003 Derived Type Calculus
Authors: Rouson Damian W.I. , Morris Karla , Xu Xiaofeng
Published: January 2015

Abstract data types developed for computational science and engineering are frequently modeled after physical objects whose state variables must satisfy governing differential equations. Generalizing the associated algebraic and differential operators to operate on the abstract data types facilitates high‐level program constructs that mimic standard mathematical notation. For non‐trivial expressions, multiple object instantiations must occur to hold intermediate results during the expression′s evaluation. When the dimension of each object′s state space is not specified at compile‐time, the programmer becomes responsible for dynamically allocating and de‐allocating memory for each instantiation. With the advent of allocatable components in Fortran 2003 derived types, the potential exists for these intermediate results to occupy a substantial fraction of a program′s footprint in memory. This issue becomes particularly acute at the highest levels of abstraction where coarse‐grained data structures predominate. This paper proposes a set of rules for de‐allocating memory that has been dynamically allocated for intermediate results in derived type calculus, while distinguishing that memory from more persistent objects. The new rules are applied to the design of a polymorphic time integrator for integrating evolution equations governing dynamical systems. Associated issues of efficiency and design robustness are discussed.
Statistical Algorithms for Long DNA Sequences: Oligonucleotide Distributions and Homogeneity Maps
Authors: Katsaloulis P. , Theoharis T. , Provata A.
Published: January 2015

The statistical properties of oligonucleotide appearances within long DNA sequences often reveal useful characteristics of the corresponding DNA areas. Two algorithms to statistically analyze oligonucleotide appearances within long DNA sequences in genome banks are presented. The first algorithm determines statistical indices for arbitrary length oligonucleotides within arbitrary length DNA sequences. The critical exponent μ of the distance distribution between consecutive occurrences of the same oligonucleotide is calculated and its value is shown to characterize the functionality of the oligonucleotide. The second algorithm searches for areas with variable homogeneity, based on the density of oligonucleotides. The two algorithms have been applied to representative eucaryotes (the animal Mus musculusand the plant Arabidopsis thaliana) and interesting results were obtained, confirmed by biological observations. All programs are open source and publicly available on our web site.
EVector: An Efficient Vector Implementation – Using Virtual Memory for Improving Memory
Authors: Kimpe Dries , Vandewalle Stefan , Poedts Stefaan
Published: January 2015

Every modern operating system provides some form of virtual memory to its applications. Usually, a hardware memory management unit (MMU) exists to efficiently support this. Although most operating systems allow user programs to indirectly control the MMU, few programs or programming languages actually make use of this facility. This article explores how the MMU can be used to enhance memory handling for resizable arrays. A reference implementation in C++ demonstrates its usability and superiority compared to the standard C++ vector class, and how to combine the scheme with an object‐oriented environment. A number of other improvements, based on newly emerged insights in C++ are also presented.
Applying Algebraic Approaches for Modeling Workflows and their Transformations in Mobile Networks
Authors: Bottoni Paolo , De Rosa Fabio , Hoffmann Kathrin , Mecella Massimo
Published: January 2015

In emergency scenarios we can obtain a more effective coordination among team members, each of them equipped with hand‐held devices, through the use of workflow management software. Team members constitute a Mobile Ad‐hoc NETwork (MANET), whose topology both influences and is influenced by the workflow. In this paper we propose an algebraic approach for modeling workflow progress as well as its modifications as required by topology transformations. The approach is based on Algebraic Higher‐Order Nets and sees both workflows and topologies as tokens, allowing their concurrent modification.
Location Based Mobile Computing–A Tuplespace Perspective
Authors: Fongen Anders , Larsen Christian , Ghinea Gheorghita , Taylor Simon J. E. , Serif Tacha
Published: January 2015

Location based or ”context aware” computing is becoming increasingly recognized as a vital part of a mobile computing environment. As a consequence, the need for location‐management middleware is widely recognized and actively researched. Location‐management is frequently offered to the application through a “location API” (e.g. JSR 179) where the mobile unit can find out its own location as coordinates or as “building, floor, room” values. It is then up to the application to map the coordinates into a set of localized variables, e.g. direction to the nearest bookshop or the local timezone. It is the opinion of the authors that a localization API should be more transparent and more integrated: The localized values should be handed to the application directly, and the API for doing so should be the same as the general storage mechanisms. Our proposed middleware for location and context management is built on top of Mobispace. Mobispace is a distributed tuplespace made for mobile units (J2me) where replication between local replicas takes place with a central server (over GPRS) or with other mobile units (using Bluetooth). Since a Bluetooth connection indicates physical proximity to another node, a set of stationary nodes may distribute locality information over Bluetooth connections, and this information may be retrieved through the ordinary tuplespace API. Besides the integration with the general framework for communication and coordination the middleware offers straightforward answers to questions like: Where is node X located? Which nodes are near me? What is the trace of node Y?
Prediction Schemes to Enhance the Routing Process in Geographical GPSR Ad Hoc Protocol
Authors: Saqour Raed , Shanuldin Mohamad , Ismail Mahamod
Published: January 2015

Geographical routing protocols have received a serious attention due to more advantages they have in comparison to the conventional routing protocols. They require information about the physical position of nodes needed to be available. Commonly, each node determines its own position through the use of Global Positioning System (GPS) or some other type of positioning service. Greedy Perimeter Stateless Routing (GPSR) protocol, which is one of geographical routing protocols, limits the forwarding decision of the packet based on the node′s own position, the destination′s position and the position of the forwarding node′s neighbors. Location information has some inaccuracy depending on the localization system and the environment exists in. This paper aims to study the impact of mobility metrics (beacon interval, and node speed) on introducing location information error in GPSR protocol using different mobility models. The effect of these metrics is identified in GPSR as Neighbor Break Link (NBL) problem. Based on simulation analysis, mobility prediction schemes are proposed to migrate the observed problem.
Alternative Data Storage Solution for Mobile Messaging Services
Authors: Ong David C. C. , Sileika Rytis , Khaddaj Souheil , Oudrhiri Radouane
Published: January 2015

In recent years, mobile devices have become relatively more powerful with additional features which have the capability to provide multimedia streaming. Better, faster and more reliable data storage solutions in the mobile messaging platform have become more essential with these additional improvements. The existing mobile messaging infrastructure, in particular the data storage platform has become less proficient in coping with the increased demand for its services. This demand especially in the mobile messaging area (i.e. SMS – Short Messaging Service, MMS – Multimedia Messaging Service), which may well exceeded 250,000 requests per second, means that the need to evaluate competing data management systems has become not only necessary but essential. This paper presents an evaluation of SMS and MMS platforms using different database management systems – DBMS and recommends the best data management strategies for these platforms.
Addressing User Expectations in Mobile Content Delivery
Authors: Agboma Florence , Liotta Antonio
Published: January 2015

Multimedia services like television programs and live streaming of mobile videos can be delivered to mobile terminals via different access technologies. The question is – how do users perceive such services on mobile terminals? The objective of this study is to find the correlation between video quality thresholds and the user context. Our study reveals the thresholds of user′s quality of experience (QoE) in a mobile environment by using different categories of content types, in relation to different access technologies and terminal capability. The mobile terminals used are: – (i) 3G Mobile Phone (ii) Personal Digital Assistant (PDA) and (iii) Laptop. We argue that quality of service (QoS) management should be driven by the user perception of quality rather than resulting from raw engineering parameters such as latency, jitter, bandwidth etc. Our results will be of great interest to network operators, service providers, terminal manufacturers, and researchers working in the area of quality of service management.
Towards Analysis-Driven Scientific Software Architecture: The Case for Abstract Data Type Calculus
Authors: Rouson Damian W.I.
Published: January 2015

This article approaches scientific software architecture from three analytical paths. Each path examines discrete time advancement of multiphysics phenomena governed by coupled differential equations. The new object-oriented Fortran 2003 constructs provide a formal syntax for an abstract data type (ADT) calculus. The first analysis uses traditional object-oriented software design metrics to demonstrate the high cohesion and low coupling associated with the calculus. A second analysis from the viewpoint of computational complexity theory demonstrates that a more representative bug search strategy than that considered by Rouson et al. (ACM Trans. Math. Soft.34(1) (2008)) reduces the number of lines searched in a code with λ total lines from O(λ2) to O(λ log2λ ), which in turn becomes nearly independent of the overall code size in the context of ADT calculus. The third analysis derives from information theory an argument that ADT calculus simplifies developer communications in part by minimizing the growth in interface information content as developers add new physics to a multiphysics package.
Performance Measurement and Analysis of Large-Scale Parallel Applications on Leadership Computing Systems
Authors: Wylie Brian J.N. , Geimer Markus , Wolf Felix
Published: January 2015

Developers of applications with large-scale computing requirements are currently presented with a variety of high-performance systems optimised for message-passing, however, effectively exploiting the available computing resources remains a major challenge. In addition to fundamental application scalability characteristics, application and system peculiarities often only manifest at extreme scales, requiring highly scalable performance measurement and analysis tools that are convenient to incorporate in application development and tuning activities. We present our experiences with a multigrid solver benchmark and state-of-the-art real-world applications for numerical weather prediction and computational fluid dynamics, on three quite different multi-thousand-processor supercomputer systems – Cray XT3/4, MareNostrum & Blue Gene/L – using the newly-developed SCALASCA toolset to quantify and isolate a range of significant performance issues.
Emergent Behavior in Massively‐Deployed Sensor Networks
Authors: Shurkova Ekaterina , Ishak Ruzana , Olariu Stephan , Salleh Shaharuddin
Published: January 2015

The phenomenal advances in MEMS and nanotechnology make it feasible to build small devices, referred to as sensors that are able to sense, compute and communicate over small distances. The massive deployment of these small devices raises the fascinating question of whether or not the sensors, as a collectivity, will display emergent behavior, just as living organisms do. In this work we report on a recent effort intended to observe emerging behavior of large groups of sensor nodes, like living cells demonstrate. Imagine a massive deployment of sensors that can be in two states "red" and "blue". At deployment time individual sensors have an initial color. The goal is to obtain a uniform coloring of the deployment area. Importantly, the sensors can only talk to sensors that are one‐hop away from them. The decisions to change colors are local, based on what the sensors can infer from collecting color information from their neighbors. We have performed extensive simulations involving 20,000 sensors in an area of 100 m × 100 m. Our simulation results show that the sensor network converges to a stable uniform coloring extremely fast.
Adaptive and Fuzzy Approaches for Nodes Affinity Management in Wireless Ad‐Hoc Networks
Authors: Natsheh Essam , Wan Tat-Chee
Published: January 2015

In most of the ad‐hoc routing protocols, a static link lifetime (LL) is used for a newly discovered neighbors. Though this works well for networks with fixed infrastructures, it is inadequate for ad‐hoc networks due to nodes mobility and frequent breaks of links. To overcome this problem, routing protocols with estimated LL using nodes affinity were introduced. However, these protocols also used the static estimated LL during the connection time. In contrast to that, in this paper two methods are presented to estimate LL based on nodes affinity and then continually update those values depending on changes of the affinity. In the first method, linear function is used to map the relationship between the signal strength fluctuation and LL. In the second method, fuzzy logic system is used to map this relationship in a nonlinear fashion. Significance of the proposed methods is validated using simulation. Results indicate that fuzzy method provides the most efficient and robust LL values for routing protocols.
Performance Evaluation of Two Fuzzy‐Based Cluster Head Selection Systems for Wireless Sensor Networks
Authors: Anno Junpei , Barolli Leonard , Durresi Arjan , Xhafa Fatos , Koyama Akio
Published: January 2015

Sensor networks supported by recent technological advances in low power wireless communications along with silicon integration of various functionalities are emerging as a critically important computer class that enable novel and low cost applications. There are many fundamental problems that sensor networks research will have to address in order to ensure a reasonable degree of cost and system quality. Cluster formation and cluster head selection are important problems in sensor network applications and can drastically affect the network′s communication energy dissipation. However, selecting of the cluster head is not easy in different environments which may have different characteristics. In this paper, in order to deal with this problem, we propose two fuzzy‐based systems for cluster head selection in sensor networks. We call these systems: FCHS System1 and FCHS System2. We evaluate the proposed systems by simulations and have shown that FCHS System2 make a good selection of the cluster head compared with FCHS System1 and another previous system.
Slogger: A Profiling and Analysis System Based on Semantic Web Technologies
Authors: Baker Mark , Boakes Richard
Published: January 2015

Increasingly, distributed systems are being used to host all manner of applications. While these platforms provide a relatively cheap and effective means of executing applications, so far there has been little work in developing tools and utilities that can help application developers understand problems with the supporting software, or the executing applications. To fully understand why an application executing on a distributed system is not behaving as would be expected it is important that not only the application, but also the underlying middleware, and the operating system are analysed too, otherwise issues could be missed and certainly overall performance profiling and fault diagnoses would be harder to understand. We believe that one approach to profiling and the analysis of distributed systems and the associated applications is via the plethora of log files generated at runtime. In this paper we report on a system (Slogger), that utilises various emerging Semantic Web technologies to gather the heterogeneous log files generated by the various layers in a distributed system and unify them in common data store. Once unified, the log data can be queried and visualised in order to highlight potential problems or issues that may be occurring in the supporting software or the application itself.
Programming the Linpack Benchmark for the IBM PowerXCell 8i Processor
Authors: Kistler Michael , Gunnels John , Brokenshire Daniel , Benton Brad
Published: January 2015

In this paper we present the design and implementation of the Linpack benchmark for the IBM BladeCenter QS22, which incorporates two IBM PowerXCell 8i1processors. The PowerXCell 8i is a new implementation of the Cell Broadband Engine™2 architecture and contains a set of special-purpose processing cores known as Synergistic Processing Elements (SPEs). The SPEs can be used as computational accelerators to augment the main PowerPC processor. The added computational capability of the SPEs results in a peak double precision floating point capability of 108.8 GFLOPS. We explain how we modified the standard open source implementation of Linpack to accelerate key computational kernels using the SPEs of the PowerXCell 8i processors. We describe in detail the implementation and performance of the computational kernels and also explain how we employed the SPEs for high-speed data movement and reformatting. The result of these modifications is a Linpack benchmark optimized for the IBM PowerXCell 8i processor that achieves 170.7 GFLOPS on a BladeCenter QS22 with 32 GB of DDR2 SDRAM memory. Our implementation of Linpack also supports clusters of QS22s, and was used to achieve a result of 11.1 TFLOPS on a cluster of 84 QS22 blades. We compare our results on a single BladeCenter QS22 with the base Linpack implementation without SPE acceleration to illustrate the benefits of our optimizations.
Building High-Resolution Sky Images Using the Cell/B.E.
Authors: Varbanescu Ana Lucia , van Amesfoort Alexander S. , Cornwell Tim , van Diepen Ger , van Nieuwpoort Rob , Elmegreen Bruce G. , Sips Henk
Published: January 2015

The performance potential of the Cell/B.E., as well as its availability, have attracted a lot of attention from various high-performance computing (HPC) fields. While computation intensive kernels proved to be exceptionally well suited for running on the Cell, irregular data-intensive applications are usually considered as poor matches. In this paper, we present our complete solution for enabling such a data-intensive application to run efficiently on the Cell/B.E. processor. Specifically, we target radioastronomy data gridding and degridding, two resembling imaging filters based on convolutional resampling. Our solution is based on building a high-level application model, used to evaluate parallelization alternatives. Next, we choose the one with the best performance potential, and we gradually exploit this potential by applying platform-specific and application-specific optimizations. After several iterations, our target application shows a speed-up factor between 10 and 20 on a dual-Cell blade when compared with the original application running on a commodity machine. Given these results, and based on our empirical observations, we are able to pinpoint a set of ten guidelines for parallelizing similar applications on the Cell/B.E. Finally, we conclude the Cell/B.E. can provide high performance for data-intensive applications at the price of increased programming efforts and with a significant aid from aggressive application-specific optimizations.
Improving Sensing Accuracy in Cognitive PANs through Modulation of Sensing Probability
Authors: Mišić Vojislav B. , Mišić Jelena
Published: January 2015

Cognitive radio technology necessitates accurate and timely sensing of primary users' activity on the chosen set of channels. The simplest selection procedure is a simple random choice of channels to be sensed, but the impact of sensing errors with respect to primary user activity or inactivity differs considerably. In order to improve sensing accuracy and increase the likelihood of finding channels which are free from primary user activity, the selection procedure is modified by assigning different sensing probabilities to active and inactive channels. The paper presents a probabilistic analysis of this policy and investigates the range of values in which the modulation of sensing probability is capable of maintaining an accurate view of the status of the working channel set. We also present a modification of the probability modulation algorithm that allows for even greater reduction of sensing error in a limited range of the duty cycle of primary users' activity. Finally, we give some guidelines as to the optimum application ranges for the original and modified algorithm, respectively.
Implementation and Performance Evaluation of Two Fuzzy-Based Handover Systems for Wireless Cellular Networks
Authors: Mino Gjergji , Barolli Leonard , Xhafa Fatos , Durresi Arjan , Koyama Akio
Published: January 2015

Wireless mobile networks and devices are becoming increasingly popular to provide users the access anytime and anywhere. We are witnessing now an unprecedented demand for wireless networks to support both data and real-time multimedia traffic. The wireless 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. Many handover algorithms are proposed in the literature. However, to make a better handover and keep the QoS in wireless networks is very difficult task. For this reason, new intelligent algorithms should be implemented to deal with this problem. In this paper, we carried out a comparison study of two handover systems based on fuzzy logic. We implement two Fuzzy-Based Handover Systems (FBHS) called FBHS1 and FBHS2. The performance evaluation via simulations shows that FBHS2 has better behavior than FBHS1 and can avoid ping-pong effect in all simulation cases.
Probability Model for Data Redundancy Detection in Sensor Networks
Authors: Kumar Suman , Park Seung-Jong
Published: January 2015

Sensor networks are made of autonomous devices that are able to collect, store, process and share data with other devices. Large sensor networks are often redundant in the sense that the measurements of some nodes can be substituted by other nodes with a certain degree of confidence. This spatial correlation results in wastage of link bandwidth and energy. In this paper, a model for two associated Poisson processes, through which sensors are distributed in a plane, is derived. A probability condition is established for data redundancy among closely located sensor nodes. The model generates a spatial bivariate Poisson process whose parameters depend on the parameters of the two individual Poisson processes and on the distance between the associated points. The proposed model helps in building efficient algorithms for data dissemination in the sensor network. A numerical example is provided investigating the advantage of this model.
Ubiquitous Supervisory System Based on Social Contexts Using Ontology
Authors: Izumi Satoru , Yamanaka Kazuhiro , Tokairin Yoshikazu , Takahashi Hideyuki , Suganuma Takuo , Shiratori Norio
Published: January 2015

As described in this paper, we propose a supervisory system that considers actual situations and social aspects of users in a ubiquitous computing environment. To realize gentle and safe supervision while providing efficient supervisory services, the system must recognize the situations of a watched person, such as the person's physical condition. To achieve this, we have proposed a ubiquitous supervisory system "uEyes", which introduces Social Context Awareness: a distinguishing feature for supervision. Using this feature, the system can combine environmental information acquired from sensors in the real world and common-sense knowledge related to human activities in daily life. As described in this paper, we specifically examine design of Social Context Awareness using ontology technologies. Based on this advanced feature, a live video streaming system is configured autonomously depending on the users' circumstances in runtime. We implemented a uEyes prototype for supervising elderly people and performed some experiments based on several scenarios. Based on those experimental results, we confirmed that the social contexts are handled effectively to support the supervision.
VHLGenetic Alteration in CCRCC Does Not Determine De-Regulation of HIF, CAIX, hnRNP A2/B1 and Osteopontin
Authors: Nyhan Michelle J. , El Mashad Shereen M. , O’Donovan Tracey R. , Ahmad Sarfraz , Collins Chris , Sweeney Paul , Rogers Eamonn , O’Sullivan Gerald C. , McKenna Sharon L.
Published: January 2015

Background: von Hippel–Lindau (VHL) tumour suppressor gene inactivation is associated with clear cell renal cell carcinoma (CCRCC) development. The VHL protein (pVHL) has been proposed to regulate the expression of several proteins including Hypoxia Inducible Factor-α (HIF-α), carbonic anhydrase (CA)IX, heterogeneous nuclear ribonucleoprotein (hnRNP) A2/B1 and osteopontin. pVHL has been characterized in vitro, however, clinical studies are limited. We evaluated the impact of VHL genetic alterations on the expression of several pVHL protein targets in paired normal and tumor tissue.

Methods: TheVHLgene was sequenced in 23 CCRCC patients andVHLtranscript levels were evaluated by real-time RT-PCR. Expression of pVHL’s protein targets were determined by Western blotting in 17 paired patient samples.

Results: VHL genetic alterations were identified in 43.5% (10/23) of CCRCCs. HIF-1α, HIF-2α and CAIX were up-regulated in 88.2% (15/17), 100% (17/17) and 88.2% (15/17) of tumors respectively and their expression is independent ofVHLstatus. hnRNP A2/B1 and osteopontin expression was variable in CCRCCs and had no association withVHLgenetic status.

Conclusion: As expression of these proposed pVHL targets can be achieved independently ofVHLmutation (and possibly by hypoxia alone), these data suggests that other pVHL targets may be more crucial in renal carcinogenesis.
Activating Mutation (V617F) in the Tyrosine Kinase JAK2 is Absent in Locally-Confined or Castration-Resistant Prostate Cancer
Authors: Gu Lei , Zhu Xian-Hua , Visakorpi Tapio , Alanen Kalle , Mirtti Tuomas , Edmonston Tina Bocker , Nevalainen Marja T.
Published: January 2015

Background: Transcription factor Stat5a/b is highly critical for the viability of human prostate cancer cells in vitro and for prostate tumor growthin vivo. Stat5 is constitutively active in clinical prostate cancers but not in the normal human prostate epithelium. Moreover, Stat5a/b activation in prostate cancer is associated with high histological grade of prostate cancer. However, the molecular mechanisms underlying constitutive activation of Stat5a/b in prostate cancer are unclear. The receptor-associated tyrosine kinase Jak2 is a known key activator of Stat5a/b in prostate cancer cells in response to ligand stimulation. Recently, a single gain-of-function point mutation ofJAK2was described in myeloproliferative diseases leading to constitutive Jak2 kinase activity, subsequent Stat5a/b activation and involvement of V617F Jak2 in the pathogenesis of myeloproliferative disorders.

Materials and Methods: We determined whetherJAK2undergoes the V617F activating mutation during clinical progression of human prostate cancer using a highly sensitive assay (amplification refractory mutation system) and a unique material of fresh specimens from organ-confined or castration-resistant prostate cancers.

Results: TheJAK2V617F mutation was not found in any of the normal or malignant prostate samples analyzed in this study.

Conclusions: Future work should focus on determining the molecular mechanisms other than V617F mutation of Jak2 resulting in continuous Stat5 activation in clinical prostate cancers.
Ultra-Fast Processing of Gigapixel Tissue MicroArray Images Using High Performance Computing
Authors: Wang Yinhai , McCleary David , Wang Ching-Wei , Kelly Paul , James Jackie , Fennell Dean A. , Hamilton Peter
Published: January 2015

Background: Tissue MicroArrays (TMAs) are a valuable platform for tissue based translational research and the discovery of tissue biomarkers. The digitised TMA slides or TMA Virtual Slides, are ultra-large digital images, and can contain several hundred samples. The processing of such slides is time-consuming, bottlenecking a potentially high throughput platform.

Methods: A High Performance Computing (HPC) platform for the rapid analysis of TMA virtual slides is presented in this study. Using an HP high performance cluster and a centralised dynamic load balancing approach, the simultaneous analysis of multiple tissue-cores were established. This was evaluated on Non-Small Cell Lung Cancer TMAs for complex analysis of tissue pattern and immunohistochemical positivity.

Results: The automated processing of a single TMA virtual slide containing 230 patient samples can be significantly speeded up by a factor of circa 22, bringing the analysis time to one minute. Over 90 TMAs could also be analysed simultaneously, speeding up multiplex biomarker experiments enormously.

Conclusion: The methodologies developed in this paper provide for the first time a genuine high throughput analysis platform for TMA biomarker discovery that will significantly enhance the reliability and speed for biomarker research. This will have widespread implications in translational tissue based research.
TGFβ-signaling in Squamous Cell Carcinoma Occurring in Recessive Dystrophic Epidermolysis Bullosa
Authors: Knaup Julia , Gruber Christina , Krammer Barbara , Ziegler Verena , Bauer Johann , Verwanger Thomas
Published: January 2015

Background: Recessive dystrophic epidermolysis bullosa (RDEB) is a hereditary skin disorder characterized by mechanical fragility of the skin, resulting in blistering and chronic wounds. The causative mutations lie in the COL7A1 gene. Patients suffering from RDEB have a high risk to develop aggressive, rapidly metastasizing squamous cell carcinomas (SCCs). Cutaneous RDEB SCCs develop preferentially in long-term skin wounds or cutaneous scars. Albeit being well differentiated, they show a more aggressive behavior than UV-induced SCCs. These findings suggest other contributing factors in SCC tumorigenesis in RDEB.Objective: To analyze factors contributing to RDEB tumorigenesis, we conducted a comprehensive gene expression study comparing a non-malignant RDEB (RDEB-CL) to a RDEB SCC cell line (SCCRDEB4) to achieve an overview on the changes of the gene expression levels in RDEB related skin cancer.Methods: We applied cDNA arrays comprising 9738 human expressed sequence tags (EST) with various functions. Selected results were verified by Real-time RT PCR.Results: Large-scale gene expression analysis revealed changes in the expression level of transforming growth factor β1 (TGFβ1) and several genes under the control of TGFβ for RDEB and SCCRDEB4 cell lines. Even untransformed RDEB keratinocytes show elevated levels of TGFβ1.Conclusion: Our findings demonstrate a prominent role of TGFβ-signaling in RDEB-related skin cancer. Once activated, TGFβ signaling either in response to wounding or in order to influence type VII collagen expression levels could facilitate cancer development and progression. Moreover, TGFβ signaling might also represent a potentially useful therapeutic target in this disease.
Imatinib Mesylate Alters the Expression of Genes Related to Disease Progression in an Animal Model of Uveal Melanoma
Authors: Fernandes Bruno F. , Di Cesare Sebastian , Belfort Rubens Neto , Maloney Shawn , Martins Claudia , Castiglione Enzo , Isenberg Jordan , Abourbih Daniel , Antecka Emilia , Burnier Jr. Miguel N.
Published: January 2015

Imatinib mesylate (IM) is a compound that inhibits both BCR-ABL tyrosine kinase and c-kit receptors. Tyrosine kinases are important in cellular signaling and mediate major cellular processes such as proliferation, differentiation, apoptosis, attachment, and migration. Twenty-six albino rabbits were injected with 1 × 106 human uveal melanoma (UM) cells (92.1) into the suprachoroidal space. Animals were immunosuppressed (cyclosporin A) over the course of the 12-week experiment and divided into two groups (n = 13). The experimental group received IM once daily by gavage while the control group received a placebo. One animal per group was sacrificed every week after the 2nd week. Upon necropsy, organs were harvested for histopathological examination. Cells from the primary tumors were recultured and tested in proliferation and invasion assays. A PCR array was used to investigate the differences in expression of 84 genes related to tumor metastasis. In the treated group, 4 rabbits developed intraocular tumors, with an average largest tumor dimension (LTD) of 2.5 mm and 5 animals reported metastatic disease. Whereas 6 rabbits in the control group developed intraocular tumors, with an average LTD of 5.8 mm and 6 animals reported metastatic disease. The recultured cells from the treated group demonstrated lower proliferation rates and were less invasive (p < 0.001 The PCR array showed differences in expression of genes related to metastasis. Notably, there was 290-fold increase inSERPINB5, a tumor suppressor gene, and a 10-fold higher expression ofKISS1, a metastasis suppressor gene, in the treated group. Proangiogenic genes such asVEGFA,PDGFAandPDGFBwere downregulated in the treated group. To the best of our knowledge, this is the first report detailing the altered expression of specific genes in UM cells after treatment with IM.
Performance Evaluation of Acoustic Underwater Data Broadcasting Exploiting the Bandwidth-Distance Relationship
Authors: Nicopolitidis P. , Christidis K. , Papadimitriou G. I. , Sarigiannidis P. G. , Pomportsis A. S.
Published: January 2015

Despite being a fundamental networking primitive, data broadcasting has so far received little attention in the context of underwater networks. This paper proposes an adaptive push system for data broadcasting in underwater acoustic wireless networks with locality of client demands. The proposed system exploits the characteristic relationship between the bandwidth of an underwater acoustic link and the transmitter-receiver distance in order to improve performance in environments with locality of client demands. Simulation results show superior performance of the proposed approach in the underwater environment compared to existing systems.
Optimizing the Performance and Robustness of Type-2 Fuzzy Group Nearest-Neighbor Queries
Authors: Ghadiri Nasser , Baraani-Dastjerdi Ahmad , Ghasem-Aghaee Nasser , Nematbakhsh Mohammad A.
Published: January 2015

In Group Nearest-Neighbor (GNN) queries, the goal is to find one or more points of interest with minimum sum of distance to the current location of mobile users. The classic forms of GNN use Euclidean distance measure which is not sufficient to capture other essential distance perceptions of human and the inherent uncertainty of it. To overcome this problem, an improved distance model can be used which is based on a richer, closer to real-world type-2 fuzzy logic distance model. However, large search spaces as well as the need for higher-order uncertainty management will increase the response times of such GNN queries. In this paper two fuzzy clustering methods combined with spatial tessellation are exploited to reduce the search space. Extensive evaluation of the proposed method shows improved response times compared to naïve method while maintaining a high quality of approximation. The proposed uncertainty management method also provides robustness to movement of mobile users, eliminating the need for full re-computation of candidate clusters when the locations of group members are changed.
Automated Area Calculation of Histopathologic Features Using SIVQ
Authors: Hipp Jason , Cheng Jerome , Daignault Stephanie , Sica Jefferey , Dugan Michael C. , Lucas David , Yagi Yukako , Hewitt Stephen , Balis Ulysses J.
Published: January 2015

Recently, with the advent of the 7th edition of the AJCC Cancer Staging manual, at least one set of criteria (e.g. breast) were modified to now require the measurement of maximal depth of stromal invasion. With the current manual interpretive morphological approaches typically employed by surgical pathologists to assess tumor extent, the specialty now potentially has stumbled upon a crossroads of practice, where the diagnostic criteria have exceeded the capabilities of our commonly available tools. While whole slide imaging (WSI) technology holds the potential to offer many improvements in clinical workflow over conventional slide microscopy including unambiguous utility for facilitating quantitative diagnostic tasks with one important example being the determination of both linear dimension and surface area. However, the availability of histology data in digital form is of little utility if time-consuming and cumbersome manual workflow steps are necessarily imposed upon the pathologist in order to generate such measurements, especially as encountered with the complex and ill-defined shapes inherent to infiltrative tumors. In this communication, we demonstrate the utility of the recently described SIVQ algorithm to serve as the basis of a highly accurate, precise and semi-automated tool for direct surface area measurement of tumor infiltration from WSI data sets. By anticipating the current trend in cancer staging that emphasizes increasingly precise feature characterization, as witnessed by the recent publication of AJCC's 7th edition of the Cancer Staging Manual, this tool holds promise to will be of value to pathologists for clinical utility.
BGN: A Novel Scatternet Formation Algorithm for Bluetooth-Based Sensor Networks
Authors: Li Yongjun , Chen Hu , Xie Rong , Wang James Z.
Published: January 2015

To address the unreliability and inefficiency of the existing algorithms for Bluetooth scatternet formation, this paper proposes a new efficient algorithm, Bluetooth Growing Network (BGN) algorithm, which constructs Bluetooth scatternet by adding reserve links among its branch nodes so that the resulting scatternet can maintain a high degree of connectivity while avoiding exccessive redundant links. Extensive simulation results demonstrate that the scatternet constructed by BGN algorithm is efficient in terms of the number of bridge nodes, average data transmission distance, network reliablity and overall network traffic.
Developing an Instrument to Measure the Adoption of Mobile Services
Authors: Gao Shang , Krogstie John , Siau Keng
Published: January 2015

Currently, there is no standard instrument for measuring user adoption of mobile services. Based on the mobile service acceptance model, this paper reports on the development of a survey instrument designed to measure user perception on mobile services acceptance. A survey instrument was developed by using some existing scales from prior instruments and by creating additional items which might appear to fit the construct definitions. In addition, a pilot study was conducted by distributing the survey to 25 users of a mobile service called Mobile Student Information Systems. As a result, a survey instrument containing 22 items were retained. Furthermore, the results showed that the reliabilities of all the scales in the survey instrument were above the target acceptance level.
Book Review
Authors: Brown Adrian
Published: January 2015

Phillip M. Morse and Herman Feshbach, Professors of Physics at the MIT, published their biblical-sized textbook ‘Methods of Theoretical Physics’ with McGraw-Hill in May 1953. At 1978 pages and published in two books, it is an intimidating twin tome that should still be atop the reading lists or the bookshelves of every mathematical physicist. What material is covered in this book? In the most concise of terms, this book is devoted to the study of differential equations and associated boundary conditions that describe physical fields. The thirteen chapters address what circumstances warrant the use of which differential equations, and most often addresses the question of coordinate system transformations, for example, how do Green's functions for Laplace's Equation transform under different coordinate systems? Under what circumstances the solutions can be expected to be separable? Many examples are covered to illustrate these points. Why is this book relevant to Software Programmers? This book is part of the background that any scientific programmer is likely to need in dealing with physical fields. This book was written before personal computers became ubiquitous, however it is still an outstanding effort to tie the methods of solving differential equations governing fields together in one book. The book never received a second edition, however, it was reprinted to an outstanding standard by Feshbach Publishing since 2004, run by the children of Herman Feshbach. Their website is feshbachpublishing.com. The majority of this review is a mini-commentary of the book showing what is covered in a very terse fashion, which may be useful as a summary even for those who have already read the full text. I then give a brief analysis of the approach to mathematical physics taken by the book. Finally, I will discuss who will benefit from reading this magnificent treatise, nearly 60 years after it was first published.
Digital Image Analysis in Pathology: Benefits and Obligation
Authors: Laurinavicius Arvydas , Laurinaviciene Aida , Dasevicius Darius , Elie Nicolas , Plancoulaine Benoît , Bor Catherine , Herlin Paulette
Published: January 2015

Pathology has recently entered the era of personalized medicine. This brings new expectations for the accuracy and precision of tissue-based diagnosis, in particular, when quantification of histologic features and biomarker expression is required. While for many years traditional pathologic diagnosis has been regarded as ground truth, this concept is no longer sufficient in contemporary tissue-based biomarker research and clinical use. Another major change in pathology is brought by the advancement of virtual microscopy technology enabling digitization of microscopy slides and presenting new opportunities for digital image analysis. Computerized vision provides an immediate benefit of increased capacity (automation) and precision (reproducibility), but not necessarily the accuracy of the analysis. To achieve the benefit of accuracy, pathologists will have to assume an obligation of validation and quality assurance of the image analysis algorithms. Reference values are needed to measure and control the accuracy. Although pathologists' consensus values are commonly used to validate these tools, we argue that the ground truth can be best achieved by stereology methods, estimating the same variable as an algorithm is intended to do. Proper adoption of the new technology will require a new quantitative mentality in pathology. In order to see a complete and sharp picture of a disease, pathologists will need to learn to use both their analogue and digital eyes.
The Software Architecture for Performing Scientific Computation with the JLAPACK Libraries in ScalaLab
Authors: Papadimitriou Stergios , Mavroudi Seferina , Theofilatos Kostas , Likothanasis Spiridon
Published: January 2015

Although LAPACK is a powerful library its utilization is difficult. JLAPACK, a Java translation obtained automatically from the Fortran LAPACK sources, retains exactly the same difficult to use interface of LAPACK routines. The MTJ library implements an object oriented Java interface to JLAPACK that hides many complicated details. ScalaLab exploits the flexibility of the Scala language to present an even more friendly and convenient interface to the powerful but complicated JLAPACK library. The article describes the interfacing of the low-level JLAPACK routines within the ScalaLab environment. This is performed rather easily by exploiting well suited features of the Scala language. Also, the paper demonstrates the convenience of using JLAPACK routines for linear algebra operations from within ScalaLab.