bluuebunny/crossref_metadata_2025 huggingface dataset:
Chromosomal Aneuploidy Affects the Global Proteome Equilibrium of Colorectal Cancer Cells
Authors: Gemoll Timo , Habermann Jens K. , Becker Susanne , Szymczak Silke , Upender Madhvi B. , Bruch Hans-Peter , Hellman Ulf , Ried Thomas , Auer Gert , Jörnvall Hans , Roblick Uwe J.
Published: January 2015

Background: Chromosomal aneuploidy has been identified as a prognostic factor in the majority of sporadic carcinomas. However, it is not known how chromosomal aneuploidy affects chromosome-specific protein expression in particular, and the cellular proteome equilibrium in general.

Objective: The aim was to detect chromosomal aneuploidy-associated expression changes in cell clones carrying trisomies found in colorectal cancer.

Methods: We used microcell-mediated chromosomal transfer to generate three artificial trisomic cell clones of the karyotypically stable, diploid, yet mismatch-deficient, colorectal cancer cell line DLD1 - each of them harboring one extra copy of either chromosome 3, 7 or 13. Protein expression differences were assessed by two-dimensional gel electrophoresis and mass spectrometry, compared to whole-genome gene expression data, and evaluated by PANTHER classification system and Ingenuity Pathway Analysis (IPA).

Results: In total, 79 differentially expressed proteins were identified between the trisomic clones and the parental cell line. Up-regulation of PCNA and HMGB1 as well as down-regulation of IDH3A and PSMB3 were revealed as trisomy-associated alterations involved in regulating genome stability.

Conclusions: These results show that trisomies affect the expression of genes and proteins that are not necessarily located on the trisomic chromosome, but reflect a pathway-related alteration of the cellular equilibrium.
The Impact of the Condenser on Cytogenetic Image Quality in Digital Microscope System
Authors: Ren Liqiang , Li Zheng , Li Yuhua , Zheng Bin , Li Shibo , Chen Xiaodong , Liu Hong
Published: January 2015

Background: Optimizing operational parameters of the digital microscope system is an important technique to acquire high quality cytogenetic images and facilitate the process of karyotyping so that the efficiency and accuracy of diagnosis can be improved.

OBJECTIVE: This study investigated the impact of the condenser on cytogenetic image quality and system working performance using a prototype digital microscope image scanning system.

Methods: Both theoretical analysis and experimental validations through objectively evaluating a resolution test chart and subjectively observing large numbers of specimen were conducted.

Results: The results show that the optimal image quality and large depth of field (DOF) are simultaneously obtained when the numerical aperture of condenser is set as 60%–70% of the corresponding objective. Under this condition, more analyzable chromosomes and diagnostic information are obtained. As a result, the system shows higher working stability and less restriction for the implementation of algorithms such as autofocusing especially when the system is designed to achieve high throughput continuous image scanning.

Conclusions: Although the above quantitative results were obtained using a specific prototype system under the experimental conditions reported in this paper, the presented evaluation methodologies can provide valuable guidelines for optimizing operational parameters in cytogenetic imaging using the high throughput continuous scanning microscopes in clinical practice.
A Weight-Aware Recommendation Algorithm for Mobile Multimedia Systems
Authors: Rosa Pedro M. P. , Rodrigues Joel J. P. C. , Basso Filippo
Published: January 2015

In the last years, information flood is becoming a common reality, and the general user, hit by thousands of possible interesting information, has great difficulties identifying the best ones, that can guide him in his/her daily choices, like concerts, restaurants, sport gatherings, or culture events. The current growth of mobile smartphones and tablets with embedded GPS receiver, Internet access, camera, and accelerometer offer new opportunities to mobile ubiquitous multimedia applications that helps gathering the best information out of an always growing list of possibly good ones. This paper presents a mobile recommendation system for events, based on few weighted context-awareness data-fusion algorithms to combine several multimedia sources. A demonstrative deployment were utilized relevance like location data, user habits and user sharing statistics, and data-fusion algorithms like the classical CombSUM and CombMNZ, simple, and weighted. Still, the developed methodology is generic, and can be extended to other relevance, both direct (background noise volume) and indirect (local temperature extrapolated by GPS coordinates in a Web service) and other data-fusion techniques. To experiment, demonstrate, and evaluate the performance of different algorithms, the proposed system was created and deployed into a working mobile application providing real time awareness-based information of local events and news.
A P2P Query Algorithm for Opportunistic Networks Utilizing betweenness Centrality Forwarding
Authors: Niu Jianwei , Liu Mingzhu , Chao Han-Chieh
Published: January 2015

With the proliferation of high-end mobile devices that feature wireless interfaces, many promising applications are enabled in opportunistic networks. In contrary to traditional networks, opportunistic networks utilize the mobility of nodes to relay messages in a store-carry-forward paradigm. Thus, the relay process in opportunistic networks faces several practical challenges in terms of delay and delivery rate. In this paper, we propose a novel P2P Query algorithm, namely Betweenness Centrality Forwarding (PQBCF), for opportunistic networking. PQBCF adopts a forwarding metric called Betweenness Centrality (BC), which is borrowed from social network, to quantify the active degree of nodes in the networks. In PQBCF, nodes with a higher BC are preferable to serve as relays, leading to higher query success rate and lower query delay. A comparison with the state-of-the-art algorithms reveals that PQBCF can provide better performance on both the query success Ratio and query delay, and approaches the performance of Epidemic Routing (ER) with much less resource consumption.
Efficient Backprojection-Based Synthetic Aperture Radar Computation with Many-Core Processors
Authors: Park Jongsoo , Tang Ping Tak Peter , Smelyanskiy Mikhail , Kim Daehyun , Benson Thomas
Published: January 2015

Tackling computationally challenging problems with high efficiency often requires the combination of algorithmic innovation, advanced architecture, and thorough exploitation of parallelism. We demonstrate this synergy through synthetic aperture radar (SAR) via backprojection, an image reconstruction method that can require hundreds of TFLOPS. Computation cost is significantly reduced by our new algorithm of approximate strength reduction; data movement cost is economized by software locality optimizations facilitated by advanced architecture support; parallelism is fully harnessed in various patterns and granularities. We deliver over 35 billion backprojections per second throughput per compute node on an Intel® Xeon® processor E5-2670-based cluster, equipped with Intel® Xeon Phi™ coprocessors. This corresponds to processing a 3K×3K image within a second using a single node. Our study can be extended to other settings: backprojection is applicable elsewhere including medical imaging, approximate strength reduction is a general code transformation technique, and many-core processors are emerging as a solution to energy-efficient computing.
Evaluations of Auto-Focusing Methods under a Microscopic Imaging Modality for Metaphase Chromosome Image Analysis
Authors: Qiu Yuchen , Chen Xiaodong , Li Yuhua , Chen Wei R. , Zheng Bin , Li Shibo , Liu Hong
Published: January 2015

Background: Auto-focusing is an important operation in high throughput imaging scanning. Although many auto-focusing methods have been developed and tested for a variety of imaging modalities, few investigations have been performed on the selection of an optimal auto-focusing method that is suitable for the pathological metaphase chromosome analysis under a high resolution scanning microscopic system.

Objective: The purpose of this study is to investigate and identify an optimal auto-focusing method for the pathological metaphase chromosome analysis.

Methods: In this study, five auto-focusing methods were applied and tested using metaphase chromosome images acquired from bone marrow and blood specimens. These methods were assessed by measuring a number of indices including execution time, accuracy, number of false maxima, and full width at half maximum (FWHM).

Results: For the specific condition investigated in this study, the results showed that the Brenner gradient and threshold pixel counting methods were the optimal methods for acquiring high quality metaphase chromosome images from the bone marrow and blood specimens, respectively.

Conclusions: Selecting an optimal auto-focusing method depends on the specific clinical tasks. This study also provides useful information for the design and implementation of the high throughput microscopic image scanning systems in the future digital pathology.
A Safe Exit Algorithm for Continuous Nearest Neighbor Monitoring in Road Networks
Authors: Cho Hyung-Ju , Kwon Se Jin , Chung Tae-Sun
Published: January 2015

Query processing in road networks has been studied extensively in recent years. However, the processing of moving queries in road networks has received little attention. In this paper, we introduce a new algorithm called the Safe Exit Algorithm (SEA), which can efficiently compute the safe exit points of a moving nearest neighbor (NN) query on road networks. The safe region of a query is an area where the query result remains unchanged, provided that the query remains inside the safe region At each safe exit point, the safe region of a query and its non-safe region meet so that a set of safe exit points represents the border of the safe region. Before reaching a safe exit point, the client (query object) does not have to request the server to re-evaluate the query This significantly reduces the server processing costs and the communication costs between the server and moving clients. Extensive experimental results show that SEA outperforms a conventional algorithm by up to two orders of magnitude in terms of communication costs and computation costs.
Containment Domains: A Scalable, Efficient and Flexible Resilience Scheme for Exascale Systems
Authors: Chung Jinsuk , Lee Ikhwan , Sullivan Michael , Ryoo Jee Ho , Kim Dong Wan , Yoon Doe Hyun , Kaplan Larry , Erez Mattan
Published: January 2015

This paper describes and evaluates a scalable and efficient resilience scheme based on the concept of containment domains. Containment domains are a programming construct that enable applications to express resilience needs and to interact with the system to tune and specialize error detection, state preservation and restoration, and recovery schemes. Containment domains have weak transactional semantics and are nested to take advantage of the machine and application hierarchies and to enable hierarchical state preservation, restoration and recovery. We evaluate the scalability and efficiency of containment domains using generalized trace-driven simulation and analytical analysis and show that containment domains are superior to both checkpoint restart and redundant execution approaches.
E-Books on the Mobile E-Reader
Authors: Kim Chulyun , Jeong Ok-Ran , Choi Jaehyuk , Kim Won
Published: January 2015

The market for e-books has been established during the past several years. Many e-book readers are commercially available, and millions of e-book titles are available for purchase or free download. E-paper technology has matured enough to be used as the screen for dedicated e-book readers which make reading possible with the familiar feel of reading printed books. In this paper, we provide a comprehensive review of the status of the e-book, including the architecture and features of e-book readers, market adoption and e-book industry ecosystem.
Mitigation of Redundant Handovers to Femtocells by Estimation of throughput Gain
Authors: Becvar Zdenek , Mach Pavel
Published: January 2015

A deployment of femtocells to mobile wireless networks can increase a throughput of indoor as well as outdoor users. On the other hand, it introduces several problems such as serious interference or high number of performed handovers. This paper is focused on mitigation of redundant handovers to femtocells with open or hybrid access. The redundant handovers decrease user's throughput due to a management overhead and due to introduced interruption. We design a novel handover decision algorithm based on an estimation of throughput gain reached by a handover to a femtocell. In the proposal, the handover is initiated only if the estimated gain in user's throughput exceeds a predefined threshold. As the results indicate, high ratio of eliminated redundant handovers is achieved by the designed procedure. Moreover, a drop in user's throughput due to the handover procedure is reduced by the proposed algorithm and thus the user's throughput is increased.
Toward Green Sensor Field by Optimizing Power Efficiency Using D-Policy M/G/1 Queuing Systems
Authors: Jiang Fuu-Cheng , Wu Hsiang-Wei , Leu Fang-Yi , Yang Chao-Tung
Published: January 2015

Power efficiency is a crucially important issue in the IEEE 802.15.4/ZigBee sensor networks (ZSNs) for majority of sensor nodes equipped with non-rechargeable batteries. To increase the lifetime of sensor networks, each node must optimize power consumption as possible. Among open literatures, much research works have focused on how to optimally increase the probability of sleeping states using multifarious wake-up strategies. Making things different, in this article, we propose a novel optimization framework for alleviating power consumption of sensor node with the D-policy M/G/1 queuing approach. Toward green sensor field, the proposed power-saving technique can be applied to prolong the lifetime of ZSN economically and effectively. For the proposed data aggregation model, mathematical framework on performance measures has been formulated. Data simulation using MATLAB tool has been conducted for exploring the feasibility of the proposed approach. And also we analyze the average traffic load per node for tree-based ZSN. Focusing on ZigBee routers deployed at the innermost shell of ZSN, network simulation results validate that the proposed approach indeed provides a feasibly cost-effective approach for prolonging lifetime of ZSNs.
Rare e14a3 (b3a3) BCR-ABL Fusion in Chronic Myeloid Leukemia in India: The Threats and Challenges in Monitoring Minimal Residual Disease (MRD)
Authors: Vaniawala Salil , Acharya Arpan , Parekh Harsh , Mukhopadhyaya Pratap N.
Published: January 2015

Objective: The primary objective of this work was to confirm the occurrence of rareBCR ABLfusion variant involving the a3 region of theABLgene in a patient positive for t(9;22) translocation but negative for common major and minor breakpoint cluster regions and the challenges and threats that it poses in a routine laboratory setting which use commercial kits for monitoring the minimal residual disease.

Methods: A patient with elevated white blood cell count was subjected to classical cytogenetics, FISH as well as RT-PCR testing using commercial kits as well as published primers and in house testing protocol. PCR amplicon generated from in the process was sequenced and analyzed.

Results: The translocation event in chromosome 9 and 22 could be successfully detected. BCR/ABL dual color, dual fusion probe generated a classical balanced translocation scenario within the nucleus of affected cells and presented a ‘1O1G2F’ signal pattern. RT-PCR with probes from commercial kit designed to detect common breakpoints within the M- and m-BCR regions involving e13a2, e14a2 and e1a2 fusion variants respectively failed to generate any signal. Further investigation revealed presence of the rare e14a3 (b3a3) fusion.

Discussion: This is the first report of rare e14a3 fusion in the BCR ABL gene in a CML patient from India. The observation indicates the need for interrogating rare BCR ABL fusions when common breakpoint cluster regions are absent such that minimal residual disease (MRD), critical for disease monitoring, can be performed and false positive remission cases can be avoided. It also emphasizes the utility and significance of cytogenetics and FISH techniques in primary diagnosis of CML and use of RT-PCR based assays only for generating secondary information within special reference to MRD.

Conclusions: The rare e14a3 (b3a3) fusion of theBCR ABLgene is present in Indian population as demonstrated from this first report and clinical laboratories using commercial kit that do not cover such rare fusions are likely to generate false result thereby declaring complete molecular remission in CML patients under therapy while conducting MRD assay using RT-PCR technology.
Direction-Optimizing Breadth-First Search
Authors: Beamer Scott , Asanović Krste , Patterson David
Published: January 2015

Breadth-First Search is an important kernel used by many graph-processing applications. In many of these emerging applications of BFS, such as analyzing social networks, the input graphs are low-diameter and scale-free. We propose a hybrid approach that is advantageous for low-diameter graphs, which combines a conventional top-down algorithm along with a novel bottom-up algorithm. The bottom-up algorithm can dramatically reduce the number of edges examined, which in turn accelerates the search as a whole. On a multi-socket server, our hybrid approach demonstrates speedups of 3.3–7.8 on a range of standard synthetic graphs and speedups of 2.4–4.6 on graphs from real social networks when compared to a strong baseline. We also typically double the performance of prior leading shared memory (multicore and GPU) implementations.
Modelling Medium Access Control in IEEE 802.15.4 Nonbeacon-Enabled Networks with Probabilistic Timed Automata
Authors: Kapus Tatjana
Published: January 2015

This paper concerns the formal modelling of medium access control in nonbeacon-enabled IEEE 802.15.4 wireless personal area networks with probabilistic timed automata supported by the PRISM probabilistic model checker. In these networks, the devices contend for the medium by executing an unslotted carrier sense multiple access with collision avoidance algorithm. In the literature, a model of a network which consists of two stations sending data to two different destination stations is introduced. We have improved this model and, based on it, we propose two ways of modelling a network with an arbitrary number of sending stations, each having its own destination. We show that the same models are valid representations of a star-shaped network with an arbitrary number of stations which send data to the same destination station. We also propose how to model such a network if some of the sending stations are not within radio range of the others, i.e. if they are hidden. We present some results obtained for these models by probabilistic model checking using PRISM.
Characterizing and Mitigating Work Time Inflation in Task Parallel Programs
Authors: Olivier Stephen L. , de Supinski Bronis R. , Schulz Martin , Prins Jan F.
Published: January 2015

Task parallelism raises the level of abstraction in shared memory parallel programming to simplify the development of complex applications. However, task parallel applications can exhibit poor performance due to thread idleness, scheduling overheads, andwork time inflation– additional time spent by threads in a multithreaded computation beyond the time required to perform the same work in a sequential computation. We identify the contributions of each factor to lost efficiency in various task parallel OpenMP applications and diagnose the causes of work time inflation in those applications. Increased data access latency can cause significant work time inflation in NUMA systems. Our locality framework for task parallel OpenMP programs mitigates this cause of work time inflation. Our extensions to the Qthreads library demonstrate that locality-aware scheduling can improve performance up to 3X compared to the Intel OpenMP task scheduler.
The Evolution of Anatomic Pathology
Authors: Cohen Stanley , Coffman Frederick
Published: January 2015

Science advances both by conceptual leaps and by improved observational and analytic tools. Mechanism and function in biological systems can best be understood in the context of the complex microenvironments in which they occur, and for this purpose morphologic analysis can be critical. Technological advances in cell and tissue imaging are currently finding application in a wide variety of basic, translational, and clinical biomedical studies. “Biophotonics in Pathology” was designed as a multi-authored work to describe the various kinds of imaging strategies that have been developed as computational power keeps increasing. Some of these overlap with radiologic techniques and others do not. The field is continuously evolving, and in this commentary I will touch on additional techniques for morphology-based interrogation of cells and tissues that have recently been described. However, it is important to note that though we are expanding our armamentarium as pathologists, our radiological colleagues have been doing this for many years. Clearly, they have embraced new imaging techniques to a greater extent than have pathologists. This commentary discusses some of the factors responsible for this, and suggests that pathology and radiology are converging towards a more holistic approach to diagnostic imaging.
Seamless MANET Autoconfiguration through Enhanced 802.11 Beaconing
Authors: Villanueva M. José , Calafate Carlos T. , Torres Álvaro , Cano José , Cano Juan-Carlos , Manzoni Pietro
Published: January 2015

The deployment of mobile ad-hoc networks involves several configuration steps, which complicate research efforts and hinder user interest. This problem prompts for new approaches offering full autoconfiguration of terminals at the different network layers involved. In this paper we propose a novel solution for the autoconfiguration of IEEE 802.11 based MANETs that relies on SSID parameter embedding. Our solution allows users to join an existing MANET without resorting to any additional technology, and even in the presence of encrypted communications. Experimental testbed results using a real implementation of the proposed solution show that it introduces significant improvements compared to other existing solutions, allowing nearby stations to be configured in about two seconds, and also enabling multi-hop dissemination of configuration data to take place quickly and efficiently.
Trypanosoma cruziNecrotizing Meningoencephalitis in a Venezuelan HIV+-AIDS Patient: Pathological Diagnosis Confirmed by PCR Using Formalin-Fixed- and Paraffin-Embedded-Tissues
Authors: Rossi Spadafora Marcello Salvatore , Céspedes Ghislaine , Romero Sandra , Fuentes Isabel , Boada-Sucre Alpidio A. , Cañavate Carmen , Flores-Chávez María
Published: January 2015

Coinfections with human immunodeficiency virus (HIV) and infectious agents have been recognized since the early 90s. In the central nervous system (CNS) of HIV+patients, parasitic protozoans likeToxoplasma gondiihave been described as responsible for the space occupying lesions (SOL) developed. However, the involvement ofTrypanosoma cruziis also described but appears to be less frequent in acquired immunodeficiency syndrome (AIDS) and transplant recipients, associated with necrotizing myocarditis and neurological symptoms related to the occurrence of necrotizing pseudotumoral encephalitis (NPE) and meningoencephalitis (NME). The present work aims to present a Venezuelan case of NME associated with the coinfection of HIV and aT. cruzi-like trypanosomatid as well as its evolution and diagnosis by histopathological techniques, electron microscopy, and PCR methods using formalin-fixed- (FF-) and paraffin-embedded- (PE-) tissues. Postmortem cytological studies of leptomeninges imprints reveal the presence of trypomastigotes ofTrypanosomasp. Histopathological and electron microscopy studies allowed us to identify an amastigote stage and to reject the involvement of other opportunistic microorganisms as the etiological agent of the SOL. The definitive confirmation ofT. cruzias the etiological agent was achieved by PCR suggesting that the NME byT. cruziwas due to a reactivation of Chagas’ disease.
Cost-Effective and Fast Handoff Scheme in Proxy Mobile IPv6 Networks with Multicasting Support
Authors: Im Illkyun , Jeong Jongpil
Published: January 2015

With recent advancements in wireless communication technologies, mobile multicasting is becoming important, in an effort to use network resources more efficiently. In the past, when various mobile IP-based multicast techniques were proposed, the focus was on the costs needed for network delivery to provide multicast services, as well as on minimizing the multicast handover delay. However, it is fundamentally difficult to resolve the problems of handover delay and tunnel convergence for techniques using MIPv6 (Mobile IPv6), a host-based mobility management protocol. To resolve these problems, the network-based mobility management protocol PMIPv6 (Proxy Mobile IPv6) was standardized. Although performance is improved in PMIPv6 over MIPv6, it still suffers from problems of handover delay and tunnel convergence. To overcome these limitations, a technique called LFH (Low-cost and Fast Handoff) is proposed in this paper, for fast and low-cost mobility management with multicasting support in PMIPv6 networks. To reduce the interactions between the complex multicast routing protocol and multicast messages, a simplified proxy method called MLD (Multicast Listener Discovery) is implemented and modified. Furthermore, a TCR (Tunnel Combination and Reconstruction) algorithm was used in the multicast handover procedure within the LMA (Local Mobility Anchor) domain, as well as in the multicast handover procedure between domains, in order to overcome the problem of tunnel convergence. It was found that, compared to other types of multicast techniques, LFH reduces multicast delay, and requires lower cost.
Adoption of Mobile Information Services: An Empirical Study
Authors: Gao Shang , Krogstie John , Siau Keng
Published: January 2015

This study investigates the adoption of mobile information services at a Norwegian university. By expanding the Technology Acceptance Model (TAM), a new research model, known as the mobile services acceptance model (MSAM), is proposed. Based on the research model, seven research hypotheses are presented. The proposed research model and research hypotheses were empirically tested using data collected from a survey of users of a mobile service, extended Mobile Student Information Systems (eMSIS), at a Norwegian university. The findings indicate that the fitness of the research model is good. Support was also found for the seven research hypotheses. Among the factors, the personal initiatives and characteristics has the strongest influence on the intention to use eMSIS.
k-Nearest Neighbor Search based on Node Density in MANETs
Authors: Komai Yuka , Sasaki Yuya , Hara Takahiro , Nishio Shojiro
Published: January 2015

In a kNN query processing method, it is important to appropriately estimate the range that includes kNNs. While the range could be estimated based on the node density in the entire network, it is not always appropriate because the density of nodes in the network is not uniform. In this paper, we propose two kNN query processing methods in MANETs where the density of nodes is ununiform; the One-Hop (OH) method and the Query Log (QL) method. In the OH method, the nearest node from the point specified by the query acquires its neighbors' location and then determines the size of a circle region (the estimated kNN circle) which includes kNNs with high probability. In the QL method, a node which relays a reply of a kNN query stores the information on the query result for future queries.
Prognostic Efficacy of Nuclear Morphometry at Invasive Front of Oral Squamous Cell Carcinoma: An Image Analysis Microscopic Study
Authors: Vedam V. K. Vaishnavi , Boaz Karen , Natarajan Srikant
Published: January 2015

Background. Oral cancer is revisited on a pathologist perspective with advanced imaging technique.Objective. The present study assessed the new malignancy grading system at tumor proper (TP) and Bryne’s grading system at invasive tumor front (ITF), morphometric features using software, to clarify their associations with prognosis of oral cancers.Methods. Histologically confirmed oral squamous cell carcinoma (OSCC) with 5-year follow-up was assessed morphometrically using image analysis at TP and ITF, correlated with the prognosis of patient.Results. On comparison of grading systems, a moderate agreement between both (Bryne and Anneroth) was seen. Among all histological parameters, we noted inverse correlation between degree of mitosis at invasive front and decrease in lymphoplasmacytic infiltrate at ITF with increase rate of recurrence and event of death. An increase in nuclear area, diameter, and perimeter along with decrease circularity in advancing OSCC was seen. Correlation of parameters showed higher values for maximum nuclear diameter, perimeter, and circularity at TP and ITF with recurrence.Conclusion. This study, while limited in sample size, concluded that a combined assessment of clinical TNM staging, histopathological grading system{excluding the parameter “mitotic activity” (due to its inverse relation)}, and nuclear morphometry at the ITF are better prognosticators. This combination proved to be an accurate predictive factor in eliciting the varied molecular characteristics of tumor heterogeneity.
Exploring the Future of Out-of-Core Computing with Compute-Local Non-Volatile Memory
Authors: Jung Myoungsoo , Wilson Ellis H. , Choi Wonil , Shalf John , Aktulga Hasan Metin , Yang Chao , Saule Erik , Catalyurek Umit V. , Kandemir Mahmut
Published: January 2015

Drawing parallels to the rise of general purpose graphical processing units (GPGPUs) as accelerators for specific high-performance computing (HPC) workloads, there is a rise in the use of non-volatile memory (NVM) as accelerators for I/O-intensive scientific applications. However, existing works have explored use of NVM within dedicated I/O nodes, which are distant from the compute nodes that actually need such acceleration. As NVM bandwidth begins to out-pace point-to-point network capacity, we argue for the need to break from the archetype of completely separated storage. Therefore, in this work we investigate co-location of NVM and compute by varying I/O interfaces, file systems, types of NVM, and both current and future SSD architectures, uncovering numerous bottlenecks implicit in these various levels in the I/O stack. We present novel hardware and software solutions, including the new Unified File System (UFS), to enable fuller utilization of the new compute-local NVM storage. Our experimental evaluation, which employs a real-world Out-of-Core (OoC) HPC application, demonstrates throughput increases in excess of an order of magnitude over current approaches.
Expression of EGFR and Molecules Downstream to PI3K/Akt, Raf-1-MEK-1-MAP (Erk1/2), and JAK (STAT3) Pathways in Invasive Lung Adenocarcinomas Resected at a Single Institution
Authors: Torres Alba Fabiola , Nogueira Cleto , Magalhaes Juliana , Costa Igor Santos , Aragao Alessa , Neto Antero Gomes , Martins Filadelfia , Tavora Fabio
Published: January 2015

Therapies targeting EGFR are effective in treating tumors that harbor molecular alterations; however, there is heterogeneity in long-term response to these therapies. We retrospectively analyzed protein expression of EGFR, Stat3, phospho-Akt, and phospho-Erk1/2 by immunohistochemistry in a series of resected cases from a single institution, correlated with clinicopathological variables. There were 96 patients, with the majority of cases being of low stage tumors (17 pT1a, 23 pT1b, 30 pT2a, and 18 pT2b). Histologic subtypes were 45 acinar predominant, 2 cribriform, 25 solid, 7 papillary, 11 lepidic, and 4 mucinous tumors. The EGFR score was higher in tumors with vascular invasion (P=0.013), in solid and cribriform acinar histology, and in high stage tumors (P=0.006andP=0.01). EGFR was more likely overexpressed in solid compared to lepidic tumors (P=0.02). Acinar tumors had the highest rate of ERK1/2 positivity (19%). There was a strong correlation among positivity for ERCC1 and other markers, including STAT3 (P=0.003), Akt (P=0.02), and ERK1/ERK2 (P=0.0005). Expression of molecules downstream to EGFR varied from 12% to 31% of tumors; however, the expression did not directly correlate to EGFR expression, which may suggest activation of the cascades through different pathways. The correlation of protein expression and the new lung adenocarcinoma classification may help in the understanding of activated pathways of each tumor type, which may act in the oncogenesis and drug resistance of these tumors.
TACO: A Scheduling Scheme for Parallel Applications on Multicore Architectures
Authors: Schönherr Jan H. , Juurlink Ben , Richling Jan
Published: January 2015

While multicore architectures are used in the whole product range from server systems to handheld computers, the deployed software still undergoes the slow transition from sequential to parallel. This transition, however, is gaining more and more momentum due to the increased availability of more sophisticated parallel programming environments. Combined with the ever increasing complexity of multicore architectures, this results in a scheduling problem that is different from what it has been, because concurrently executing parallel programs and features such as non-uniform memory access, shared caches, or simultaneous multithreading have to be considered. In this paper, we compare different ways of scheduling multiple parallel applications on multicore architectures. Due to emerging parallel programming environments, we primarily consider applications where the parallelism degree can be changed on the fly. We propose TACO, a topology-aware scheduling scheme that combines equipartitioning and coscheduling, which does not suffer from the drawbacks of the individual concepts. Additionally, TACO is conceptually compatible with contention-aware scheduling strategies. We find that topology-awareness increases performance for all evaluated workloads. The combination with coscheduling is more sensitive towards the executed workloads and NUMA effects. However, the gained versatility allows new use cases to be explored, which were not possible before.
Salivary RNA Signatures in Oral Cancer Detection
Authors: Panta Prashanth , Venna Venkat Raghavender
Published: January 2015

Oral squamous cell carcinomas (OSCC) are common malignancies that affect almost a million people every year. The key issue in reducing mortality and morbidity associated with OSCC is to develop novel strategies to identify OSCC at an early stage. One such strategy is the identification of biomarkers. So far, more than 100 biomarkers are recognized in the detection of oral cancer and they range from proteins to nucleic acids (DNAs, RNAs). Detection of ribose nucleic acids in saliva is a recent trend in diagnosing oral cancer. Studies have shown statistically significant changes in the levels of salivary transcriptomes in patients with oral squamous cell carcinomas. These biomarkers have displayed high sensitivity and specificity. Also, new point-of-care platforms such as oral fluid nanosensor test are now available that will soon emerge as chair-side tools for early detection of oral cancer. The aim of this review is to highlight the importance of salivary transcriptomes in oral cancer detection.
Numerical and Experimental Study on Confinement in Y-Shaped Post Wall Branching Waveguide
Authors: Maeda Hiroshi , Chen Huili , Tomiura Kazuya , Yasumoto Kiyotoshi
Published: January 2015

Post wall waveguides consist of dielectric or metallic cylinders for microwave around 4 GHz were experimentally and numerically investigated. The structure attracts interests for application of transmission circuit for three-dimensionally integrated planar circuit in millimeter wavelength. In straight waveguide with dielectric cylinders, confinement of microwave is poor, when the post wall was composed of a pair of single row of cylinders. The confinement was improved as increase of rows of post wall. In metallic cylinders, microwave was well confined even when a pair of single row of cylinders composed the waveguide. After confirming confinement of the electromagnetic field, Y-shaped branches of post wall waveguide consisted of dielectric cylinders for microwave were similarly investigated for dielectric rods. The confinement was also improved by increase of post wall up to 3 layers. These results are applicable for fundamental design and fabrication of integrated circuit for microwave and millimeter wave.
Lightweight MIPv6 with IPSec Support
Authors: Jara Antonio J. , Fernandez David , Lopez Pablo , Zamora Miguel A. , Skarmeta Antonio F.
Published: January 2015

Mobility management is a desired feature for the emerging Internet of Things (IoT). Mobility aware solutions increase the connectivity and enhance adaptability to changes of the location and infrastructure. IoT is enabling a new generation of dynamic ecosystems in environments such as smart cities and hospitals. Dynamic ecosystems require ubiquitous access to Internet, seamless handover, flexible roaming policies, and an interoperable mobility protocol with existing Internet infrastructure. These features are challenges for IoT devices, which are usually constrained devices with low memory, processing, communication and energy capabilities. This work presents an analysis of the requirements and desirable features for the mobility support in the IoT, and proposes an efficient solution for constrained environments based on Mobile IPv6 and IPSec. Compatibility with IPv6-existing protocols has been considered a major requirement in order to offer scalable and inter-domain solutions that were not limited to specific application domains in order to enable a new generation of application and services over Internet-enabled dynamic ecosystems, and security support based on IPSec has been also considered, since dynamic ecosystems present several challenges in terms of security and privacy. This work has, on the one hand, analysed suitability of Mobile IPv6 and IPSec for constrained devices, and on the other hand, analysed, designed, developed and evaluated a lightweight version of Mobile IPv6 and IPSec. The proposed solution of lightweight Mobile IPv6 with IPSec is aware of the requirements of the IoT and presents the best solution for dynamic ecosystems in terms of efficiency and security adapted to IoT-devices capabilities. This presents concerns in terms of higher overhead and memory requirements. But, it is proofed and concluded that even when higher memory is required and major overhead is presented, the integration of Mobile IPv6 and IPSec for constrained devices is feasible.
Aristotle: A performance Impact Indicator for the OpenCL Kernels Using Local Memory
Authors: Fang Jianbin , Sips Henk , Varbanescu Ana Lucia
Published: January 2015

Due to the increasing complexity of multi/many-core architectures (with their mix of caches and scratch-pad memories) and applications (with different memory access patterns), the performance of many workloads becomes increasingly variable. In this work, we address one of the main causes for this performance variability: the efficiency of the memory system. Specifically, based on an empirical evaluation driven by memory access patterns, we qualify and partially quantify the performance impact of using local memory in multi/many-core processors. To do so, we systematically describe memory access patterns (MAPs) in an application-agnostic manner. Next, for each identified MAP, we use OpenCL (for portability reasons) to generate two microbenchmarks: a “naive” version (without local memory) and “an optimized” version (using local memory). We then evaluate both of them on typically used multi-core and many-core platforms, and we log their performance. What we eventually obtain is a local memory performance database, indexed by various MAPs and platforms. Further, we propose a set of composing rules for multiple MAPs. Thus, we can get an indicator of whether using local memory is beneficial in the presence of multiple memory access patterns. This indication can be used to either avoid the hassle of implementing optimizations with too little gain or, alternatively, give a rough prediction of the performance gain.
Tools and Methods for Measuring and Tuning the Energy Efficiency of HPC Systems
Authors: Schöne Robert , Treibig Jan , Dolz Manuel F. , Guillen Carla , Navarrete Carmen , Knobloch Michael , Rountree Barry
Published: January 2015

Energy costs nowadays represent a significant share of the total costs of ownership of High Performance Computing (HPC) systems. In this paper we provide an overview on different aspects of energy efficiency measurement and optimization. This includes metrics that define energy efficiency and a description of common power and energy measurement tools. We discuss performance measurement and analysis suites that use these tools and provide users the possibility to analyze energy efficiency weaknesses in their code. We also demonstrate how the obtained power and performance data can be used to locate inefficient resource usage or to create a model to predict optimal operation points. We further present interfaces in these suites that allow an automated tuning for energy efficiency and how these interfaces are used. We finally discuss how a hard power limit will change our view on energy efficient HPC in the future.
Collective Mind: Towards Practical and Collaborative Auto-Tuning
Authors: Fursin Grigori , Miceli Renato , Lokhmotov Anton , Gerndt Michael , Baboulin Marc , Malony Allen D. , Chamski Zbigniew , Novillo Diego , Del Vento Davide
Published: January 2015

Empirical auto-tuning and machine learning techniques have been showing high potential to improve execution time, power consumption, code size, reliability and other important metrics of various applications for more than two decades. However, they are still far from widespread production use due to lack of native support for auto-tuning in an ever changing and complex software and hardware stack, large and multi-dimensional optimization spaces, excessively long exploration times, and lack of unified mechanisms for preserving and sharing of optimization knowledge and research material. We present a possible collaborative approach to solve above problems using Collective Mind knowledge management system. In contrast with previous cTuning framework, this modular infrastructure allows to preserve and share through the Internet the whole auto-tuning setups with all related artifacts and their software and hardware dependencies besides just performance data. It also allows to gradually structure, systematize and describe all available research material including tools, benchmarks, data sets, search strategies and machine learning models. Researchers can take advantage of shared components and data with extensible meta-description to quickly and collaboratively validate and improve existing auto-tuning and benchmarking techniques or prototype new ones. The community can now gradually learn and improve complex behavior of all existing computer systems while exposing behavior anomalies or model mispredictions to an interdisciplinary community in a reproducible way for further analysis. We present several practical, collaborative and model-driven auto-tuning scenarios. We also decided to release all material atc-mind.org/repoto set up an example for a collaborative and reproducible research as well as our new publication model in computer engineering where experimental results are continuously shared and validated by the community.
2HOT: An Improved Parallel Hashed Oct-Tree N-Body Algorithm for Cosmological Simulation
Authors: Warren Michael S.
Published: January 2015

We report on improvements made over the past two decades to our adaptive treecode N-body method (HOT). A mathematical and computational approach to the cosmological N-body problem is described, with performance and scalability measured up to 256k (218) processors. We present error analysis and scientific application results from a series of more than ten 69 billion (40963) particle cosmological simulations, accounting for 4×1020floating point operations. These results include the first simulations using the new constraints on the standard model of cosmology from the Planck satellite. Our simulations set a new standard for accuracy and scientific throughput, while meeting or exceeding the computational efficiency of the latest generation of hybrid TreePM N-body methods.
Assessing the Effects of Data Compression in Simulations Using Physically Motivated Metrics
Authors: Laney Daniel , Langer Steven , Weber Christopher , Lindstrom Peter , Wegener Al
Published: January 2015

This paper examines whether lossy compression can be used effectively in physics simulations as a possible strategy to combat the expected data-movement bottleneck in future high performance computing architectures. We show that, for the codes and simulations we tested, compression levels of 3–5X can be applied without causing significant changes to important physical quantities. Rather than applying signal processing error metrics, we utilize physics-based metrics appropriate for each code to assess the impact of compression. We evaluate three different simulation codes: a Lagrangian shock-hydrodynamics code, an Eulerian higher-order hydrodynamics turbulence modeling code, and an Eulerian coupled laser-plasma interaction code. We compress relevant quantities after each time-step to approximate the effects of tightly coupled compression and study the compression rates to estimate memory and disk-bandwidth reduction. We find that the error characteristics of compression algorithms must be carefully considered in the context of the underlying physics being modeled.
Context-Aware Mobile Service Adaptation via a Co-Evolution eXtended Classifier System in Mobile Network Environments
Authors: Wang Shangguang , Zheng Zibin , Wu Zhengping , Sun Qibo , Zou Hua , Yang Fangchun
Published: January 2015

With the popularity of mobile services, an effective context-aware mobile service adaptation is becoming more and more important for operators. In this paper, we propose a Co-evolution eXtended Classifier System (CXCS) to perform context-aware mobile service adaptation. Our key idea is to learn user context, match adaptation rule, and provide the best suitable mobile services for users. Different from previous adaptation schemes, our proposed CXCS can produce a new user's initial classifier population to quicken its converging speed. Moreover, it can make the current user to predict which service should be selected, corresponding to an uncovered context. We compare CXCS based on a common mobile service adaptation scenario with other five adaptation schemes. The results show the adaptation accuracy of CXCS is higher than 70% on average, and outperforms other schemes.