bluuebunny/crossref_metadata_2025 huggingface dataset:
Large Science Databases – Are Cloud Services Ready for Them?
Authors: Thakar Ani , Szalay Alex , Church Ken , Terzis Andreas
Published: January 2015

We report on attempts to put an astronomical database – the Sloan Digital Sky Survey science archive – in the cloud. We find that it is very frustrating to impossible at this time to migrate a complex SQL Server database into current cloud service offerings such as Amazon (EC2) and Microsoft (SQL Azure). Certainly it is impossible to migrate a large database in excess of a TB, but even with (much) smaller databases, the limitations of cloud services make it very difficult to migrate the data to the cloud without making changes to the schema and settings that would degrade performance and/or make the data unusable. Preliminary performance comparisons show a large performance discrepancy with the Amazon cloud version of the SDSS database. These difficulties suggest that much work and coordination needs to occur between cloud service providers and their potential clients before science databases – not just large ones but even smaller databases that make extensive use of advanced database features for performance and usability – can successfully and effectively be deployed in the cloud. We describe a powerful new computational instrument that we are developing in the interim – the Data-Scope – that will enable fast and efficient analysis of the largest (petabyte scale) scientific datasets.
Nuclear Morphology Measurements with Angle-Resolved Low Coherence Interferometry For Application To Cell Biology And Early Cancer Detection
Authors: Wax Adam , Chalut Kevin J.
Published: January 2015

The study of intact, living cells using non-invasive optical spectroscopic methods offers the opportunity to assess cellular structure and organization in a way that is not possible with commonly used cell biology imaging techniques. We have developed a novel spectroscopic technique for diagnosing disease at the cellular level based on using low-coherence interferometry (LCI) to detect the angular distribution of scattered light. Angle-resolved LCI (a/LCI) combines the ability of LCI to isolate scattering from sub-surface tissue layers with the ability of light scattering spectroscopy to obtain structural information on sub-wavelength scales. In application to examining cellular structure, a/LCI enables quantitative measurements of changes in the size and texture of cell nuclei. These quantitative measurements are characteristic of different pathological states. The capabilities of a/LCI were demonstrated using a clinical system that can be applied in endoscopic surveillance of esophageal tissue, producing high sensitivity and specificity for detecting dysplastic tissuesin vivo. Experiments within vitrocell samples also show the utility of a/LCI in observing structural changes due to environmental stimuli as well as detecting apoptosis due to chemotherapeutic agents.
A Mobile Relational Algebra
Authors: Morvan Franck , Hameurlain Abdelkader
Published: January 2015

Most of the dynamic query optimization methods proposed in the literature are centralized. This centralization, in a large-scale environment, generates a bottleneck due to relatively important message exchange on a network with a weak bandwidth and strong latency. It becomes thus convenient to render autonomous and self-adaptable the query execution on a large-scale network. In this perspective, we propose a mobile relational algebra to decentralize the control of dynamic query optimization processes. Experiments, in local and large-scale distributed environments, allow: (i) to validate the proposed proactive migration policy, and (ii) to identify the efficiency intervals of proposed mobile relational algebra.
Use of GPU Computing for Uncertainty Quantification in Computational Mechanics: A Case Study
Authors: Gaurav  , Wojtkiewicz Steven F.
Published: January 2015

Graphics processing units (GPUs) are rapidly emerging as a more economical and highly competitive alternative to CPU-based parallel computing. As the degree of software control of GPUs has increased, many researchers have explored their use in non-gaming applications. Recent studies have shown that GPUs consistently outperform their best corresponding CPU-based parallel computing alternatives in single-instruction multiple-data (SIMD) strategies. This study explores the use of GPUs for uncertainty quantification in computational mechanics. Five types of analysis procedures that are frequently utilized for uncertainty quantification of mechanical and dynamical systems have been considered and their GPU implementations have been developed. The numerical examples presented in this study show that considerable gains in computational efficiency can be obtained for these procedures. It is expected that the GPU implementations presented in this study will serve as initial bases for further developments in the use of GPUs in the field of uncertainty quantification and will (i) aid the understanding of the performance constraints on the relevant GPU kernels and (ii) provide some guidance regarding the computational and the data structures to be utilized in these novel GPU implementations.
An Analytical Approach Differentiates Between Individual and Collective Cancer Invasion
Authors: Katz Elad , Verleyen Wim , Blackmore Colin G. , Edward Michael , Smith V. Anne , Harrison David J.
Published: January 2015

Tumour cells employ a variety of mechanisms to invade their environment and to form metastases. An important property is the ability of tumour cells to transition between individual cell invasive mode and collective mode. The switch from collective to individual cell invasion in the breast was shown recently to determine site of subsequent metastasis. Previous studies have suggested a range of invasion modes from single cells to large clusters. Here, we use a novel image analysis method to quantify and categorise invasion. We have developed a process using automated imaging for data collection, unsupervised morphological examination of breast cancer invasion using cognition network technology (CNT) to determine how many patterns of invasion can be reliably discriminated. We used Bayesian network analysis to probabilistically connect morphological variables and therefore determine that two categories of invasion are clearly distinct from one another. The Bayesian network separated individual and collective invading cell groups based on the morphological measurements, with the level of cell-cell contact the most discriminating morphological feature. Smaller invading groups were typified by smoother cellular surfaces than those invading collectively in larger groups. Interestingly, elongation was evident in all invading cell groups and was not a specific feature of single cell invasion as a surrogate of epithelial-mesenchymal transition. In conclusion, the combination of cognition network technology and Bayesian network analysis provides an insight into morphological variables associated with transition of cancer cells between invasion modes. We show that only two morphologically distinct modes of invasion exist.
GSSIM – A Tool for Distributed Computing Experiments
Authors: Bąk Sławomir , Krystek Marcin , Kurowski Krzysztof , Oleksiak Ariel , Piątek Wojciech , Wąglarz Jan
Published: January 2015

In this paper we present the Grid Scheduling Simulator (GSSIM), a comprehensive and advanced simulation tool for distributed computing problems. Based on a classification of simulator features proposed in the paper, we define problems that can be simulated using GSSIM and compare it to other simulation tools. We focus on an extension of our previous works including advanced workload generation methods, simulation of a network with advance reservation features, handling specific application performance models and energy efficiency modeling. Some important features of GSSIM are demonstrated by three diverse experiments conducted with the use of the tool. We also present an advanced web tool for the remote management and execution of simulation experiments, which makes GSSIM the comprehensive distributed computing simulator available on the Web.
CD133 Expression and Identification of CD133/nestin Positive Cells in Rhabdomyosarcomas and Rhabdomyosarcoma Cell Lines
Authors: Sana Jiri , Zambo Iva , Skoda Jan , Neradil Jakub , Chlapek Petr , Hermanova Marketa , Mudry Peter , Vasikova Alzbeta , Zitterbart Karel , Hampl Ales , Sterba Jaroslav , Veselska Renata
Published: January 2015

Background: Co-expression of CD133, cell surface glycoprotein, and nestin, an intermediate filament protein, was determined to be a marker of neural stem cells and of cancer stem cells in neurogenic tumors.Methods: We examined the expression of CD133 and nestin in ten tumor tissue samples taken from patients with rhabdomyosarcomas and in five rhabdomyosarcoma cell lines. Immunohistochemistry and immunofluorescence were used to examine FFPE tumor tissue samples. Cell lines were analyzed by immunofluorescence, immunoblotting, flow cytometry, and RT-PCR. Functional assays (clonogenicin vitroassay and tumorigenicin vivoassay) were also performed using these cell lines.Results: CD133 and nestin were detected in all 10 tumor tissue samples and in all 5 cell lines; however, the frequency of CD133+, Nes+, and CD133+/Nes+ cells, as well as the intensity of fluorescence varied in individual samples or cell lines. The expression of CD133 and nestin was subsequently confirmed in all cell lines by immunoblotting. Furthermore, we observed an increasing expression of CD133 in relation to the cultivation. All cell lines were positive for Oct3/4 and nucleostemin; NSTS-11 cells were also able to form xenograft tumors in mice.Conclusion: Our results represent the first evidence of CD133 expression in rhabdomyosarcoma tissue and in rhabdomyosarcoma cell lines. In addition, the co-expression of CD133 and nestin as well as results of the functional assays suggest a possible presence of cancer cells with a stem-like phenotype in these tumors.
Whole Slide Images and Digital Media in Pathology Education, Testing, and Practice: The Oklahoma Experience
Authors: Fung Kar-Ming , Hassell Lewis A. , Talbert Michael L. , Wiechmann Allan F. , Chaser Brad E. , Ramey Joel
Published: January 2015

Examination of glass slides is of paramount importance in pathology training. Until the introduction of digitized whole slide images that could be accessed through computer networks, the sharing of pathology slides was a major logistic issue in pathology education and practice. With the help of whole slide images, our department has developed several online pathology education websites. Based on a modular architecture, this program provides online access to whole slide images, still images, case studies, quizzes and didactic text at different levels. Together with traditional lectures and hands-on experiences, it forms the back bone of our histology and pathology education system for residents and medical students. The use of digitized whole slide images has a.lso greatly improved the communication between clinicians and pathologist in our institute.
A GPS Sensing Strategy for Accurate and Energy-Efficient Outdoor-to-Indoor Handover in Seamless Localization Systems
Authors: Kim Yungeun , Lee Songhee , Lee Seokjoon , Cha Hojung
Published: January 2015

Indoor localization systems typically locate users on their own local coordinates, while outdoor localization systems use global coordinates. To achieve seamless localization from outdoors to indoors, a handover technique that accurately provides a starting position to the indoor localization system is needed. However, existing schemes assume that a starting position is known a priori or uses a naïve approach to consider the last location obtained from GPS as the handover point. In this paper, we propose an accurate handover scheme that monitors the signal-to-noise ratio (SNR) of the effective GPS satellites that are selected according to their altitude. We also propose an energy-efficient handover mechanism that reduces the GPS sampling interval gradually. Accuracy and energy efficiency are experimentally validated with the GPS logs obtained in real life.
Virtual Microscopy Beyond the Pyramids, Applications of WSI in Cairo University for E-Education & Telepathology
Authors: Ayad Essam , Yagi Yukako
Published: January 2015

Background: Telepathology, the practice of pathology at a long distance, has advanced continuously since 1986. The progress of telepathology passed through four stages: Static, Dynamic, Hybrid & Whole Slide Imaging.

Materials and Methods: A pilot project between the Italian Hospital in Cairo & the Civico Hospital in Palermo was completed successfully, applying the static & dynamic techniques of telepathology. This project began in 2003 and continued till now. In 2004, centers in Venice, London and Pittsburgh participated actively in our project.

Results: Over eight years we consulted on many problematic pathological cases with specialized pathological centers in Italy, UK & USA. In addition to the highly specialized scientific value, we saved a lot of time and money.

Conclusion: We concluded from our experience that telepathology is a very useful and applicable tool for additional consulting on difficult pathological cases especially for emerging countries. In view of this success we have already established our Digital Telepathology Unit in Cairo University, using the WSI technique in teaching which was greatly successful and encouraged us to build a huge digital pathology library which will expand our telepathology & E-learning programs to cover staff and students in Egypt and Eastern Mediterranean.
Condensation-Based Routing in Mobile Ad-Hoc Networks
Authors: Palmieri Francesco , Castiglione Aniello
Published: January 2015

The provision of efficient broadcast containment schemes that can dynamically cope with frequent topology changes and limited shared channel bandwidth, is one of the most challenging research topics in MANETs, and is crucial to the basic operations of networks serving fully mobile devices within areas having no fixed communication infrastructure. This problem particularly impacts the design of dynamic routing protocol that can efficiently establish routes to deliver data packets among mobile nodes with minimum communication overhead, and at the same time, ensure high throughput and low end-to-end delay. Accordingly, this work exploits and analyzes an adaptive probabilistic broadcast containment technique based on a particular condensation phenomenon borrowed from Quantum Mechanics and transposed in self-organizing random networks, that has the potential to effectively drive the on-demand route discovery process. Simulation-based performance analysis has shown that the proposed technique can introduce significant benefits on the general performance of broadcast-based reactive routing protocols in MANETs.
Modern Trends in Imaging XI: Impedance Measurements in the Biomedical Sciences
Authors: Coffman Frederick D. , Cohen Stanley
Published: January 2015

Biological organisms and their component organs, tissues and cells have unique electrical impedance properties. Impedance properties often change with changes in structure, composition, and metabolism, and can be indicative of the onset and progression of disease states. Over the past 100 years, instruments and analytical methods have been developed to measure the impedance properties of biological specimens and to utilize these measurements in both clinical and basic science settings. This chapter will review the applications of impedance measurements in the biomedical sciences, from whole body analysis to impedance measurements of single cells and cell monolayers, and how cellular impedance measuring instruments can now be used in high throughput screening applications.
Amesos2 and Belos: Direct and Iterative Solvers for Large Sparse Linear Systems
Authors: Bavier Eric , Hoemmen Mark , Rajamanickam Sivasankaran , Thornquist Heidi
Published: January 2015

Solvers for large sparse linear systems come in two categories: direct and iterative. Amesos2, a package in the Trilinos software project, provides direct methods, and Belos, another Trilinos package, provides iterative methods. Amesos2 offers a common interface to many different sparse matrix factorization codes, and can handle any implementation of sparse matrices and vectors, via an easy-to-extend C++ traits interface. It can also factor matrices whose entries have arbitrary “Scalar” type, enabling extended-precision and mixed-precision algorithms. Belos includes many different iterative methods for solving large sparse linear systems and least-squares problems. Unlike competing iterative solver libraries, Belos completely decouples the algorithms from the implementations of the underlying linear algebra objects. This lets Belos exploit the latest hardware without changes to the code. Belos favors algorithms that solve higher-level problems, such as multiple simultaneous linear systems and sequences of related linear systems, faster than standard algorithms. The package also supports extended-precision and mixed-precision algorithms. Together, Amesos2 and Belos form a complete suite of sparse linear solvers.
Integration of Architectural and Cytologic Driven Image Algorithms for Prostate Adenocarcinoma Identification
Authors: Hipp Jason , Monaco James , Kunju L. Priya , Cheng Jerome , Yagi Yukako , Rodriguez-Canales Jaime , Emmert-Buck Michael R. , Hewitt Stephen , Feldman Michael D. , Tomaszewski John E. , Toner Mehmet , Tompkins Ronald G. , Flotte Thomas , Lucas David , Gilbertson John R. , Madabhushi Anant , Balis Ulysses
Published: January 2015

Introduction: The advent of digital slides offers new opportunities within the practice of pathology such as the use of image analysis techniques to facilitate computer aided diagnosis (CAD) solutions. Use of CAD holds promise to enable new levels of decision support and allow for additional layers of quality assurance and consistency in rendered diagnoses. However, the development and testing of prostate cancer CAD solutions requires a ground truth map of the cancer to enable the generation of receiver operator characteristic (ROC) curves. This requires a pathologist to annotate, or paint, each of the malignant glands in prostate cancer with an image editor software - a time consuming and exhaustive process.

Recently, two CAD algorithms have been described: probabilistic pairwise Markov models (PPMM) and spatially-invariant vector quantization (SIVQ). Briefly, SIVQ operates as a highly sensitive and specific pattern matching algorithm, making it optimal for the identification of any epithelial morphology, whereas PPMM operates as a highly sensitive detector of malignant perturbations in glandular lumenal architecture.

Methods: By recapitulating algorithmically how a pathologist reviews prostate tissue sections, we created an algorithmic cascade of PPMM and SIVQ algorithms as previously described by Doyle el al. [1] where PPMM identifies the glands with abnormal lumenal architecture, and this area is then screened by SIVQ to identify the epithelium.

Results: The performance of this algorithm cascade was assessed qualitatively (with the use of heatmaps) and quantitatively (with the use of ROC curves) and demonstrates greater performance in the identification of malignant prostatic epithelium.

Conclusion: This ability to semi-autonomously paint nearly all the malignant epithelium of prostate cancer has immediate applications to future prostate cancer CAD development as a validated ground truth generator. In addition, such an approach has potential applications as a pre-screening/quality assurance tool.
Targeting Focal Adhesion Assembly by Ethoxyfagaronine Prevents Lymphoblastic Cell Adhesion to Fibronectin
Authors: Ouchani F. , Devy J. , Rusciani A. , Helesbeux J. J. , Salesse S. , Letinois I. , Gras-Billart D. , Duca L. , Duval O. , Martiny L. , Charpentier E.
Published: January 2015

Background: Leukemic cell adhesion to proteins of the bone marrow microenvironment provides signals which control morphology, motility and cell survival. We described herein the ability of ethoxyfagaronine (etxfag), a soluble synthetic derivative of fagaronine, to prevent leukemic cell adhesion to fibronectin peptide (FN/V).

Methods: Phosphorylation of fak and pyk2 were evaluated by immunoblotting. Labelled proteins were localized by confocal microscopy. PI 3-kinase activity was evaluated byin vitrokinase assay.

Results: Subtoxic concentration of etxfag reduced L1210 cell adhesion to FN/V dependently of β1 integrin engagement. Etxfag impaired FN-dependent formation of β1 clustering without modifying β1 expression at the cell membrane. This was accompanied by a decrease of focal adhesion number, a diminution of fak and pyk2 phosphorylation at Tyr-576, Tyr-861 and Tyr-579, respectively leading to their dissociations from β1 integrin and inhibition of PI 3-kinase activity. Etxfag also induced a cell retraction accompanied by a redistribution of phosphorylated fak and pyk2 in the perinuclear region and lipid raft relocalization.

Conclusion: Through its anti-adhesive potential, etxfag, combined with conventional cytotoxic drugs could be potentially designed as a new anti-leukemic drug.
A New Overview of The Trilinos Project
Authors: Heroux Michael A. , Willenbring James M.
Published: January 2015

SinceAn Overview of the Trilinos Project[ACM Trans. Math. Softw. 31(3) (2005), 397–423] was published in 2005, Trilinos has grown significantly. It now supports the development of a broad collection of libraries for scalable computational science and engineering applications, and a full-featured software infrastructure for rigorous lean/agile software engineering. This growth has created significant opportunities and challenges. This paper focuses on some of the most notable changes to the Trilinos project in the last few years. At the time of the writing of this article, the current release version of Trilinos was 10.12.2.
Multispectral Enhancement Method to Increase the Visual Differences of Tissue Structures in Stained Histopathology Images
Authors: Bautista Pinky A. , Yagi Yukako
Published: January 2015

In this paper we proposed a multispectral enhancement scheme in which the spectral colors of the stained tissue-structure of interest and its background can be independently modified by the user to further improve their visualization and color discrimination. The colors of the background objects are modified by transforming theirN-band spectra through anNxNtransformation matrix, which is derived by mapping the representative samples of their original spectra to the spectra of their target colors using least mean square method. On the other hand, the color of the tissue structure of interest is modified by modulating the transformed spectra with the sum of the pixel’s spectral residual-errors at specific bands weighted through anNxNweighting matrix; the spectral error is derived by taking the difference between the pixel’s original spectrum and its reconstructed spectrum using the firstMdominant principal component vectors in principal component analysis. Promising results were obtained on the visualization of the collagen fiber and the non-collagen tissue structures, e.g., nuclei, cytoplasm and red blood cells (RBC), in a hematoxylin and eosin (H&E) stained image.
Context-Aware HCI Service Selection
Authors: Shen Yao , Wang Minjie , Tang Xiaoxin , Luo Yi , Guo Minyi
Published: January 2015

Context-awareness has become a key issue in Human-Computer Interaction(HCI) to provide better user experience under multi-device and multi-modal environment. With this intuition, we have proposed a web service based framework, which associates interactions with services, and provided service selection mechanism using context knowledge to achieve smart interaction migration [1]. A fundamental problem of such a service-oriented framework for interaction migration is to design an effective while scalable algorithm for service selection. In this paper, we propose a service selection algorithm considering not only context information and user preferences but also inter-service relations such as relative location. Our algorithm detects interaction hot spots within user active scope and presents the best service combination based on evaluation of interaction effectiveness. We also conduct simulation and the results illustrate that our algorithm is effective and scalable for interaction service selection.
Optimization of Complex Cancer Morphology Detection Using the SIVQ Pattern Recognition Algorithm
Authors: Hipp Jason , Smith Steven Christopher , Cheng Jerome , Tomlins Scott Arthur , Monaco James , Madabhushi Anant , Kunju Lakshmi Priya , Balis Ulysses J.
Published: January 2015

For personalization of medicine, increasingly clinical and demographic data are integrated into nomograms for prognostic use, while molecular biomarkers are being developed to add independent diagnostic, prognostic, or management information. In a number of cases in surgical pathology, morphometric quantitation is already performed manually or semi-quantitatively, with this effort contributing to diagnostic workup. Digital whole slide imaging, coupled with emerging image analysis algorithms, offers great promise as an adjunctive tool for the surgical pathologist in areas of screening, quality assurance, consistency, and quantitation. We have recently reported such an algorithm, SIVQ (Spatially Invariant Vector Quantization), which avails itself of the geometric advantages of ring vectors for pattern matching, and have proposed a number of potential applications. One key test, however, remains the need for demonstration and optimization of SIVQ for discrimination between foreground (neoplasm- malignant epithelium) and background (normal parenchyma, stroma, vessels, inflammatory cells). Especially important is the determination of relative contributions of each key SIVQ matching parameter with respect to the algorithm’s overall detection performance. Herein, by combinatorial testing of SIVQ ring size, sub-ring number, and inter-ring wobble parameters, in the setting of a morphologically complex bladder cancer use case, we ascertain the relative contributions of each of these parameters towards overall detection optimization using urothelial carcinoma as a use case, providing an exemplar by which this algorithm and future histology-oriented pattern matching tools may be validated and subsequently, implemented broadly in other appropriate microscopic classification settings.
The Prognostic Value of Adaptive Nuclear Texture Features from Patient Gray Level Entropy Matrices in Early Stage Ovarian Cancer
Authors: Nielsen Birgitte , Albregtsen Fritz , Kildal Wanja , Abeler Vera M. , Kristensen Gunnar B. , Danielsen Håvard E.
Published: January 2015

Background: Nuclear texture analysis gives information about the spatial arrangement of the pixel gray levels in a digitized microscopic nuclear image, providing texture features that may be used as quantitative tools for prognosis of human cancer. The aim of the study was to evaluate the prognostic value of adaptive nuclear texture features in early stage ovarian cancer.

Methods: 246 cases of early stage ovarian cancer were included in the analysis. Isolated nuclei (monolayers) were prepared from 50 μm tissue sections and stained with Feulgen-Schiff. Local gray level entropy was measured within small windows of each nuclear image and stored in gray level entropy matrices. A compact set of adaptive features was computed from these matrices.

Results: Univariate Kaplan-Meier analysis showed significantly better relapse-free survival (p < 0.001) for patients with low adaptive feature values compared to patients with high adaptive feature values. The 10-year relapse-free survival was about 78% for patients with low feature values and about 52% for patients with high feature values. Adaptive features were found to be of independent prognostic significance for relapse-free survival in a multivariate analysis.

Conclusion: Adaptive nuclear texture features from entropy matrices contain prognostic information and are of independent
prognostic significance for relapse-free survival in early stage ovarian cancer.
Book Review
Authors: Brown Adrian
Published: January 2015

The second edition ofComputational Physicsby Rubin Landau, Manuel Paez and Cristian C. Bordeianu (published by Wiley) hit bookshelves in 2007, and is steadily making its way into physics classrooms across the United States. Your reviewer first encountered the book at the Stanford Campus Book Store, where it is presumably being put to good use by students and faculty. The first edition was published in 1997 with Landau and Paez as authors [Computational Physics, 1st edn, Wiley, New York, 1997]. Rubin Landau is a very experienced computational physicist and staff member of the Oregon State University in Corvallis, where he directs theComputational Physicsfor Undergraduates course and teaches using this book. Landau is an incredibly active teacher to put it mildly – the code for the book is supplied in an accompanying DVD and he also posts applets and video lectures for his courses on his web page (http://www.physics.orst.edu/~rubin/).
Detection of Cross Site Scripting Attack in Wireless Networks Using n-Gram and SVM
Authors: Choi Jun-Ho , Choi Chang , Ko Byeong-Kyu , Kim Pan-Koo
Published: January 2015

Large parts of attacks targeting the web are aiming at the weak point of web application. Even though SQL injection, which is the form of XSS (Cross Site Scripting) attacks, is not a threat to the system to operate the web site, it is very critical to the places that deal with the important information because sensitive information can be obtained and falsified. In this paper, the method to detect themalicious SQL injection script code which is the typical XSS attack using n-Gram indexing and SVM (Support Vector Machine) is proposed. In order to test the proposed method, the test was conducted after classifying each data set as normal code and malicious code, and the malicious script code was detected by applying index term generated by n-Gram and data set generated by code dictionary to SVM classifier. As a result, when the malicious script code detection was conducted using n-Gram index term and SVM, the superior performance could be identified in detecting malicious script and the more improved results than existing methods could be seen in the malicious script code detection recall.
An Ultra-High Speed Whole Slide Image Viewing System
Authors: Yagi Yukako , Yoshioka Shigeatsu , Kyusojin Hiroshi , Onozato Maristela , Mizutani Yoichi , Osato Kiyoshi , Yada Hiroaki , Mark Eugene J. , Frosch Matthew P. , Louis David N.
Published: January 2015

Background: One of the goals for a Whole Slide Imaging (WSI) system is implementation in the clinical practice of pathology. One of the unresolved problems in accomplishing this goal is the speed of the entire process, i.e., from viewing the slides through making the final diagnosis. Most users are not satisfied with the correct viewing speeds of available systems. We have evaluated a new WSI viewing station and tool that focuses on speed.

Method: A prototype WSI viewer based on PlayStation®3 with wireless controllers was evaluated at the Department of Pathology at MGH for the following reasons: 1. For the simulation of signing-out cases; 2. Enabling discussion at a consensus conference; and 3. Use at slide seminars during a Continuing Medical Education course.

Results: Pathologists were being able to use the system comfortably after 0–15 min training. There were no complaints regarding speed. Most pathologists were satisfied with the functionality, usability and speed of the system. The most difficult situation was simulating diagnostic sign-out.

Conclusion: The preliminary results of adapting the Sony PlayStation®3 (PS3®) as an ultra-high speed WSI viewing system were promising. The achieved speed is consistent with what would be needed to use WSI in daily practice.
Constructing Workflows from Script Applications
Authors: Baranowski Mikołaj , Belloum Adam , Bubak Marian , Malawski Maciej
Published: January 2015

For programming and executing complex applications on grid infrastructures, scientific workflows have been proposed as convenient high-level alternative to solutions based on general-purpose programming languages, APIs and scripts. GridSpace is a collaborative programming and execution environment, which is based on a scripting approach and it extends Ruby language with a high-level API for invoking operations on remote resources. In this paper we describe a tool which enables to convert the GridSpace application source code into a workflow representation which, in turn, may be used for scheduling, provenance, or visualization. We describe how we addressed the issues of analyzing Ruby source code, resolving variable and method dependencies, as well as building workflow representation. The solutions to these problems have been developed and they were evaluated by testing them on complex grid application workflows such as CyberShake, Epigenomics and Montage. Evaluation is enriched by representing typical workflow control flow patterns.
Investigation and Identification of let-7a Related Functional Proteins in Gastric Carcinoma by Proteomics
Authors: Zhu Yimin , Xiao Xingyuan , Dong Lairong , Liu Zhiming
Published: January 2015

MicroRNAs are small noncoding RNA molecules that control expression of target genes. Our previous studies show that let-7a decreased in gastric carcinoma and that up-regulation of let-7a by gene augmentation inhibited gastric carcinoma cell growth bothin vitroandin vivo, whereas it remains largely unclear as to how let-7a affects tumor growth. In this study, proteins associated with the function of let-7a were detected by high throughout screening. The cell line of SGC-7901 stablely overexpressing let-7a was successfully established by gene cloning. Two-dimensional gel electrophoresis (2-DEy was used to separate the total proteins of SGC-7901/let-7a, SGC-7901/EV and SGC-7901, and PDQuest software was applied to analyze 2-DE images. Ten different protein spots were identified by MALDI-TOF-MS, and they may be the proteins associated with let-7a function. The overexpressed proteins included Antioxidant protein 2, Insulin–like growth factor binding protein 2, Protein disulfide isomerase A2, C-1-tetrahydrofolate synthase, Cyclin-dependent kinase inhibitor1 (CDKN1) and Rho–GTPase activating protein 4. The underexpressed proteins consisted of S-phase kinase-associated protein 2 (Spk2), Platelet membrane glycoprotein, Fibronectin and Cks1 protein. Furthermore, the different expression levels of the partial proteins (CDKN1, Spk2 and Fibronectin) were confirmed by western blot analysis. The data suggest that these differential proteins are involved in a novel let-7a signal pathway and these findings provide the basis to investigate the functional mechanisms of let-7a in gastric carcinoma.
Using Computerized Workflow Simulations to Assess the Feasibility of Whole Slide Imaging Full Adoption in a High-Volume Histology Laboratory
Authors: McClintock David S. , Lee Roy E. , Gilbertson John R.
Published: January 2015

Background: Whole slide Imaging (WSI) has been touted by many as the future of pathology, with estimates of full adoption occurring sometime in the next 5 to 15 years. While WSI devices have become increasingly capable since their inception, there has been little consideration of how WSI will be implemented and subsequently affect the workflow of high volume histology laboratories.

Methods: Histology workflow process data was collected from a high-volume histology laboratory (Massachusetts General Hospital) and a process model developed using business process management software. Computerized workflow simulations were performed and total histology process time evaluated under a number of different WSI conditions.

Results: Total histology process time increased approximately 10-fold to 20-fold over baseline with the presence of one WSI robot in the histology workflow. Depending on the specifications of the WSI robot, anywhere from 9 to 14 WSI robots were required within the histology workflow to minimize the effects of WSI.

Conclusion: Placing a WSI robot into the current workflow of a high-volume histology laboratory with the intent of full adoption is not feasible. Implementing WSI without making significant changes to the current workflow of the histology laboratory would prove to be both disruptive and costly to surgical pathology.
Flexible Multi-Authority Attribute-Based Signature Schemes for Expressive Policy
Authors: Cao Dan , Zhao Baokang , Wang Xiaofeng , Su Jinshu
Published: January 2015

Attribute-based signature (ABS) is a new cryptographic primitive, in which a signer can sign a message with his attributes, and the verifier can only known whether the signer owns attributes satisfying his policy. Moreover, the signature cannot be forged by any user not having attributes satisfying the policy. ABS has many applications, such as anonymous authentication, and attribute-based messaging systems. But many applications may require a user obtaining attributes from different authorities, which calls for multi-authority ABS schemes.
A Scheduling Method to Reduce Waiting Time for Close-Range Broadcasting
Authors: Gotoh Yusuke , Yoshihisa Tomoki , Taniguchi Hideo , Kanazawa Masanori , Rahayu Wenny , Chen Yi-Ping Phoebe
Published: January 2015

Due to the recent popularization of digital broadcasting systems, close-range broadcasting using continuous media data, i.e. audio and video, has attracted great attention. For example, in a drama, after a user watches interesting content such as a highlight scene, he/she will watch the main program continuously. In close-range broadcasting, the necessary bandwidth for continuously playing the two types of data increases. Conventional methods reduce the necessary bandwidth by producing an effective broadcast schedule for continuous media data. However, these methods do not consider the broadcast schedule for two types of continuous media data. When the server schedules two types of continuous media data, waiting time that occurs from finishing the highlight scene to starting the main scene, may increase. In this paper, we propose a scheduling method to reduce the waiting time for close-range broadcasting. In our proposed method, by dividing two types of data and producing an effective broadcast schedule considering the available bandwidth, we can reduce the waiting time.
Cooperation as a Service in VANET: Implementation and Simulation Results
Authors: Mousannif Hajar , Khalil Ismail , Olariu Stephan
Published: January 2015

The past decade has witnessed the emergence of Vehicular Ad-hoc Networks (VANET), specializing from the well-known Mobile Ad Hoc Networks (MANET) to Vehicle-to-Vehicle (V2V) and Vehicle-to-Infrastructure (V2I) wireless communications. While the original motivation for Vehicular Networks was to promote traffic safety, recently it has become increasingly obvious that Vehicular Networks open new vistas for Internet access, providing weather or road condition, parking availability, distributed gaming, and advertisement. In previous papers [27,28], we introduced Cooperation as a Service (CaaS); a new service-oriented solution which enables improved and new services for the road users and an optimized use of the road network through vehicle's cooperation and vehicle-to-vehicle communications. The current paper is an extension of the first ones; it describes an improved version of CaaS and provides its full implementation details and simulation results. CaaS structures the network into clusters, and uses Content Based Routing (CBR) for intra-cluster communications and DTN (Delay–and disruption-Tolerant Network) routing for inter-cluster communications. To show the feasibility of our approach, we implemented and tested CaaS using Opnet modeler software package. Simulation results prove the correctness of our protocol and indicate that CaaS achieves higher performance as compared to an Epidemic approach.
Standardization Efforts of Digital Pathology in Europe
Authors: Rojo Marcial García , Daniel Christel , Schrader Thomas
Published: January 2015

Background: EURO-TELEPATH is a European COST Action IC0604. It started in 2007 and will end in November 2011. Its main objectives are evaluating and validating the common technological framework and communication standards required to access, transmit, and manage digital medical records by pathologists and other medical specialties in a networked environment.

Business Modelling: Working Group 1, “Business Modelling in Pathology,” has designed main pathology processes – Frozen Study, Formalin Fixed Specimen Study, Telepathology, Cytology, and Autopsy – using Business Process Modelling Notation (BPMN).

Informatics Standards in Pathology: Working Group 2 has been dedicated to promoting the application of informatics standards in pathology, collaborating with Integrating Healthcare Enterprise (IHE), Digital Imaging and Communications in Medicine (DICOM), Health Level Seven (HL7), and other standardization bodies.

Conclusion: Health terminology standardization research has become a topic of great interest. Future research work should focus on standardizing automatic image analysis and tissue microarrays imaging.
Performance Evaluation of WMN-GA for Different Mutation and Crossover Rates Considering Number of Covered Users Parameter
Authors: Oda Tetsuya , Barolli Admir , Xhafa Fatos , Barolli Leonard , Ikeda Makoto , Takizawa Makoto
Published: January 2015

Node placement problems have been long investigated in the optimization field due to numerous applications in location science and classification. Facility location problems are showing their usefulness to communication networks, and more especially from Wireless Mesh Networks (WMNs) field. Recently, such problems are showing their usefulness to communication networks, where facilities could be servers or routers offering connectivity services to clients. In this paper, we deal with the effect of mutation and crossover operators in GA for node placement problem. We evaluate the performance of the proposed system using different selection operators and different distributions of router nodes considering number of covered users parameter. The simulation results show that for Linear and Exponential ranking methods, the system has a good performance for all rates of crossover and mutation.
Multifractal Feature Descriptor for Histopathology
Authors: Atupelage Chamidu , Nagahashi Hiroshi , Yamaguchi Masahiro , Sakamoto Michiie , Hashiguchi Akinori
Published: January 2015

Background: Histologic image analysis plays an important role in cancer diagnosis. It describes the structure of the body tissues and abnormal structure gives the suspicion of the cancer or some other diseases. Observing the structural changes of these chaotic textures from the human eye is challenging process. However, the challenge can be defeat by forming mathematical descriptor to represent the histologic texture and classify the structural changes via a sophisticated computational method.

Objective: In this paper, we propose a texture descriptor to observe the histologic texture into highly discriminative feature space.

Methods: Fractal dimension describes the self-similar structures in different and more accurate manner than topological dimension. Further, the fractal phenomenon has been extended to natural structures (images) as multifractal dimension. We exploited the multifractal analysis to represent the histologic texture, which derive more discriminative feature space for classification.

Results: We utilized a set of histologic images (belongs to liver and prostate specimens) to assess the discriminative power of the multifractal features. The experiment was organized to classify the given histologic texture as cancer and non-cancer. The results show the discrimination capability of multifractal features by achieving approximately 95% of correct classification rate.

Conclusion: Multifractal features are more effective to describe the histologic texture. The proposed feature descriptor showed high classification rate for both liver and prostate data sample datasets.
Joint Redundant and Random Network Coding for Robust Video Transmission over Lossy Networks
Authors: Zhang Xingjun , Jing Cuiping , Tang Feilong , Fowler Scott , Cui Huali , Dong Xiaoshe
Published: January 2015

In this paper a novel unequal packet loss protection scheme R2NC based on low-triangular global coding matrix with ladder-shaped partition is presented, which combines redundant and random network coding for robust H.264/SVC video transmission. Firstly, the error-correcting capabilities of redundant network coding make our scheme resilient to loss. Secondly, the implementation of random network coding at the intermediate nodes with multiple input links can reduce the cost of network bandwidth, thus reducing the end-to-end delay for video transmission. Thirdly, the low-triangular global coding matrix with ladder-shaped partition is maintained throughout the R2NC processes to reduce the impact of global coding matrix's rank deficiency on video transmission and provide unequal erasure protection for H.264/SVC priority layers. The redundant network coding avoids the retransmission of lost packets and improves error-correcting capabilities of lost packets. Based only on the knowledge of the packet loss rates on the output links, the source node and intermediate nodes can make decisions for redundant network coding and random network coding (i.e., how much redundancy to add at this node). However, the redundancy caused by redundant network coding makes the network load increases. In order to improve network throughput, we performed random network coding at the intermediate nodes. Our approach is grounded on the overall distortion of reconstructed video minimization by optimizing the amount of redundancy assigned to each layer. The convex optimization model is constructed under the constraint of network coding and scalable video coding. Experimental results are shown to demonstrate the significant improvement of H.264/SVC video reconstruction quality with R2NC over packet lossy networks.
Mining Low-Variance Biclusters to Discover Coregulation Modules in Sequencing Datasets
Authors: Hu Zhen , Bhatnagar Raj
Published: January 2015

High-throughput sequencing (CHIP-Seq) data exhibit binding events with possible binding locations and their strengths, followed by interpretation of the locations of peaks. Recent methods tend to summarize all CHIP-Seq peaks detected within a limited up and down region of each gene into one real-valued score in order to quantify the probability of regulation in a region. Applying subspace clustering techniques on these scores can help discover important knowledge such as the potential co-regulation or co-factor mechanisms. The ideal biclusters generated would contain subsets of genes and transcription factors (TF) such that the cell-values in biclusters are distributed around a mean value with very low variance. Such biclusters would indicate TF sets regulating gene sets with very similar probability values. However, most existing biclustering algorithms neither enforce low variance as the desired property of a bicluster, nor use variance as a guiding metric while searching for the desirable biclusters. In this paper we present an algorithm that searches a space of all overlapping biclusters organized in a lattice, and uses an upper bound on variance values of biclusters as the guiding metric. We show the algorithm to be an efficient and effective method for discovering the possibly overlapping biclusters under pre-defined variance bounds. We present in this paper our algorithm, its results with synthetic, CHIP-Seq and motif datasets, and compare them with the results obtained by other algorithms to demonstrate the power and effectiveness of our algorithm.