bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparison of Different Promoter Methylation Assays in Breast Cancer
Authors: Suijkerbuijk Karijn P. M. , Pan Xiaojuan , van der Wall Elsken , van Diest Paul J. , Vooijs Marc
Published: January 2015

Background: Promoter hypermethylation has emerged as a promising cancer biomarker. Currently, a large variety of quantitative and non-quantitative techniques is used to measure methylation in clinical specimens. Here we directly compared three commonly used methylation assays and assessed the influence of tissue fixation, target sequence location and the amount of DNA on their performance.

Methods: We used Methylation-Specific PCR (MSP), Quantitative Multiplex MSP (QM-MSP) and Methylation-Specific Multiplex Ligation-dependent Probe Amplification (MS-MLPA) to compare methylation of CCND2, SCGB3A1, RARB and RASSF1 on DNA from 40 breast carcinomas.

Results: A comparison between MSP and QM-MSP on the same samples showed a high discrepancy: 20% of tumors that showed no methylation in MSP gave >10% methylation in QM-MSP. In contrast, QM-MSP correlated strongly with MS-MLPA when targeting the same sequence in DNA from paraffin embedded as well as fresh frozen tissue. This correlation declined when target sequences were non-overlapping. In titration experiments, MSP and MS-MLPA performed robust with 10 ng of DNA, while QM-MSP was at least ten-fold more sensitive.

Conclusion: Despite the difference in molecular basis, QM-MSP and MS-MLPA showed moderate to strong correlations. In contrast, there was a poor concordance between either of these techniques and non-quantitative MSP. For biological samples with scarce DNA, QM-MSP is the method of choice.
Enabling Locality-Aware Computations in OpenMP
Authors: Huang Lei , Jin Haoqiang , Yi Liqi , Chapman Barbara
Published: January 2015

Locality of computation is key to obtaining high performance on a broad variety of parallel architectures and applications. It is moreover an essential component of strategies for energy-efficient computing. OpenMP is a widely available industry standard for shared memory programming. With the pervasive deployment of multi-core computers and the steady growth in core count, a productive programming model such as OpenMP is increasingly expected to play an important role in adapting applications to this new hardware. However, OpenMP does not provide the programmer with explicit means to program for locality. Rather it presents the user with a “flat” memory model. In this paper, we discuss the need for explicit programmer control of locality within the context of OpenMP and present some ideas on how this might be accomplished. We describe potential extensions to OpenMP that would enable the user to manage a program's data layout and to align tasks and data in order to minimize the cost of data accesses. We give examples showing the intended use of the proposed features, describe our current implementation and present some experimental results. Our hope is that this work will lead to efforts that would help OpenMP to be a major player on emerging, multi- and many-core architectures.
Robust Video Communication over an Urban VANET
Authors: Qadri N. , Altaf M. , Fleury M. , Ghanbari M.
Published: January 2015

Video communication within a Vehicular Ad Hoc Network (VANET) has the potential to be of considerable benefit in an urban emergency, as it allows emergency vehicles approaching the scene to better understand the nature of the emergency. However, the lack of centralized routing and network resource management within a VANET is an impediment to video streaming. To overcome these problems the paper pioneers source-coding techniques for VANET video streaming. The paper firstly investigates two practical multiple-path schemes, Video Redundancy Coding (VRC) and the H.264/AVC codec's redundant frames. The VRC scheme is reinforced by gradual decoder refresh to improve the delivered video quality. Evaluation shows that multiple-path 'redundant frames' achieves acceptable video quality at some destinations, whereas VRC is insufficient. The paper also demonstrates a third source coding scheme, single-path streaming with Flexible Macroblock Ordering, which is also capable of delivery of reasonable quality video. Therefore, video communication between vehicles is indeed shown to be feasible in an urban emergency if the suitable source coding techniques are selected.
Experiences with Resource Provisioning for Scientific Workflows Using Corral
Authors: Juve Gideon , Deelman Ewa , Vahi Karan , Mehta Gaurang
Published: January 2015

The development of grid and workflow technologies has enabled complex, loosely coupled scientific applications to be executed on distributed resources. Many of these applications consist of large numbers of short-duration tasks whose runtimes are heavily influenced by delays in the execution environment. Such applications often perform poorly on the grid because of the large scheduling overheads commonly found in grids. In this paper we present a provisioning system based on multi-level scheduling that improves workflow runtime by reducing scheduling overheads. The system reserves resources for the exclusive use of the application, and gives applications control over scheduling policies. We describe our experiences with the system when running a suite of real workflow-based applications including in astronomy, earthquake science, and genomics. Provisioning resources with Corral ahead of the workflow execution, reduced the runtime of the astronomy application by up to 78% (45% on average) and of a genome mapping application by an order of magnitude when compared to traditional methods. We also show how provisioning can benefit applications both on a small local cluster as well as a large-scale campus resource.
The Design and Implementation of Tamper Resistance for Mobile Game Service
Authors: Chang Hang Bae , Kwon Hyuk Jun , Kang Jong Gu
Published: January 2015

The commensurate number of the attacks and infringement targeting a vulnerability of the game service has been increasing constantly, due to the dramatic growth and expansion of the impact of the game industry. However, there exist no subsequent researches for the differentiated technology, which is to prevent the reverse function of the game service. Therefore, in this study, we examined the current status of infringement toward online game services which are provided in the market currently and designed the proper technical measures ('Software Tamper Resistance') for a manipulation of the game service which is the most vulnerable part. In detail, we have encrypted an execution file and decrypted it in real time process. After that we implemented antibebugging, disassemble, and antidump technology.
Gene Expression in Oligodendroglial Tumors
Authors: Shaw Elisabeth J. , Haylock Brian , Husband David , du Plessis Daniel , Sibson D. Ross , Warnke Peter C. , Walker Carol
Published: January 2015

Background: Oligodendroglial tumors with 1p/19q loss are more likely to be chemosensitive and have longer survival than those with intact 1p/19q, but not all respond to chemotherapy, warranting investigation of the biological basis of chemosensitivity.

Methods: Gene expression profiling was performed using amplified antisense RNA from 28 oligodendroglial tumors treated with chemotherapy (26 serial stereotactic biopsy, 2 resection). Expression of differentially expressed genes was validated by real-time PCR.

Results: Unsupervised hierarchical clustering showed clustering of multiple samples from the same case in 14/17 cases and identified subgroups associated with tumor grade and 1p/19q status. 176 genes were differentially expressed, 164 being associated with 1p/19q loss (86% not on 1p or 19q). 94 genes differed between responders and non-responders to chemotherapy; 12 were not associated with 1p/19q loss. Significant differential expression was confirmed in 11/13 selected genes. Novel genes associated with response to therapy includedSSBP2,GFRA1,FAPandRASD1.IQGAP1,INA,TGIF1,NR2F2andMYCBPwere differentially expressed in oligodendroglial tumors with 1p/19q loss.

Conclusion: Gene expression profiling using serial stereotactic biopsies indicated greater homogeneity within tumors than between tumors. Genes associated with 1p/19q status or response were identified warranting further elucidation of their role in oligodendroglial tumors.
MANET Performance for Source and Destination Moving Scenarios Considering OLSR and AODV protocols
Authors: Kulla Elis , Hiyama Masahiro , Ikeda Makoto , Barolli Leonard , Kolici Vladi , Miho Rozeta
Published: January 2015

Recently, a great interest is shown in MANETs potential usage and applications in several fields such as military activities, rescue operations and time-critical applications. In this work, we implement and analyse a MANET testbed considering AODV and OLSR protocols for wireless multi-hop networking. We investigate the effect of mobility and topology changing in MANET and evaluate the performance of the network through experiments in a real environment. The performance assessment of our testbed is done considering throughput, number of dropped packets and delay. We designed four scenarios: Static, Source Moving, Destination Moving and Source-Destination Moving. From our experimental results, we concluded that when the communicating nodes are moving and the routes change quickly, OLSR (as a proactive protocol) performs better than AODV, which is a reactive protocol.
Experiences Using Hybrid MPI/OpenMP in the Real World: Parallelization of a 3D CFD Solver for Multi-Core Node Clusters
Authors: Jost Gabriele , Robins Bob
Published: January 2015

Today most systems in high-performance computing (HPC) feature a hierarchical hardware design: shared-memory nodes with several multi-core CPUs are connected via a network infrastructure. When parallelizing an application for these architectures it seems natural to employ a hierarchical programming model such as combining MPI and OpenMP. Nevertheless, there is the general lore that pure MPI outperforms the hybrid MPI/OpenMP approach. In this paper, we describe the hybrid MPI/OpenMP parallelization of IR3D (Incompressible Realistic 3-D) code, a full-scale real-world application, which simulates the environmental effects on the evolution of vortices trailing behind control surfaces of underwater vehicles. We discuss performance, scalability and limitations of the pure MPI version of the code on a variety of hardware platforms and show how the hybrid approach can help to overcome certain limitations.
Scheduling Two-Sided Transformations Using Tile Algorithms on Multicore Architectures
Authors: Ltaief Hatem , Kurzak Jakub , Dongarra Jack , Badia Rosa M.
Published: January 2015

The objective of this paper is to describe, in the context of multicore architectures, three different scheduler implementations for the two-sided linear algebra transformations, in particular the Hessenberg and Bidiagonal reductions which are the first steps for the standard eigenvalue problems and the singular value decompositions respectively. State-of-the-art dense linear algebra softwares, such as the LAPACK and ScaLAPACK libraries, suffer performance losses on multicore processors due to their inability to fully exploit thread-level parallelism. At the same time the fine-grain dataflow model gains popularity as a paradigm for programming multicore architectures. Buttari et al. (Parellel Comput. Syst. Appl. 35 (2009), 38–53) introduced the concept oftile algorithmsin which parallelism is no longer hidden inside Basic Linear Algebra Subprograms but is brought to the fore to yield much better performance. Along with efficient scheduling mechanisms for data-driven execution, these tile two-sided reductions achieve high performance computing by reaching up to 75% of the DGEMM peak on a 12000×12000 matrix with 16 Intel Tigerton 2.4 GHz processors. The main drawback of thetile algorithmsapproach for two-sided transformations is that the full reduction cannot be obtained in one stage. Other methods have to be considered to further reduce the band matrices to the required forms.
Adipose Tissue-Derived Stem Cells Differentiate into Carcinoma-Associated Fibroblast-Like Cells under the Influence of Tumor-Derived Factors
Authors: Jotzu Constantin , Alt Eckhard , Welte Gabriel , Li Jie , Hennessy Bryan T. , Devarajan Eswaran , Krishnappa Srinivasalu , Pinilla Severin , Droll Lilly , Song Yao-Hua
Published: January 2015

Carcinoma-associated fibroblasts (CAF) are considered to contribute to tumor growth, invasion and metastasis. However, the cell type of origin remains unknown. Since human adipose tissue-derived stem cells (hASCs) are locally adjacent to breast cancer cells and might directly interact with tumor cells, we investigated whether CAFs may originate from hASCs. We demonstrated that a significant percentage of hASCs differentiated into a CAF-like myofibroblastic phenotype (e.g., expression of alpha smooth muscle actin and tenascin-C) when exposed to conditioned medium from the human breast cancer lines MDAMB231 and MCF7. The conditioned medium from MDAMB231 and MCF7 contains significant amounts of transforming growth factor-beta 1 (TGFβ1) and the differentiation of hASCs towards CAFs is dependent on TGFβ1 signaling via Smad3 in hASCs. The induction of CAFs can be abolished using a neutralizing antibody to TGFβ1 as well as by pretreatment of the hASCs with SB431542, a TGFβ1 receptor kinase inhibitor. Additionally, we found that these hASC-derived CAF-like cells exhibit functional properties of CAFs, including the ability to promote tumor cell invasion in anin vitroinvasion assay, as well as increased expression of stromal-cell-derived factor 1 (SDF-1) and CCL5. Taken together, these data suggest that hASCs are a source of CAFs which play an important role in the tumor invasion.
TS Gene Polymorphisms Are Not Good Markers of Response to 5-FU Therapy in Stage III Colon Cancer Patients
Authors: Fariña-Sarasqueta A. , Gosens M. J. E. M. , Moerland E. , van Lijnschoten I. , Lemmens V. E. P. P. , Slooter G. D. , Rutten H. J. T. , van den Brule A. J. C.
Published: January 2015

Aim: Although the predictive and prognostic value of thymidylate synthase (TS) expression and gene polymorphism in colon cancer has been widely studied, the results are inconclusive probably because of methodological differences. With this study, we aimed to elucidate the role of TS gene polymorphisms genotyping in therapy response in stage III colon carcinoma patients treated with 5-FU adjuvant chemotherapy.

Patients and Methods: 251 patients diagnosed with stage III colon carcinoma treated with surgery followed by 5-FU based adjuvant therapy were selected. The variable number of tandem repeats (VNTR) and the single nucleotide polymorphism (SNP) in the 5′-untranslated region of the TS gene were genotyped.

Results: There was a positive association between tumor T stage and the VNTR genotypes (p=0.05). In both univariate and multivariate survival analysis no effects of the studied polymorphisms on survival were found. However, there was an association between both polymorphisms and age. Among patients younger than 60 years, the patients homozygous for 2R seemed to have a better overall survival, whereas among the patients older than 67 this longer survival was seen by the carriers of other genotypes.

Conclusion: We conclude that the TS VNTR and SNP do not predict response to 5-FU therapy in patients with stage III colon carcinoma. However, age appears to modify the effects of TS polymorphisms on survival.
p21/waf1 and Smooth-Muscle Actin α Expression in Stromal Fibroblasts of Oral Cancers
Authors: Chatzistamou Ioulia , Dioufa Nikolina , Trimis George , Sklavounou Alexandra , Kittas Christos , Kiaris Hippokratis , Papavassiliou Athanasios G.
Published: January 2015

Background: Concerted alterations between stromal fibroblasts and neoplastic cells underline the carcinogenic process. Activation of alpha-smooth muscle actin (SMA) expression, a cytoskeleton protein normally expressed only in myoepithelial cells, is considered a landmark for the activation of stromal fibroblasts with little however being known regarding the mechanism governing the expression of SMA in the stroma.

Methods: We have evaluated by immunohistochemistry the expression of SMA in the stroma of oral malignant and pre-malignant lesions, in association with the expression of p53 and p21 tumor suppressors that were shown previously to be deregulated and/or mutated in stromal fibroblasts of various cancers. The effects of p21 knockdown in SMA expression and cell migration and the mRNA levels of endogenous p21 in fibroblasts co-cultured with cancer cells were also assessed.

Results: We found that both p21 and SMA expression was elevated in the stroma, but not the epithelium, of malignant as compared to pre-malignant lesions. We also noted that the expression of both was positively correlated, implying that SMA expression may be regulated by p21. Consistently with this notion we found that siRNA-mediated p21 suppression resulted in the reduction of SMA levels and also inhibited cell migration.

Conclusion: Our results show that p21 deregulation is associated with the activation of stromal fibroblasts of oral cancers by a mechanism that involves the stimulation of SMA expression.
Rapid Quantification of Myocardial Fibrosis: A New Macro-Based Automated Analysis
Authors: Hadi Awal M. , Mouchaers Koen T. B. , Schalij Ingrid , Grunberg Katrien , Meijer Gerrit A. , Vonk-Noordegraaf Anton , van der Laarse Willem J. , Beliën Jeroen A. M.
Published: January 2015

Background: Fibrosis is associated with various cardiac pathologies and dysfunction. Current quantification methods are time-consuming and laborious. We describe a semi-automated quantification technique for myocardial fibrosis and validated this using traditional methods.

Methods: Pulmonary Hypertension (PH) was induced in adult Wistar rats by subcutaneous monocrotaline (MCT) injection (40 mg/kg). Cryosections of myocardial tissue (5 μm) of PH rats (n=9) and controls (n=9) were stained using Picrosirius red and scanned with a digital microscopic Mirax slide scanner. From these sections 21 images were taken randomly of each heart. Using ImageJ software a macro for automated image analysis of the amount of fibrosis was developed. For comparison, fibrosis was quantified using traditional polarisation microscopy. Both methods were correlated and validated against stereology as the gold standard. Furthermore, the method was tested in paraffin-embedded human tissues.

Results: Automated analysis showed a significant increase of fibrosis in PH hearts vs. control. Automated analysis correlated with traditional polarisation and stereology analysis (r2=0.92 and r2=0.95, respectively). In human heart, lungs, kidney and liver, a similar correlation with stereology (r2=0.91) was observed. Time required for automated analysis was 22 and 33% of the time needed for stereology and polarisation analysis, respectively.

Conclusion: Automated quantification of fibrosis is feasible, objective and time-efficient.
Tumor Necrosis Factor-αis Associated with Positive Lymph Node Status in Patients with Recurrence of Colorectal Cancer – Indications for Anti-TNF-αAgents in Cancer Treatment
Authors: Grimm M. , Lazariotou M. , Kircher S. , Höfelmayr A. , Germer C. T. , von Rahden B. H. A. , Waaga-Gasser A. M. , Gasser M.
Published: January 2015

Introduction: The progressive growth of malignancies is accompanied by a decline in the immune response through mechanisms which are poorly understood. Apoptosis and induction of inflammation by tumor released cytokines as tumor escape mechanisms have been proposed to play an important role in colorectal carcinogenesis.

Methods: Expression of Tumor necrosis factor-alpha (TNF-α) was analyzed in colorectal cancer specimen and the cancer cell line HT-29 by immunohistochemistry and RT-PCR. TNF-αexpression on protein and mRNA level were correlated with clinical characteristics and impact on survival. TNFR-1 was co-labelled with TNF-αand CD8+ cytotoxic T cells in immunofluorescence double staining experiments.

Results: 94% (n=98/104) of the patients with CRC expressed TNF-α. High TNF-αexpression was significantly associated with positive lymph node stage and recurrence of the tumor. Multivariate analysis revealed high TNF-αexpression as an independent prognostic factor. Immunohistochemistry was correlated with RT-PCR results (τ=0.794). Immunofluorescence double staining experiments revealed increased TNFR-1 expression by CD8+ cells.

Conclusion: TNF-αexpression by tumor cells may be an efficient immunological escape mechanism by inflammation-enhanced metastases and probably by induction of apoptosis in tumor-infiltrating CD8+ immune cells resulting in a down regulation of the tumoral immune response. Our data support the role of tumor-derived TNF-αexpression as an important promoter of tumoral immune escape mechanisms and malignant progression, and suggest that analysis on either protein (immunohistochemistry) or RNA level (RT-PCR) can be used effectively in this respect. Targeting TNF-αmay be a promising option, especially in cases with high TNF-αexpression and positive lymph node metastases.
Architecture for Mobile Heterogeneous Multi Domain Networks
Authors: Durresi Arjan , Zhang Ping , Durresi Mimoza , Barolli Leonard
Published: January 2015

Multi domain networks can be used in several scenarios including military, enterprize networks, emergency networks and many other cases. In such networks, each domain might be under its own administration. Therefore, the cooperation among domains is conditioned by individual domain policies regarding sharing information, such as network topology, connectivity, mobility, security, various service availability and so on. We propose a new architecture for Heterogeneous Multi Domain (HMD) networks, in which one the operations are subject to specific domain policies. We propose a hierarchical architecture, with an infrastructure of gateways at highest-control level that enables policy based interconnection, mobility and other services among domains. Gateways are responsible for translation among different communication protocols, including routing, signalling, and security. Besides the architecture, we discuss in more details the mobility and adaptive capacity of services in HMD. We discuss the HMD scalability and other advantages compared to existing architectural and mobility solutions. Furthermore, we analyze the dynamic availability at the control level of the hierarchy.
Diffie-Hellman Key Based Authentication in Proxy Mobile IPv6
Authors: Kim HyunGon , Lee Jong-Hyouk
Published: January 2015

Wireless communication service providers have been showing strong interest in Proxy Mobile IPv6 for providing network-based IP mobility management. This could be a prominent way to support IP mobility to mobile nodes, because Proxy Mobile IPv6 requires minimal functionalities on the mobile node. While several extensions for Proxy Mobile IPv6 are being developed in the Internet Engineering Task Force, there has been little attentions paid to developing efficient authentication mechanisms. An authentication scheme for a mobility protocol must protect signaling messages against various security threats, e.g., session stealing attack, intercept attack by redirection, replay attack, and key exposure, while minimizing authentication latency. In this paper, we propose a Diffie-Hellman key based authentication scheme that utilizes the low layer signaling to exchange Diffie-Hellman variables and allows mobility service provisioning entities to exchange mobile node's profile and ongoing sessions securely. By utilizing the low layer signaling and context transfer between relevant nodes, the proposed authentication scheme minimizes authentication latency when the mobile node moves across different networks. In addition, thanks to the use of the Diffie-Hellman key agreement, pre-established security associations between mobility service provisioning entities are not required in the proposed authentication scheme so that network scalability in an operationally efficient manner is ensured. To ascertain its feasibility, security analysis and performance analysis are presented.
Inhibition of IGF-1R-Dependent PI3K Activation Sensitizes Colon Cancer Cells Specifically to DR5-Mediated Apoptosis But Not to rhTRAIL
Authors: Pennarun Bodvael , Kleibeuker Jan H. , Oenema Tjitske , Stegehuis Janet H. , de Vries Elisabeth G.E. , de Jong Steven
Published: January 2015

Background: Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) initiates apoptosis in tumor cells upon binding to its cognate agonistic receptors, death receptors 4 and 5 (DR4 and DR5). The activity of the insulin-like growth factor 1 (IGF-1) survival pathway is often increased in cancer, influencing both cell proliferation and apoptosis. We hypothesized that inhibiting the IGF-1 receptor (IGF-1R) using NVP-AEW541, a small molecular weight tyrosine kinase inhibitor of the IGF-1R, could increase death receptor (DR)-mediated apoptosis in colon cancer cells.

Methods: The analyses were performed by caspase assay, flow cytometry, Western blotting, immunoprecipitation and fluorescent microscopy.

Results: Preincubation with NVP-AEW541 surprisingly decreased apoptosis induced by recombinant human TRAIL (rhTRAIL) or an agonistic DR4 antibody while sensitivity to an agonistic DR5 antibody was increased. NVP-AEW541 could inhibit IGF-1-induced activation of the phosphatidylinositol 3-kinase (PI3K) pathway. The effects of the PI3K inhibitor LY294002 on TRAIL-induced apoptosis were similar to those of NVP-AEW541, further supporting a role for IGF-1R-mediated activation of PI3K. We show that PI3K inhibition enhances DR5-mediated caspase 8 processing but also lowers DR4 membrane expression and DR4-mediated caspase 8 processing. Inhibition of PI3K reduced rhTRAIL sensitivity independently of the cell line preference for either DR4- or DR5-mediated apoptosis signaling.

Conclusion: Our study indicates that individual effects on DR4 and DR5 apoptosis signaling should be taken into consideration when combining DR-ligands with PI3K inhibition.
Fault Reconnaissance Agent for Sensor Networks
Authors: Shakshuki Elhadi M. , Xing Xinyu , Sheltami Tarek R.
Published: January 2015

One of the key prerequisite for a scalable, effective and efficient sensor network is the utilization of low-cost, low-overhead and high-resilient fault-inference techniques. To this end, we propose an intelligent agent system with a problem solving capability to address the issue of fault inference in sensor network environments. The intelligent agent system is designed and implemented at base-station side. The core of the agent system – problem solver – implements a fault-detection inference engine which harnesses Expectation Maximization (EM) algorithm to estimate fault probabilities of sensor nodes. To validate the correctness and effectiveness of the intelligent agent system, a set of experiments in a wireless sensor testbed are conducted. The experimental results show that our intelligent agent system is able to precisely estimate the fault probability of sensor nodes.
Detection of The TNFSF Members BAFF, APRIL, TWEAK and Their Receptors in Normal Kidney and Renal Cell Carcinomas
Authors: Pelekanou Vassiliki , Notas George , Theodoropoulou Katerina , Kampa Marilena , Takos Dimitrios , Alexaki Vassilia-Ismini , Radojicic Jelena , Sofras Frank , Tsapis Andreas , Stathopoulos Efstathios N. , Castanas Elias
Published: January 2015

In advanced renal cell carcinoma (RCC), surgery combined with systemic chemotherapy and immunotherapy have had limited effectiveness. Therapeutic modalities targeting VEGF, PDGF, and c-kit using tyrosine kinase inhibitors and m-TOR using specific biologic factors are in development. Therapeutic approaches targeting TNF-alpha have shown limited efficacy, while anti-TRAIL (TNFSF10) antibodies have shown enhanced activity. The presence and potential significance of other members of the TNFSF has not been investigated. Here, we assayed the TNFSF members APRIL, BAFF, TWEAK and their receptors (BCMA, TACI, BAFFR, Fn14) in 86 conventional type clear cell RCC, using immunohistochemistry and correlated our findings with histological data and, in a limited series, follow-up of patients. We observed a differential expression of these TNFSF ligands and receptors in cancerous and non-cancerous structures. BAFF was found in all RCC; APRIL expression is associated with an aggressive phenotype, correlating negatively with patients' disease-free survival, while TWEAK and its receptor Fn14 are heterogeneously expressed, correlating negatively with the grade and survival of RCC patients. This is the first study, presenting together the TNFSF members APRIL, BAFF, TWEAK and their receptors in different areas of normal renal tissue and RCC, suggesting a potential role of these TNFSF members in renal tumor biology.
GeoVanet: A Routing Protocol for Query Processing in Vehicular Networks
Authors: Delot Thierry , Mitton Nathalie , Ilarri Sergio , Hien Thomas
Published: January 2015

In a vehicular ad hoc network (VANET), cars can exchange information by using short-range wireless communications. Along with the opportunities offered by vehicular networks, a number of challenges also arise. In particular, most works so far have focused on a push model, where potentially useful data are pushed towards vehicles. The use of pull models, that would allow users to send queries to a set of cars in order to find the desired information, has not been studied in depth. The main challenge for pull models is the difficulty to route the different results towards the query originator in a highly dynamic network where the nodes move very quickly. To solve this issue, we propose GeoVanet, an anonymous and non-intrusive geographic routing protocol which ensures that the sender of a query can get a consistent answer. Our goal is to ensure that the user will be able to retrieve the query results within a bounded time. To prove the effectiveness of GeoVanet, an extensive experimental evaluation has been performed, that proves the interest of the proposal for both rural and urban areas. It shows that up to 80% of the available query results are delivered to the user.
Early Observations on the Performance of Windows Azure
Authors: Hill Zach , Li Jie , Mao Ming , Ruiz-Alvarez Arkaitz , Humphrey Marty
Published: January 2015

A significant open issue in cloud computing is the real performance of the infrastructure. Few, if any, cloud providers or technologies offer quantitative performance guarantees. Regardless of the potential advantages of the cloud in comparison to enterprise-deployed applications, cloud infrastructures may ultimately fail if deployed applications cannot predictably meet behavioral requirements. In this paper, we present the results of comprehensive performance experiments we conducted on Windows Azure from October 2009 to February 2010. In general, we have observed good performance of the Windows Azure mechanisms, although the average 10 min VM startup time must be accounted for in application design. We also present performance and reliability observations and analysis from our deployment of a large-scale scientific application hosted on Azure, called ModisAzure, that show unusual and sporadic VM execution slowdown of over 4× in some cases and affected up to 16% of task executions at times. In addition to a detailed performance evaluation of Windows Azure, we provide recommendations for potential users of Windows Azure based on these early observations. Although the discussion and analysis is tailored to scientific applications, the results are broadly applicable to the range of existing and future applications running in Windows Azure.
Lymphatic Expression of CLEVER-1 in Breast Cancer and Its Relationship with Lymph Node Metastasis
Authors: Ammar Aula , Mohammed Rabab A. A. , Salmi Marko , Pepper Michael , Paish Emma C. , Ellis Ian O. , Martin Stewart G.
Published: January 2015

Background: Mechanisms regulating breast cancer lymph node metastasis are unclear. Staining of CLEVER-1 (common lymphatic endothelial and vascular endothelial receptor-1) in human breast tumors was used, along within vitrotechniques, to assess involvement in the metastatic process.Methods: 148 sections of primary invasive breast cancers, with 10 yr follow-up, were stained with anti-CLEVER-1. Leukocyte infiltration was assessed, along with involvement of specific subpopulations by staining with CD83 (mature dendritic cells, mDC), CD209 (immature DC, iDC) and CD68 (macrophage, M&phis;).in vitroexpression of CLEVER-1 on lymphatic (LEC) and blood endothelial cells (BEC) was examined by flow cytometry.Results:in vitroresults showed that although both endothelial cell types express CLEVER-1, surface expression was only evident on LEC. In tumour sections CLEVER-1 was expressed in blood vessels (BV, 61.4% of samples), lymphatic vessels (LV, 18.2% of samples) and in M&phis;/DCs (82.4% of samples). However, only CLEVER-1 expression in LV was associated with LN metastasis (p =0.027) and with M&phis; indices (p =0.021). Although LV CLEVER-1 was associated with LN positivity there was no significant correlation with recurrence or overall survival, BV CLEVER-1 expression was, however, associated with increased risk of recurrence (p =0.049). The density of inflammatory infiltrate correlated with CLEVER-1 expression in BV (p < 0.001) and LV (p =0.004).Conclusions: The associations between CLEVER-1 expression on endothelial vessels and macrophage/leukocyte infiltration is suggestive of its regulation by inflammatory conditions in breast cancer, most likely by macrophage-associated cytokines. Its upregulation on LV, related surface expression, and association with LN metastasis suggest that it may be an important mediator of tumor cell metastasis to LN.
Event Sharing in Vehicular Networks using Geographic Vectors and Maps
Authors: Delot Thierry , Ilarri Sergio , Cenerario Nicolas , Hien Thomas
Published: January 2015

By exchanging events in a vehicular ad hoc network (VANET), drivers can receive information that allows them to find relevant places (e.g., parking spaces) or avoid dangerous/undesirable situations (e.g., an accident or a traffic jam). However, developing this kind of information services for drivers calls for new data management approaches, such as an appropriate dissemination protocol and some mechanism to decide when a driver should be alerted.
Scalability of Parallel Scientific Applications on the Cloud
Authors: Srirama Satish Narayana , Batrashev Oleg , Jakovits Pelle , Vainikko Eero
Published: January 2015

Cloud computing, with its promise of virtually infinite resources, seems to suit well in solving resource greedy scientific computing problems. To study the effects of moving parallel scientific applications onto the cloud, we deployed several benchmark applications like matrix–vector operations and NAS parallel benchmarks, and DOUG (Domain decomposition On Unstructured Grids) on the cloud. DOUG is an open source software package for parallel iterative solution of very large sparse systems of linear equations. The detailed analysis of DOUG on the cloud showed that parallel applications benefit a lot and scale reasonable on the cloud. We could also observe the limitations of the cloud and its comparison with cluster in terms of performance. However, for efficiently running the scientific applications on the cloud infrastructure, the applications must be reduced to frameworks that can successfully exploit the cloud resources, like the MapReduce framework. Several iterative and embarrassingly parallel algorithms are reduced to the MapReduce model and their performance is measured and analyzed. The analysis showed that Hadoop MapReduce has significant problems with iterative methods, while it suits well for embarrassingly parallel algorithms. Scientific computing often uses iterative methods to solve large problems. Thus, for scientific computing on the cloud, this paper raises the necessity for better frameworks or optimizations for MapReduce.
Proteomic Analysis of MCF-7 Breast Cancer Cell Line Exposed To Leptin
Authors: Valle A. , Sastre-Serra J. , Pol C. , Miró A. M. , Oliver J. , Roca P.
Published: January 2015

Background: Obesity is a well-known factor risk for breast cancer in postmenopausal women. Circulating leptin levels are increased in obese and it has been suggested to play an important role in mammary tumor formation and progression. To contribute to the understanding of the molecular mechanisms underlying leptin action in breast cancer, our aim was to identify proteins regulated by leptin in MCF-7 human breast cancer cells.Methods: We used two-dimensional gel electrophoresis (2-DE) and matrix assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) to identify proteins affected by leptin.Results: Thirty proteins were found differentially expressed in MCF-7 cells after 48 h leptin exposure. Proteins regulated by leptin included proteins previously implicated in breast cancer such as catechol-o-methyltransferase, cathepsin D, hsp27, serine/threonine-protein phosphatase and regulatory proteins of the Ras signaling pathway. Proteins involved in other cellular functions such as stress response, cytosqueleton remodeling and proteins belonging to ubiquitin-proteasome system, were also identified. Furthermore, leptin-treated cells showed a substantial uptake of the serum carrier proteins albumin and alpha-2-HS-glycoprotein.Conclusions: This screening reveals that leptin influences the levels of key proteins involved in breast cancer which opens new avenues for the study of the molecular mechanisms linking obesity to breast cancer.
Performance Models for the Spike Banded Linear System Solver
Authors: Manguoglu Murat , Saied Faisal , Sameh Ahmed , Grama Ananth
Published: January 2015

With availability of large-scale parallel platforms comprised of tens-of-thousands of processors and beyond, there is significant impetus for the development of scalable parallel sparse linear system solvers and preconditioners. An integral part of this design process is the development of performance models capable of predicting performance and providing accurate cost models for the solvers and preconditioners. There has been some work in the past on characterizing performance of the iterative solvers themselves. In this paper, we investigate the problem of characterizing performance and scalability of banded preconditioners. Recent work has demonstrated the superior convergence properties and robustness of banded preconditioners, compared to state-of-the-art ILU family of preconditioners as well as algebraic multigrid preconditioners. Furthermore, when used in conjunction with efficient banded solvers, banded preconditioners are capable of significantly faster time-to-solution. Our banded solver, the Truncated Spike algorithm is specifically designed for parallel performance and tolerance to deep memory hierarchies. Its regular structure is also highly amenable to accurate performance characterization. Using these characteristics, we derive the following results in this paper: (i) we develop parallel formulations of the Truncated Spike solver, (ii) we develop a highly accurate pseudo-analytical parallel performance model for our solver, (iii) we show excellent predication capabilities of our model – based on which we argue the high scalability of our solver. Our pseudo-analytical performance model is based on analytical performance characterization of each phase of our solver. These analytical models are then parameterized using actual runtime information on target platforms. An important consequence of our performance models is that they reveal underlying performance bottlenecks in both serial and parallel formulations. All of our results are validated on diverse heterogeneous multiclusters – platforms for which performance prediction is particularly challenging. Finally, we provide predict the scalability of the Spike algorithm using up to 65,536 cores with our model. In this paper we extend the results presented in the Ninth International Symposium on Parallel and Distributed Computing.
CaKernel – A Parallel Application Programming Framework for Heterogenous Computing Architectures
Authors: Blazewicz Marek , Brandt Steven R. , Kierzynka Michal , Kurowski Krzysztof , Ludwiczak Bogdan , Tao Jian , Weglarz Jan
Published: January 2015

With the recent advent of new heterogeneous computing architectures there is still a lack of parallel problem solving environments that can help scientists to use easily and efficiently hybrid supercomputers. Many scientific simulations that use structured grids to solve partial differential equations in fact rely on stencil computations. Stencil computations have become crucial in solving many challenging problems in various domains, e.g., engineering or physics. Although many parallel stencil computing approaches have been proposed, in most cases they solve only particular problems. As a result, scientists are struggling when it comes to the subject of implementing a new stencil-based simulation, especially on high performance hybrid supercomputers. In response to the presented need we extend our previous work on a parallel programming framework for CUDA – CaCUDA that now supports OpenCL. We present CaKernel – a tool that simplifies the development of parallel scientific applications on hybrid systems. CaKernel is built on the highly scalable and portable Cactus framework. In the CaKernel framework, Cactus manages the inter-process communication via MPI while CaKernel manages the code running on Graphics Processing Units (GPUs) and interactions between them. As a non-trivial test case we have developed a 3D CFD code to demonstrate the performance and scalability of the automatically generated code.
IEEE 802.15.4 Modifications and Their Impact
Authors: Goyal M. , Xie W. , Hosseini H.
Published: January 2015

IEEE 802.15.4 is a popular choice for MAC/PHY protocols in low power and low data rate wireless sensor networks. In this paper, we suggest several modifications to beaconless IEEE 802.15.4 MAC operation and evaluate their impact on the performance via stochastic modeling and simulations. We found that the utility of these modifications is strongly dependent on the traffic load on the network. Accordingly, we make recommendations regarding how these modifications should be used in view of the prevalent traffic load on the network.
Programming Heterogeneous Clusters with Accelerators Using Object-Based Programming
Authors: Kunzman David M. , Kalé Laxmikant V.
Published: January 2015

Heterogeneous clusters that include accelerators have become more common in the realm of high performance computing because of the high GFlop/s rates such clusters are capable of achieving. However, heterogeneous clusters are typically considered hard to program as they usually require programmers to interleave architecture-specific code within application code. We have extended the Charm++ programming model and runtime system to support heterogeneous clusters (with host cores that differ in their architecture) that include accelerators. We are currently focusing on clusters that include commodity processors, Cell processors, and Larrabee devices. When our extensions are used to develop code, the resulting code is portable between various homogeneous and heterogeneous clusters that may or may not include accelerators. Using a simple example molecular dynamics (MD) code, we demonstrate our programming model extensions and runtime system modifications on a heterogeneous cluster comprised of Xeon and Cell processors. Even though there is no architecture-specific code in the example MD program, it is able to successfully make use of three core types, each with a different ISA (Xeon, PPE, SPE), three SIMD instruction extensions (SSE, AltiVec/VMX and the SPE's SIMD instructions), and two memory models (cache hierarchies and scratchpad memories) in a single execution. Our programming model extensions abstract away hardware complexities while our runtime system modifications automatically adjust application data to account for architectural differences between the various cores.
Smart Object Reminders with RFID and Mobile Technologies
Authors: Hsu Hui-Huang , Lee Cheng-Ning , Hung Jason C. , Shih Timothy K.
Published: January 2015

In this paper, we present a reminder system that sends a reminder list to the user's mobile device based on the history data collected from the same user and the events in the user's calendar on that day. The system provides an individualized service. The list is to remind the user with objects he/she might have forgotten at home. The objects that the user brings along with are detected by passive RFID technology. Objects are classified into three different levels based on their frequencies in the history data. Rules of the three levels are then followed to decide if a certain object should be in the reminder list or not. A feedback mechanism is also designed to lower the possibility of unnecessary reminding.
Strategies for H-score Normalization of Preanalytical Technical Variables with Potential Utility to Immunohistochemical-Based Biomarker Quantitation in Therapeutic Reponse Diagnostics
Authors: Pierceall William E. , Wolfe Michele , Suschak Jessica , Chang Hua , Chen Yan , Sprott Kam M. , Kutok Jeffery L. , Quan Stella , Weaver David T. , Ward Brian E.
Published: January 2015

Digital quantitative immunohistochemical analysis of protein biomarker expression offers a broad dynamic range against which clinical outcomes may be measured. Semi-quantitative expression data represented as an H-score is produced by computer generated average intensity of positive staining given weight by the percentage of cells showing positive staining. While patient H-scores vary for biological reasons, variation may also arise from preanalytic technical issues, such as differences in fixation protocols. In this study, we present data on two candidate calibrator nuclear-localized proteins, SNRPA and SnRNP70, with robust and consistent expression levels across breast cancers. Quantitative expression measurement of these two candidate biomarkers may potentially be used to eliminate the effect of differences in preanalytic processing of specimens by normalizing H-scores derived from test biomarkers of interest. To examine the effects of preanalytical fixation variation on biomarker quantitation and potential utility of candidate calibrators to address such issues, 6 surgically-resected human breast cancer patient specimens were divided into 6 portions and fixed under distinct conditions (fixation following resection in formalin for 2 hr, 8 hr or 48 hr, or held overnight at 4°C in buffered saline prior to formalin fixation for 2 hr, 8 hr, or 48 hr). We find H-score variation between fixation conditions within individual patient's tumors that were stained for XPF, ATM, BRCA1, pMK2 and PARP1. Most interestingly, detectable expression of SNRPA and SnRNP70 is covariant to test biomarkers under distinct fixation conditions and so these hold the potential for serving as calibration standards for general antigen preservation and reactivity.