bluuebunny/crossref_metadata_2025 huggingface dataset:
A Skeleton Based Programming Paradigm for Mobile Multi‐Agents on Distributed Systems and Its Realization within the MAGDA Mobile Agents Platform
Authors: Aversa R. , Di Martino B. , Mazzocca N. , Venticinque S.
Published: January 2015

Parallel programming effort can be reduced by using high level constructs such as algorithmic skeletons. Within the MAGDA toolset, supporting programming and execution of mobile agent based distributed applications, we provide a skeleton‐based parallel programming environment, based on specialization of Algorithmic Skeleton Java interfaces and classes. Their implementation include mobile agent features for execution on heterogeneous systems, such as clusters of WSs and PCs, and support reliability and dynamic workload balancing. The user can thus develop a parallel, mobile agent based application by simply specialising a given set of classes and methods and using a set of added functionalities.
Norms for Modeling Agents′ Interaction in Ubiquitous Environments
Authors: Ibrahim Ismail Khalil
Published: January 2015

In ubiquitous environments a vast amount of mobile human and software entities, each with limited resources and knowledge, needs to interact with each other to achieve common and/or individual goals within a specific context. Due to their autonomy, proactiveness, mobility, social capability, and the successful implementation of agent mediated applications and services over the Web, different scenarios have been proposed in literature for the use of agents in ubiquitous environments for a wide range of applications such as user interfaces, mobile computing, information retrieval and filtering, smart messaging, telecommunication and m‐commerce. In this paper, we address the problem of modeling agents′ interaction in ubiquitous environments. We argue agents′ interactions can be modeled using norms, which are represented mathematically as zero set of n‐variate functions. We utilize the barycentic coordinates to show how agents should behave based on established protocols, rules of conduct or accepted social practices.
Implementation of the Two-Point Angular Correlation Function on a High-Performance Reconfigurable Computer
Authors: Kindratenko Volodymyr V. , Myers Adam D. , Brunner Robert J.
Published: January 2015

We present a parallel implementation of an algorithm for calculating the two-point angular correlation function as applied in the field of computational cosmology. The algorithm has been specifically developed for a reconfigurable computer. Our implementation utilizes a microprocessor and two reconfigurable processors on a dual-MAP SRC-6 system. The two reconfigurable processors are used as two application-specific co-processors. Two independent computational kernels are simultaneously executed on the reconfigurable processors while data pre-fetching from disk and initial data pre-processing are executed on the microprocessor. The overall end-to-end algorithm execution speedup achieved by this implementation is over 90× as compared to a sequential implementation of the algorithm executed on a single 2.8 GHz Intel Xeon microprocessor.
Efficient SIMDization and Data Management of the Lattice QCD Computation on the Cell Broadband Engine
Authors: Ibrahim Khaled Z. , Bodin François
Published: January 2015

Lattice Quantum Chromodynamic (QCD) models subatomic interactions based on a four-dimensional discretized space–time continuum. The Lattice QCD computation is one of the grand challenges in physics especially when modeling a lattice with small spacing. In this work, we study the implementation of the main kernel routine of Lattice QCD that dominates the execution time on the Cell Broadband Engine. We tackle the problem of efficient SIMD execution and the problem of limited bandwidth for data transfers with the off-chip memory. For efficient SIMD execution, we present runtime data fusion technique that groups data processed similarly at runtime. We also introduce analysis needed to reduce the pressure on the scarce memory bandwidth that limits the performance of this computation. We studied two implementations for the main kernel routine that exhibit different patterns of accessing the memory and thus allowing different sets of optimizations. We show the attributes that make one implementation more favorable in terms of performance. For lattice size that is significantly larger than the local store, our implementation achieves 31.2 GFlops for single precision computations and 16.6 GFlops for double precision computations on the PowerXCell 8i, an order of magnitude better than the performance achieved on most general-purpose processors.
Estimation of Spectrum Requirements for Mobile Networks With Self-Similar Traffic, Handover, and Frequency Reuse
Authors: Yang Won Seok , Yang Eun Saem , Kim Hwa J. , Kim Dae K.
Published: January 2015

This paper considers self-similarity in data traffic, handover, and frequency reuse to estimate the spectrum requirements of mobile networks. An approximate average cell capacity subject to a delay requirement and self-similar traffic is presented. It is shown that handover traffic can be an additional load. Spectrum requirements are calculated based on carrier demand instead of spectral efficiency, as at least one carrier is necessary to transmit even 1 bit. The cell-split operation is considered under frequency reuse of one. Estimation methods are presented using cell traffic in two cases. First, a procedure is presented that estimates cell traffic from previous networks. Second, cell traffic is assumed to follow probability distributions. Numerical examples demonstrate the impact of self-similarity, handover, and the proportion of cell-split occurrences on the spectrum requirements.
EBV-Infection in Cardiac and Non-Cardiac Gastric Adenocarcinomas is Associated with Promoter Methylation ofp16,p14andAPC, but nothMLH1
Authors: Geddert Helene , Hausen Axel zur , Gabbert Helmut E. , Sarbia Mario
Published: January 2015

Background: Epstein–Barr virus (EBV)-associated gastric carcinomas (GC) constitute a distinct clinicopathological entity of gastric cancer. In order to determine underlying distinct aberrant promoter methylation we tested cardiac and non-cardiac GC with regard to the presence of EBV.

Methods: One hundred GC were tested by RNA-in situ hybridization for the presence of EBV by EBV-encoded small RNA (EBER). Aberrant promoter methylation was investigated by methylation-specific real-time PCR for p16, p14, APC and hMLH1. P16 protein expression was assessed by immunohistochemistry.

Results: In our selected study cohort, EBER-transcripts were detected in 19.6% (18/92) of GC. EBV-positive GC revealed significantly more often gene hypermethylation of p16, p14 and APC (p < 0.0001, p < 0.0001 and p = 0.02, respectively) than EBV-negative GC. The majority of GC with p16 hypermethylation showed a p16 protein loss (22/28). In contrast, no correlation between the presence of EBV and hMLH1 hypermethylation was found (p = 0.7). EBV-positive GC showed a trend towards non-cardiac location (p = 0.06) and lower stages (I/II) according to the WHO (p = 0.05).

Conclusion: Hypermethylation of tumor suppressor genes is significantly more frequent in EBV-associated GC compared to EBV-negative GC. Our data add new insights to the role of EBV in gastric carcinogenesis and underline that EBV-associated GC comprise a distinct molecular-pathologic as well as a distinct clinicopathological entity of GC.
Gene Copy Number Variation in Male Breast Cancer by aCGH
Authors: Tommasi Stefania , Mangia Anita , Iannelli Giuseppina , Chiarappa Patrizia , Rossi Elena , Ottini Laura , Mottolese Marcella , Zoli Wainer , Zuffardi Orsetta , Paradiso Angelo
Published: January 2015

Background: Male breast cancer (MBC) is a rare disease and little is known about its etiopathogenesis. Array comparative genomic hybridization (aCGH) provides a method to quantitatively measure the changes of DNA copy number and to map them directly onto the complete linear genome sequences. The aim of this study was to investigate DNA imbalances by aCGH and compare them with a female breast cancer dataset.

Methods: We used Agilent Human Genome CGH Microarray Kit 44B and 44K to compare genomic alterations in 25 male breast cancer tissues studied at NCC of Bari and 16 female breast cancer deposited with the Gene Expression Omnibus (GSE12659). Data analysis was performed with Nexus Copy Number 5.0 software.

Results: All the 25 male and 16 female breast cancer samples displayed some chromosomal instability (110.93 alterations per patient in female, 69 in male). However, male samples presented a lower frequency of genetic alterations both in terms of loss and gains.

Conclusion: aCGH is an effective tool for analysis of cytogenetic aberrations in MBC, which involves different biological processes than female. Male most significant altered regions contained genes involved in cell communication, cell division and immunological response, while female cell–cell junction maintenance, regulation of transcription and neuron development.
State-of-the-art in Heterogeneous Computing
Authors: Brodtkorb Andre R. , Dyken Christopher , Hagen Trond R. , Hjelmervik Jon M. , Storaasli Olaf O.
Published: January 2015

Node level heterogeneous architectures have become attractive during the last decade for several reasons: compared to traditional symmetric CPUs, they offer high peak performance and are energy and/or cost efficient. With the increase of fine-grained parallelism in high-performance computing, as well as the introduction of parallelism in workstations, there is an acute need for a good overview and understanding of these architectures. We give an overview of the state-of-the-art in heterogeneous computing, focusing on three commonly found architectures: the Cell Broadband Engine Architecture, graphics processing units (GPUs), and field programmable gate arrays (FPGAs). We present a review of hardware, available software tools, and an overview of state-of-the-art techniques and algorithms. Furthermore, we present a qualitative and quantitative comparison of the architectures, and give our view on the future of heterogeneous computing.
A Computational Framework for Flood Risk Assessment in The Netherlands
Authors: Markus A.A. , Courage W.M.G. , van Mierlo M.C.L.M.
Published: January 2015

The safety of dikes in The Netherlands, located in the delta of the rivers Rhine, Meuse and Scheldt, has been the subject of debate for more than ten years. The safety (or flood risk) of a particular area may depend on the safety of other areas. This is referred to as effects of river system behaviour on flood risk (quantified as the estimated number of casualties and economic damage). A computational framework was developed to assess these effects. It consists of several components that are loosely coupled via data files and Tcl scripts to manage the individual programs and keep track of the state of the computations. The computations involved are lengthy (days or even weeks on a Linux cluster), which makes the framework currently more suitable for planning and design than for real-time operation. While the framework was constructedad hoc, it can also be viewed more formally as atuplespaceRealising this makes it possible to adopt the philosophy for other similar frameworks.
Localization of ORC1 During the Cell Cycle in Human Leukemia Cells
Authors: Coffman Frederick D. , Reyes Mai-Ling , Brown Monique , Lambert W. Clark , Cohen Stanley
Published: January 2015

The interaction of the origin recognition complex (ORC) with replication origins is a critical parameter in eukaryotic replication initiation. In mammals the ORC remains bound except during mitosis, thus the localization of ORC complexes allows localization of origins. A monoclonal antibody that recognizes human ORC1 was used to localize ORC complexes in populations of human MOLT-4 cells separated by cell cycle position using centrifugal elutriation. ORC1 staining in cells in early G1 is diffuse and primarily peripheral. As the cells traverse G1, ORC1 accumulates and becomes more localized towards the center of the nucleus, however around the G1/S boundary the staining pattern changes and ORC1 appears peripheral. By mid to late S phase ORC1 immunofluorescence is again concentrated at the nuclear center. During anaphase, ORC1 staining is localized mainly in the pericentriolar regions. These findings suggest that concerted movements of origin DNA sequences in addition to the previously documented assembly and disassembly of protein complexes are an important aspect of replication initiation loci in eukaryotes.
An Approach for Leukemia Classification Based on Cooperative Game Theory
Authors: Torkaman Atefeh , Charkari Nasrollah Moghaddam , Aghaeipour Mahnaz
Published: January 2015

Hematological malignancies are the types of cancer that affect blood, bone marrow and lymph nodes. As these tissues are naturally connected through the immune system, a disease affecting one of them will often affect the others as well. The hematological malignancies include; Leukemia, Lymphoma, Multiple myeloma. Among them, leukemia is a serious malignancy that starts in blood tissues especially the bone marrow, where the blood is made. Researches show, leukemia is one of the common cancers in the world. So, the emphasis on diagnostic techniques and best treatments would be able to provide better prognosis and survival for patients. In this paper, an automatic diagnosis recommender system for classifying leukemia based on cooperative game is presented. Through out this research, we analyze the flow cytometry data toward the classification of leukemia into eight classes. We work on real data set from different types of leukemia that have been collected at Iran Blood Transfusion Organization (IBTO). Generally, the data set contains 400 samples taken from human leukemic bone marrow. This study deals with cooperative game used for classification according to different weights assigned to the markers. The proposed method is versatile as there are no constraints to what the input or output represent. This means that it can be used to classify a population according to their contributions. In other words, it applies equally to other groups of data. The experimental results show the accuracy rate of 93.12%, for classification and compared to decision tree (C4.5) with (90.16%) in accuracy. The result demonstrates that cooperative game is very promising to be used directly for classification of leukemia as a part of Active Medical decision support system for interpretation of flow cytometry readout. This system could assist clinical hematologists to properly recognize different kinds of leukemia by preparing suggestions and this could improve the treatment of leukemic patients.
Using a New Event-Based Simulation Framework for Investigating Resource Provisioning in Clouds
Authors: Ostermann Simon , Plankensteiner Kassian , Prodan Radu
Published: January 2015

Today, Cloud computing proposes an attractive alternative to building large-scale distributed computing environments by which resources are no longer hosted by the scientists' computational facilities, but leased from specialised data centres only when and for how long they are needed. This new class of Cloud resources raises new interesting research questions in the fields of resource management, scheduling, fault tolerance, or quality of service, requiring hundreds to thousands of experiments for finding valid solutions. To enable such research, a scalable simulation framework is typically required for early prototyping, extensive testing and validation of results before the real deployment is performed. The scope of this paper is twofold. In the first part we present GroudSim, a Grid and Cloud simulation toolkit for scientific computing based on a scalable simulation-independent discrete-event engine. GroudSim provides a comprehensive set of features for complex simulation scenarios from simple job executions on leased computing resources to file transfers, calculation of costs and background load on resources. Simulations can be parameterised and are easily extendable by probability distribution packages for failures which normally occur in complex distributed environments. Experimental results demonstrate the improved scalability of GroudSim compared to a related process-based simulation approach. In the second part, we show the use of the GroudSim simulator to analyse the problem of dynamic provisioning of Cloud resources to scientific workflows that do not benefit from sufficient Grid resources as required by their computational demands. We propose and study four strategies for provisioning and releasing Cloud resources that take into account the general leasing model encountered in today's commercial Cloud environments based on resource bulks, fuzzy descriptions and hourly payment intervals. We study the impact of our techniques to the overall execution time, overall cost and cost per unit of saved time with respect to various instance types offered by the Amazon EC2.
Performance and Cost Analysis of the Supernova Factory on the Amazon AWS Cloud
Authors: Jackson Keith R. , Muriki Krishna , Ramakrishnan Lavanya , Runge Karl J. , Thomas Rollin C.
Published: January 2015

Today, our picture of the Universe radically differs from that of just over a decade ago. We now know that the Universe is not only expanding as Hubble discovered in 1929, but that the rate of expansion is accelerating, propelled by mysterious new physics dubbed “Dark Energy”. This revolutionary discovery was made by comparing the brightness of nearby Type Ia supernovae (which exploded in the past billion years) to that of much more distant ones (from up to seven billion years ago). The reliability of this comparison hinges upon a very detailed understanding of the physics of the nearby events. To further this understanding, the Nearby Supernova Factory (SNfactory) relies upon a complex pipeline of serial processes that execute various image processing algorithms in parallel on ~10 TBs of data. This pipeline traditionally runs on a local cluster. Cloud computing [Above the clouds: a Berkeley view of cloud computing, Technical Report UCB/EECS-2009-28, University of California, 2009] offers many features that make it an attractive alternative. The ability to completely control the software environment in a cloud is appealing when dealing with a community developed science pipeline with many unique library and platform requirements. In this context we study the feasibility of porting the SNfactory pipeline to the Amazon Web Services environment. Specifically we: describe the tool set we developed to manage a virtual cluster on Amazon EC2, explore the various design options available for application data placement, and offer detailed performance results and lessons learned from each of the above design options.
Reshaping Text Data for Efficient Processing on Amazon EC2
Authors: Turcu Gabriela , Foster Ian , Nestorov Svetlozar
Published: January 2015

Text analysis tools are nowadays required to process increasingly large corpora which are often organized as small files (abstracts, news articles, etc.). Cloud computing offers a convenient, on-demand, pay-as-you-go computing environment for solving such problems. We investigate provisioning on the Amazon EC2 cloud from the user perspective, attempting to provide a scheduling strategy that is both timely and cost effective. We derive an execution plan using an empirically determined application performance model. A first goal of our performance measurements is to determine an optimal file size for our application to consume. Using the subset-sum first fit heuristic we reshape the input data by merging files in order to match as closely as possible the desired file size. This also speeds up the task of retrieving the results of our application, by having the output be less segmented. Using predictions of the performance of our application based on measurements on small data sets, we devise an execution plan that meets a user specified deadline while minimizing cost.
Point-of-Care Pathology with Miniature Microscopes
Authors: Liu Jonathan T. C. , Loewke Nathan O. , Mandella Michael J. , Levenson Richard M. , Crawford James M. , Contag Christopher H.
Published: January 2015

Advances in optical designs are enabling the development of miniature microscopes that can examine tissue in situ for early anatomic and molecular indicators of disease, in real time, and at cellular resolution. These new devices will lead to major changes in how diseases are detected and managed, driving a shift from today's diagnostic paradigm of biopsy followed by histopathology and recommended therapy, to non-invasive point-of-care diagnosis with possible same-session definitive treatment. This shift may have major implications for the training requirements of future physicians to enable them to interpret real-timein vivomicroscopic data, and will also shape the emerging fields of telepathology and telemedicine. Implementation of new technologies into clinical practice is a complex process that requires bridging gaps between clinicians, engineers and scientists. This article provides a forward-looking discussion of these issues, with a focus on malignant and pre-malignant lesions, by first highlighting some of the clinical areas where point-of-carein vivomicroscopy could address unmet needs, and then by reviewing the technological challenges that are being addressed, or need to be addressed, forin vivomicroscopy to become a standard clinical tool.
Distributed Authentication Mechanism for Secure Channel Establishment in Ubiquitous Medical Sensor Networks
Authors: Doh Inshil , Lim Jiyoung , Chae Kijoon
Published: January 2015

In medical sensor networks, sensor nodes on a body of the patient sense the vital data and deliver them to the server system through mobile devices or gateways in the middle. However, when these linking devices do not function because of the battery outage or the system fault, the server system could not get patients' data during that period, and this situation could lead to serious problems. In this paper, to cope with this problem, we propose a distributed authentication mechanism in which substituted devices could be authenticated to deliver patients' data to the server system in the unusual situation.
Tool Support for Software Lookup Table Optimization
Authors: Wilcox Chris , Strout Michelle Mills , Bieman James M.
Published: January 2015

A number of scientific applications are performance-limited by expressions that repeatedly call costly elementary functions. Lookup table (LUT) optimization accelerates the evaluation of such functions by reusing previously computed results. LUT methods can speed up applications that tolerate an approximation of function results, thereby achieving a high level of fuzzy reuse. One problem with LUT optimization is the difficulty of controlling the tradeoff between performance and accuracy. The current practice of manual LUT optimization adds programming effort by requiring extensive experimentation to make this tradeoff, and such hand tuning can obfuscate algorithms. In this paper we describe a methodology and tool implementation to improve the application of software LUT optimization. Our Mesa tool implements source-to-source transformations for C or C++ code to automate the tedious and error-prone aspects of LUT generation such as domain profiling, error analysis, and code generation. We evaluate Mesa with five scientific applications. Our results show a performance improvement of 3.0× and 6.9× for two molecular biology algorithms, 1.4× for a molecular dynamics program, 2.1× to 2.8× for a neural network application, and 4.6× for a hydrology calculation. We find that Mesa enables LUT optimization with more control over accuracy and less effort than manual approaches.
Tyrosine Phosphatases in the HER2-Directed Motility of Ovarian Cancer Cells: Involvement of PTPN12, ERK5 and FAK
Authors: Villa-Moruzzi Emma
Published: January 2015

Background: HER2 activation in tumours supports multiple signalling pathways, including those regulating invasion and metastasis. Among the involved genes, Tyrosine and Dual Specificity Phosphatases (PTPs and DSPs) may play a relevant, though not completely clear role. Methods: HER2 was silenced in ovarian SKOV-3 cells, a genome-wide expression analysis of PTPs and DSPs was performed, the effects on cell motility were analysed and compared with those of PTPN12-silencing, focusing on FAK. Results: HER2-silencing altered the expression of 4 PTPs and 6 DSPs; PTPN12 displayed also 3-4-fold protein increase. Conversely, PTPN12-silencing enhanced migration, suggesting that PTPN12 down-modulation by HER2 favours motility. HER2-silencing inactivated FAK, in quiescent and migrating cells, involving FAK dephosphorylation at Y397 and S910. Conversely, in PTPN12-silenced cells FAK activity was close to control, altogether suggesting that PTPN12 targets Y397. As regards to S910, cell-treatment with the MEK inhibitor UO126 and ERK5-silencing indicated its targeting by ERK5. Loss of pS910 and decreased ERK5 kinase activity in HER2-silenced cells confirmed their control by HER2. Conclusions: The results indicate the contribution of PTPN12, targeting FAK Y397, and ERK5, targeting FAK S910, to the HER2-driven cell motility, thus depicting new aspects of the complex cross­talk between HER2 and the motility machinery.
Modern Trends in Imaging VI: Raman Scattering in Pathology
Authors: Smith Zachary J. , Huser Thomas R. , Wachsmann-Hogiu Sebastian
Published: January 2015

Raman scattering is the inelastic scattering of light by chemical bonds, and can therefore show molecular specificity. It can be used both in pure spectroscopy mode, and in imaging mode. While many applications of Raman spectroscopy and imaging in the biomedical field have been so far demonstrated, the use of this technology for pathology applications is still in early stages. In this paper we review some of the most important recent developments in this field, including a description of relevant technologies, applications to molecular sensing, characterization of cells and tissues of interest, and disease detection via Raman scattering.
A Methodology to Counter DoS Attacks in Mobile IP Communication
Authors: Parvin Sazia , Hussain Farookh Khadeer , Ali Sohrab
Published: January 2015

Similar to wired communication, Mobile IP communication is susceptible to various kinds of attacks. Of these attacks, Denial of Service (DoS) attack is considered as a great threat to mobile IP communication. The number of approaches hitherto proposed to prevent DoS attack in the area of mobile IP communication is much less compared to those for the wired domain and mobile ad hoc networks. In this work, the effects of Denial of Service attack on mobile IP communication are analyzed in detail. We propose to use packet filtering techniques that work in different domains and base stations of mobile IP communication to detect suspicious packets and to improve the performance. If any packet contains a spoofed IP address which is created by DoS attackers, the proposed scheme can detect this and then filter the suspected packet. The proposed system can mitigate the effect of Denial of Service (DoS) attack by applying three methods: (i) by filtering in the domain periphery router (ii) by filtering in the base station and (iii) by queue monitoring at the vulnerable points of base-station node. We evaluate the performance of our proposed scheme using the network simulator NS-2. The results indicate that the proposed scheme is able to minimize the effects of Denial of Service attacks and improve the performance of mobile IP communication.
Multispectral Enhancement towards Digital Staining
Authors: Bautista Pinky A. , Yagi Yukako
Published: January 2015

Background: Digital staining can be considered as a special form of image enhancement wherein the concern is not only to increase the contrast between the background objects and objects of interest, but to also impart the colors that mark the objects’ unique reactions to a specific stain. In this paper, we extended the previously proposed multispectral enhancement methods such that the colors of the background pixels can also be changed.

Methods: In the previous multispectral enhancement methods a shifting factor is provided to the original spectrum. To implement digital staining, a spectral transformation process is introduced prior to spectral shifting.

Results: The enhancement method is applied to multispectral images of H&E stained liver tissue. The resulting digitally stained images show good correlation with the serial-section images of the tissue which are physically stained with Masson's trichrome.

Conclusion: We have presented a multispectral enhancement method that can be adjusted to produce digitally stained-images. The current experimental results show the viability of the method. However, to achieve robust enhancement performance issues that arise from variations in staining conditions has to be addressed as well. This would be part of our future work.
A Friendly Location-Aware System to Facilitate the Work of Technical Directors when Broadcasting Sport Events
Authors: Ilarri Sergio , Mena Eduardo , Illarramendi Arantza , Yus Roberto , Laka Maider , Marcos Gorka
Published: January 2015

The production costs of broadcasting sport events that require tracking moving objects are continuously increasing. Although those events are very demanded by the audience, broadcasting organizations have economical difficulties to afford them. For that reason, they are demanding the development of new professional (software and hardware) equipments that lead to a considerable reduction of the production costs.
Solving PDEs with Intrepid
Authors: Bochev P. , Edwards H.C. , Kirby R.C. , Peterson K. , Ridzal D.
Published: January 2015

Intrepid is a Trilinos package for advanced discretizations of Partial Differential Equations (PDEs). The package provides a comprehensive set of tools for local, cell-based construction of a wide range of numerical methods for PDEs. This paper describes the mathematical ideas and software design principles incorporated in the package. We also provide representative examples showcasing the use of Intrepid both in the context of numerical PDEs and the more general context of data analysis.
Microarray Core Detection by Geometric Restoration
Authors: Azar Jimmy C. , Busch Christer , Carlbom Ingrid B.
Published: January 2015

Whole-slide imaging of tissue microarrays (TMAs) holds the promise of automated image analysis of a large number of histopathological samples from a single slide. This demands high-throughput image processing to enable analysis of these tissue samples for diagnosis of cancer and other conditions. In this paper, we present a completely automated method for the accurate detection and localization of tissue cores that is based on geometric restoration of the core shapes without placing any assumptions on grid geometry. The method relies on hierarchical clustering in conjunction with the Davies-Bouldin index for cluster validation in order to estimate the number of cores in the image wherefrom we estimate the core radius and refine this estimate using morphological granulometry. The final stage of the algorithm reconstructs circular discs from core sections such that these discs cover the entire region of each core regardless of the precise shape of the core. The results show that the proposed method is able to reconstruct core locations without any evidence of localization. Furthermore, the algorithm is more efficient than existing methods based on the Hough transform for circle detection. The algorithm’s simplicity, accuracy, and computational efficiency allow for automated high-throughput analysis of microarray images.
Modern Trends in Imaging VIII: Lensfree Computational Microscopy Tools for Cell and Tissue Imaging at the Point-of-Care and in Low-Resource Settings
Authors: Isikman Serhan O. , Greenbaum Alon , Lee Myungjun , Bishara Waheb , Mudanyali Onur , Su Ting-Wei , Ozcan Aydogan
Published: January 2015

The recent revolution in digital technologies and information processing methods present important opportunities to transform the way optical imaging is performed, particularly toward improving the throughput of microscopes while at the same time reducing their relative cost and complexity. Lensfree computational microscopy is rapidly emerging toward this end, and by discarding lenses and other bulky optical components of conventional imaging systems, and relying on digital computation instead, it can achieve both reflection and transmission mode microscopy over a large field-of-view within compact, cost-effective and mechanically robust architectures. Such high throughput and miniaturized imaging devices can provide a complementary toolset for telemedicine applications and point-of-care diagnostics by facilitating complex and critical tasks such as cytometry and microscopic analysis of e.g., blood smears, Pap tests and tissue samples. In this article, the basics of these lensfree microscopy modalities will be reviewed, and their clinically relevant applications will be discussed.
Modern Trends in Imaging X: Spectral Imaging in Preclinical Research and Clinical Pathology
Authors: Levenson Richard , Beechem Joseph , McNamara George
Published: January 2015

Spectral imaging methods are attracting increased interest from researchers and practitioners in basic science, pre-clinical and clinical arenas. A combination of better labeling reagents and better optics creates opportunities to detect and measure multiple parameters at the molecular and cellular level. These tools can provide valuable insights into the basic mechanisms of life, and yield diagnostic and prognostic information for clinical applications. There are many multispectral technologies available, each with its own advantages and limitations. This chapter will present an overview of the rationale for spectral imaging, and discuss the hardware, software and sample labeling strategies that can optimize its usefulness in clinical settings.
Absolute Quantification of Choline-Related Biomarkers in Breast Cancer Biopsies by Liquid Chromatography Electrospray Ionization Mass Spectrometry
Authors: Mimmi Maria Chiara , Finato Nicoletta , Pizzolato Gloria , Beltrami Carlo Alberto , Fogolari Federico , Corazza Alessandra , Esposito Gennaro
Published: January 2015

It has been repeatedly demonstrated that choline metabolism is altered in a wide variety of cancers. In breast tumours, the choline metabolite profile is characterized by an elevation of phosphocholine and total choline-compounds. This pattern is increasingly being exploited as biomarker in cancer diagnosis.

The majority of in vitro metabolomics studies, for biomarkers quantification in cell cultures or tissues, entail proton NMR spectroscopy. Although many “targeted” approaches have been proposed to quantify metabolites from standard one-dimensional (1D) NMR experiments, the task is often made difficult by the high degree of overlap characterizing 1H NMR spectra of biological samples.

Here we present an optimized protocol for tissue extraction and absolute quantification of choline, phosphocholine and glycerophosphocholine by means of liquid chromatography electrospray ionization mass spectrometry (LC-ESI-MS). The selected chromatographic separation system with a HILIC (hydrophilic interaction chromatography) amide column effectively separates free choline and its phopshorylated derivatives, contrary to failure observed using standard reversed-phase chromatography. The metabolite absolute quantification is based on external calibration with commercial standards, and is validated by a parallel 1D proton NMR analysis.

The LC-MS/NMR analysis is applied to three breast carcinoma specimens obtained by surgical excision, each one accompanied by a control tissue sample taken outside the tumor margin. The metabolite concentrations measured are in good agreement with previous results on metabolic profile changes of breast cancer. Each of the three cancerous biopsies, when compared with the control tissue, exhibit a highly increased levels phosphocholine, total choline and phosphocholine/glycerophosphocholine ratio.
Structured Illumination-Based Super-Resolution Optical Microscopy for Hemato- and Cyto-Pathology Applications
Authors: Zhang Tieqiao , Osborn Samantha , Brandow Chloe , Dwyre Denis , Green Ralph , Lane Stephen , Wachsmann-Hogiu Sebastian
Published: January 2015

Structured illumination fluorescence microscopy utilizes interfering light and the moiré effect to enhance spatial resolution to about a half of that of conventional light microscopy, i.e. approximately 90 nm. In addition to the enhancement in thexandydirections, it also allows enhancement of resolution in thez- direction by the same factor of two (to approximately 220 nm), making it a powerful tool for 3-D morphology studies of fluorescently labeled cells or thin tissue sections. In this report, we applied this technique to several types of blood cells that are commonly seen in hematopathology. Compared with standard brightfield and ordinary fluorescence microscopy images, the 3-D morphology results clearly reveal the morphological features of different types of normal blood cells. We have also used this technique to evaluate morphologies of abnormal erythrocytes and compare them with those recorded on normal cells. The results give a very intuitive presentation of morphological structures of erythrocytes with great details. This research illustrates the potential of this technique to be used in hematology and cyto-pathology studies aimed at identifying nanometer-sized features that cannot be distinguished otherwise with conventional optical microscopy.
Personalized Behavior Pattern Recognition and Unusual Event Detection for Mobile Users
Authors: Ahn Junho , Han Richard
Published: January 2015

Mobile phones have become widely used for obtaining help in emergencies, such as accidents, crimes, or health emergencies. The smartphone is an essential device that can record emergency situations, which can be used for clues or evidence, or as an alert system in such situations. In this paper, we focus on mobile-based identification of potentially unusual, or abnormal events, occurring in a mobile user's daily behavior patterns. For purposes of this research, we have classified events as “unusual” for a mobile user when an event is an infrequently occurring one from the user's normal behavior patterns–all of which are collected and recorded on a user's mobile phone. We build a general unusual event classification model to be automated on the smartphone for use by any mobile phone users. To classify both normal and unusual events, we analyzed the activity, location, and audio sensor data collected from 20 mobile phone users to identify these users' personalized normal daily behavior patterns and any unusual events occurring in their daily activity. We used binary fusion classification algorithms on the subjects' recorded experimental data and ultimately identified the most accurately performing fusion algorithm for unusual event detection.
Advanced Methods in Fluorescence Microscopy
Authors: Fritzky Luke , Lagunoff David
Published: January 2015

It requires a good deal of will power to resist hyperbole in considering the advances that have been achieved in fluorescence microscopy in the last 25 years. Our effort has been to survey the modalities of microscopic fluorescence imaging available to cell biologists and perhaps useful for diagnostic pathologists. The gamut extends from established confocal laser scanning through multiphoton and TIRF to the emerging technologies of super-resolution microscopy that breech the Abbé limit of resolution. Also considered are the recent innovations in structured and light sheet illumination, the use of FRET and molecular beacons that exploit specific characteristics of designer fluorescent proteins, fluorescence speckles, and second harmonic generation for native anisometric structures like collagen, microtubules and sarcomeres.
A Mobile Picture Tagging System Using Tree-Structured Layered Bayesian Networks
Authors: Lee Young-Seol , Cho Sung-Bae
Published: January 2015

Advances in digital media technology have increased in multimedia content. Tagging is one of the most effective methods to manage a great volume of multimedia content. However, manual tagging has limitations such as human fatigue and subjective and ambiguous keywords. In this paper, we present an automatic tagging method to generate semantic annotation on a mobile phone. In order to overcome the constraints of the mobile environment, the method uses two layered Bayesian networks. In contrast to existing techniques, this approach attempts to design probabilistic models with fixed tree structures and intermediate nodes. To evaluate the performance of this method, an experiment is conducted with data collected over a month. The result shows the efficiency and effectiveness of our proposed method. Furthermore, a simple graphic user interface is developed to visualize and evaluate recognized activities and probabilities.
The Evolutionary Random Interval Fingerprint for a More Secure Wireless Communication
Authors: Tseng Kuo-Kun , Pan Jeng-Shyang , Wei Wei , Hsu Hui-Huang
Published: January 2015

In this paper, we propose a novel evolutionary Random Interval Fingerprint (RIF) for active RFID and ZigBee systems. This new approach can enable more secure multi-party communication since, if the wireless packets are forged by another wireless communication party, the interval fingerprint can provide another way to detect the spoofing packet. Moreover, the random evolutionary algorithms, both genetic and memetic, are also proposed as a means to generate the random interval fingerprint. Compared to the conventional random generator, our approach is flexible in generating uniform random and long cycle numbers, and more robust for the anti-cracking. It is difficult for the forged party to produce the fake random intervals. Finally, we provide an application example, a completed work survey, pseudo-code and analysis result to prove that our concept is feasible for the Wireless communication.
Python for Scientific Computing Education: Modeling of Queueing Systems
Authors: Dolgopolovas Vladimiras , Dagienė Valentina , Minkevičius Saulius , Sakalauskas Leonidas
Published: January 2015

In this paper, we present the methodology for the introduction to scientific computing based on model-centered learning. We propose multiphase queueing systems as a basis for learning objects. We use Python and parallel programming for implementing the models and present the computer code and results of stochastic simulations.
Types and Patterns of Colonic Polyps Encountered at a Tertiary Care Center in a Developing Country in South Asia
Authors: Wickramasinghe Dakshitha Praneeth , Samaranayaka Sanjeev F. , Lakmal Chamila , Mathotaarachchi Sashi , Kanishka Lal Chula , Keppetiyagama Chathuranga , Samarasekera Dharmabandhu Nandadeva
Published: January 2015

Purpose. To identify the prevalence, types, and patterns of colonic polyps in a cohort of patients presenting to a tertiary care referral center in Sri Lanka.Methods. Endoscopy and pathology reports of a single unit from 2006 to 2013 were analyzed retrospectively. Spearman’s correlation coefficient and chi-square test were used to identify correlations.Results. There were a total of 158 patients (M : F, 10 : 57) who had polyps encountered on colonoscopy (n=1408) and flexible sigmoidoscopy (n=2402) with an incidence of 4.1%. Mean age was 56.5 years (SD 16.4) and the incidence of polyps increased with age. The majority (81.6%) had one polyp. A total of 188 polyps were assessed and most were seen in the rectum (33.5%) followed by sigmoid colon (22.9%). The commonest histological type was tubulovillous adenoma (33.5%) followed by tubular adenoma (24.5%). Most polyps were benign (91.5%). There was no statistically significant correlation with age or gender with malignancy, site, or histology.Discussion and Conclusion. The incidence of colorectal polyps was lower than the values reported in the west. More polyps were identified in males. There was no statistically significant association between age, gender, or multiplicity and malignant change in the polyps.
Constructing the Web of Events from Raw Data in the Web of Things
Authors: Sun Yunchuan , Yan Hongli , Lu Cheng , Bie Rongfang , Zhou Zhangbing
Published: January 2015

An exciting paradise of data is emerging into our daily life along with the development of the Web of Things. Nowadays, volumes of heterogeneous raw data are continuously generated and captured by trillions of smart devices like sensors, smart controls, readers and other monitoring devices, while various events occur in the physical world. It is hard for users including people and smart things to master valuable information hidden in the massive data, which is more useful and understandable than raw data for users to get the crucial points for problems-solving. Thus, how to automatically and actively extract the knowledge of events and their internal links from the big data is one key challenge for the future Web of Things. This paper proposes an effective approach to extract events and their internal links from large scale data leveraging predefined event schemas in the Web of Things, which starts with grasping the critical data for useful events by filtering data with well-defined event types in the schema. A case study in the context of smart campus is presented to show the application of proposed approach for the extraction of events and their internal semantic links.
A Comparative and Evaluative Study of Two Cytological Grading Systems in Breast Carcinoma with Histological Grading: An Important Prognostic Factor
Authors: Pandey Pinki , Dixit Alok , Chandra Subrat , Kaur Swarn
Published: January 2015

Objective. Cytonuclear gradings in the breast carcinoma raise the level of FNA reportage and improves patient management. Our aim was to evaluate and compare two cytological grading methods (Robinson’s and Mouriquand’s) in breast carcinoma and correlate it with Nottingham modification of Scarff-Bloom-Richardson (SBR) histological grading.Materials and Methods. 30 cytologically proven cases of infiltrating ductal carcinoma were graded cytologically and histologically. Cytograding was done by Robinson’s and Mouriquand’s methods (grades I to III) followed by comparison of the two methods. Cytogradings were correlated with SBR grading method. Sensitivity, specificity, diagnostic accuracy, and concordance and discordance rates were evaluated.Results. An overall concordance of 76.66% between cytogradings, of 83.33% between Robinson’s method and SBR, and of 66.66% between Mouriquand’s method and SBR was seen. Robinson’s method correlated best with SBR in all the three nuclear grades. Robinson’s method showed a diagnostic accuracy of 90% with 91.30% sensitivity while Mouriquand’s method had an accuracy of 76.66% with 95.65% sensitivity. The specificity by Mouriquand’s method was quite low (14.28%) as compared to Robinson’s method (85.71%).Conclusion. Comprehensive cytological grading of breast cancer by Robinson’s method seems better because of more objective set of criteria, easy reproducibility, and specificity.