bluuebunny/crossref_metadata_2025 huggingface dataset:
PetaShare: A Reliable, Efficient and Transparent Distributed Storage Management System
Authors: Kosar Tevfik , Akturk Ismail , Balman Mehmet , Wang Xinqi
Published: January 2015

Modern collaborative science has placed increasing burden on data management infrastructure to handle the increasingly large data archives generated. Beside functionality, reliability and availability are also key factors in delivering a data management system that can efficiently and effectively meet the challenges posed and compounded by the unbounded increase in the size of data generated by scientific applications. We have developed a reliable and efficient distributed data storage system, PetaShare, which spans multiple institutions across the state of Louisiana. At the back-end, PetaShare provides a unified name space and efficient data movement across geographically distributed storage sites. At the front-end, it provides light-weight clients the enable easy, transparent and scalable access. In PetaShare, we have designed and implemented an asynchronously replicated multi-master metadata system for enhanced reliability and availability, and an advanced buffering system for improved data transfer performance. In this paper, we present the details of our design and implementation, show performance results, and describe our experience in developing a reliable and efficient distributed data management system for data-intensive science.
Autonomic Management of Application Workflows on Hybrid Computing Infrastructure
Authors: Kim Hyunjoo , el-Khamra Yaakoub , Rodero Ivan , Jha Shantenu , Parashar Manish
Published: January 2015

In this paper, we present a programming and runtime framework that enables the autonomic management of complex application workflows on hybrid computing infrastructures. The framework is designed to address system and application heterogeneity and dynamics to ensure that application objectives and constraints are satisfied. The need for such autonomic system and application management is becoming critical as computing infrastructures become increasingly heterogeneous, integrating different classes of resources from high-end HPC systems to commodity clusters and clouds. For example, the framework presented in this paper can be used to provision the appropriate mix of resources based on application requirements and constraints. The framework also monitors the system/application state and adapts the application and/or resources to respond to changing requirements or environment. To demonstrate the operation of the framework and to evaluate its ability, we employ a workflow used to characterize an oil reservoir executing on a hybrid infrastructure composed of TeraGrid nodes and Amazon EC2 instances of various types. Specifically, we show how different applications objectives such as acceleration, conservation and resilience can be effectively achieved while satisfying deadline and budget constraints, using an appropriate mix of dynamically provisioned resources. Our evaluations also demonstrate that public clouds can be used to complement and reinforce the scheduling and usage of traditional high performance computing infrastructure.
Design of a Secure RFID Authentication Scheme Preceding Market Transactions
Authors: Chen Chin-Ling
Published: January 2015

In recent years, as RFID reader equipment is ever more widely deployed in handled devices, the importance of security problems among RFID reader, tags and server have obviously gained increased attention. However, there are still many security issues preceding transactions; these issues are well worth discussing. In this paper, we propose a novel authentication scheme, conforming EPC C1G2 standards, at a low implementation cost for market application. In order to achieve mutual authentication, the proposed scheme integrates fingerprint biometrics, related cryptology and a hash function mechanism to ensure the security of the transmitted messages. The proposed scheme also can resist known attacks.
Digital Pathology – Implementation Challenges in Low-Resource Countries
Authors: Fontelo Paul , Faustorilla John , Gavino Alex , Marcelo Alvin
Published: January 2015

Background: Medical education in pathology and histology in low-resource countries face many obstacles because of equipment cost and telecommunication deficiencies. Digital Pathology may provide solutions. We report student experience to virtual slides on a local network and a remote image server.

Methods: Using an iPad tablet device, fifty 3rd and 4th year medical students viewed digital pathology slides from a Web server at the National Library of Medicine and a mirror server on the local network.

Results: The quality of images from both servers was found to be satisfactory, but the local server was deemed faster and preferred by the participants in this study (p< 0.005).

Conclusions: Virtual slides on a local network server may provide solutions to equipment and technical obstacles and could enhance student learning in developing countries.
Color Standardization Method and System for Whole Slide Imaging Based on Spectral Sensing
Authors: Tani Shinsuke , Fukunaga Yasuhiro , Shimizu Saori , Fukunishi Munenori , Ishii Kensuke , Tamiya Kosei
Published: January 2015

In the field of whole slide imaging, the imaging device or staining process cause color variations for each slide that affect the result of image analysis made by pathologist. In order to stabilize the analysis, we developed a color standardization method and system as described below: 1) Color standardization method based on RGB imaging and multi spectral sensing, which utilize less band (16 bands) than conventional method (60 bands), 2) High speed spectral sensing module. As a result, we confirmed the following effect: 1) We confirmed the performance improvement of nucleus detection by the color standardization. And we can conduct without training data set which is needed in conventional method, 2) We can get detection performance of H&E component equivalent to conventional method (60 bands). And measurement process is more than 255 times faster.
Automating Embedded Analysis Capabilities and Managing Software Complexity in Multiphysics Simulation, Part I: Template-Based Generic Programming
Authors: Pawlowski Roger P. , Phipps Eric T. , Salinger Andrew G.
Published: January 2015

An approach for incorporating embedded simulation and analysis capabilities in complex simulation codes through template-based generic programming is presented. This approach relies on templating and operator overloading within the C++ language to transform a given calculation into one that can compute a variety of additional quantities that are necessary for many state-of-the-art simulation and analysis algorithms. An approach for incorporating these ideas into complex simulation codes through general graph-based assembly is also presented. These ideas have been implemented within a set of packages in the Trilinos framework and are demonstrated on a simple problem from chemical engineering.
FluorescenceIn SituHybridization (FISH) Signal Analysis Using Automated Generated Projection Images
Authors: Wang Xingwei , Chen Xiaodong , Li Yuhua , Liu Hong , Li Shibo , Zhang Roy R. , Zheng Bin
Published: January 2015

Fluorescencein situhybridization (FISH) tests provide promising molecular imaging biomarkers to more accurately and reliably detect and diagnose cancers and genetic disorders. Since current manual FISH signal analysis is low-efficient and inconsistent, which limits its clinical utility, developing automated FISH image scanning systems and computer-aided detection (CAD) schemes has been attracting research interests. To acquire high-resolution FISH images in a multi-spectral scanning mode, a huge amount of image data with the stack of the multiple three-dimensional (3-D) image slices is generated from a single specimen. Automated preprocessing these scanned images to eliminate the non-useful and redundant data is important to make the automated FISH tests acceptable in clinical applications. In this study, a dual-detector fluorescence image scanning system was applied to scan four specimen slides with FISH-probed chromosome X. A CAD scheme was developed to detect analyzable interphase cells and map the multiple imaging slices recorded FISH-probed signals into the 2-D projection images. CAD scheme was then applied to each projection image to detect analyzable interphase cells using an adaptive multiple-threshold algorithm, identify FISH-probed signals using a top-hat transform, and compute the ratios between the normal and abnormal cells. To assess CAD performance, the FISH-probed signals were also independently visually detected by an observer. The Kappa coefficients for agreement between CAD and observer ranged from 0.69 to 1.0 in detecting/counting FISH signal spots in four testing samples. The study demonstrated the feasibility of automated FISH signal analysis that applying a CAD scheme to the automated generated 2-D projection images.
Automated Sputum Cytometry for Detection of Intraepithelial Neoplasias in the Lung
Authors: Li Gerald , Guillaud Martial , LeRiche Jean , McWilliams Annette , Gazdar Adi , Lam Stephen , MacAulay Calum
Published: January 2015

Background: Despite the benefits of early lung cancer detection, no effective strategy for early screening and treatment exists, partly due to a lack of effective surrogate biomarkers. Our novel sputum biomarker, the Combined Score (CS), uses automated image cytometric analysis of ploidy and nuclear morphology to detect subtle intraepithelial changes that often precede lung tumours.

Methods: 2249 sputum samples from 1795 high-risk patients enrolled in ongoing chemoprevention trials were subjected to automated quantitative image cytometry after Feulgen-thionin staining. Samples from normal histopathology patients were compared against samples from carcinomain situ(CIS) and cancer patients to train the CS.

Results: CS correlates with several lung cancer risk factors, including histopathological grade, age, smoking status, and p53 and Ki67 immunostaining. At 50% specificity, CS detected 78% of all highest-risk subjects—those with CIS or worse plus those with moderate or severe dysplasia and abnormal nuclear morphology.

Conclusion: CS is a powerful yet minimally invasive tool for rapid and inexpensive risk assessment for the presence of precancerous lung lesions, enabling enrichment of chemoprevention trials with highest-risk dysplasias. CS correlates with other biomarkers, so CS may find use as a surrogate biomarker for patient assessment and as an endpoint in chemoprevention clinical trials.
A Distributed Approach to Continuous Monitoring of Constrained k-Nearest Neighbor Queries in Road Networks
Authors: Cho Hyung-Ju , Choe Seung-Kwon , Chung Tae-Sun
Published: January 2015

Given two positive parameters k and r, a constrained k-nearest neighbor (CkNN) query returns the k closest objects within a network distance r of the query location in road networks. In terms of the scalability of monitoring these CkNN queries, existing solutions based on central processing at a server suffer from a sudden and sharp rise in server load as well as messaging cost as the number of queries increases. In this paper, we propose a distributed and scalable scheme called DAEMON for the continuous monitoring of CkNN queries in road networks. Our query processing is distributed among clients (query objects) and server. Specifically, the server evaluates CkNN queries issued at intersections of road segments, retrieves the objects on the road segments between neighboring intersections, and sends responses to the query objects. Finally, each client makes its own query result using this server response. As a result, our distributed scheme achieves close-to-optimal communication costs and scales well to large numbers of monitoring queries. Exhaustive experimental results demonstrate that our scheme substantially outperforms its competitor in terms of query processing time and messaging cost.
Design Considerations for a Flexible Multigrid Preconditioning Library
Authors: Gaidamour Jérémie , Hu Jonathan , Siefert Chris , Tuminaro Ray
Published: January 2015

MueLu is a library within the Trilinos software project [An overview of Trilinos, Technical Report SAND2003-2927, Sandia National Laboratories, 2003] and provides a framework for parallel multigrid preconditioning methods for large sparse linear systems. While providing efficient implementations of modern multigrid methods based on smoothed aggregation and energy minimization concepts, MueLu is designed to be customized and extended. This article gives an overview of design considerations for the MueLu package: user interfaces, internal design, data management, usage of modern software constructs, leveraging Trilinos capabilities, linear algebra operations and advanced application.
Exploring Capabilities within ForTrilinos by Solving the 3D Burgers Equation
Authors: Morris Karla , Rouson Damian W.I. , Lemaster M. Nicole , Filippone Salvatore
Published: January 2015

We present the first three-dimensional, partial differential equation solver to be built atop the recently released, open-source ForTrilinos package (http://trilinos.sandia.gov/packages/fortrilinos). ForTrilinos currently provides portable, object-oriented Fortran 2003 interfaces to the C++ packages Epetra, AztecOO and Pliris in the Trilinos library and framework [ACM Trans. Math. Softw.31(3) (2005), 397–423]. Epetra provides distributed matrix and vector storage and basic linear algebra calculations. Pliris provides direct solvers for dense linear systems. AztecOO provides iterative sparse linear solvers. We demonstrate how to build a parallel application that encapsulates the Message Passing Interface (MPI) without requiring the user to make direct calls to MPI except for startup and shutdown. The presented example demonstrates the level of effort required to set up a high-order, finite-difference solution on a Cartesian grid. The example employs an abstract data type (ADT) calculus [Sci. Program.16(4) (2008), 329–339] that empowers programmers to write serial code that lower-level abstractions resolve into distributed-memory, parallel implementations. The ADT calculus uses compilable Fortran constructs that resemble the mathematical formulation of the partial differential equation of interest.
Sundance: High-Level Software for PDE-Constrained Optimization
Authors: Long Kevin , Boggs Paul T. , van Bloemen Waanders Bart G.
Published: January 2015

Sundance is a package in the Trilinos suite designed to provide high-level components for the development of high-performance PDE simulators with built-in capabilities for PDE-constrained optimization. We review the implications of PDE-constrained optimization on simulator design requirements, then survey the architecture of the Sundance problem specification components. These components allow immediate extension of a forward simulator for use in an optimization context. We show examples of the use of these components to develop full-space and reduced-space codes for linear and nonlinear PDE-constrained inverse problems.
Mitotic Figure Recognition: Agreement among Pathologists and Computerized Detector
Authors: Malon Christopher , Brachtel Elena , Cosatto Eric , Graf Hans Peter , Kurata Atsushi , Kuroda Masahiko , Meyer John S. , Saito Akira , Wu Shulin , Yagi Yukako
Published: January 2015

Despite the prognostic importance of mitotic count as one of the components of the Bloom – Richardson grade [3], several studies ([2, 9, 10]) have found that pathologists’ agreement on the mitotic grade is fairly modest. Collecting a set of more than 4,200 candidate mitotic figures, we evaluate pathologists' agreement on individual figures, and train a computerized system for mitosis detection, comparing its performance to the classifications of three pathologists. The system’s and the pathologists’ classifications are based on evaluation of digital micrographs of hematoxylin and eosin stained breast tissue. On figures where the majority of pathologists agree on a classification, we compare the performance of the trained system to that of the individual pathologists. We find that the level of agreement of the pathologists ranges from slight to moderate, with strong biases, and that the system performs competitively in rating the ground truth set. This study is a step towards automatic mitosis count to accelerate a pathologist's work and improve reproducibility.
A Comparison of Digitized Frozen Section and Smear Preparations for Intraoperative Neurotelepathology
Authors: Gould Peter V. , Saikali Stephan
Published: January 2015

Background: Intraoperative consultations in neuropathology are often assessed by smear preparations rather than by frozen sections. Both techniques are standard practice for light microscopic examination on site, but there is little data comparing these techniques in a telepathology setting.

Methods: Thirty cases of brain tumours submitted for intraoperative consultation at our institution between July and December 2010 were identified in which both frozen section and tissue smear preparations were available for digitization at 20× magnification. Slides were digitized using a Hamamatsu Nanozoomer 2.0 HT whole slide scanner, and resulting digital images were visualized at 1680 × 1050 pixel resolution with NDP. view software.

Results: The original intraoperative diagnosis was concordant with the sign out diagnosis in 29/30 cases; one tumeur was initially interpreted as a high grade glioma but proved to be a lymphoma at sign out.

Digitized frozen section slides were sufficient for diagnosis at 10× magnification in 27/30 cases. Digitized tissue smears were sufficient for diagnosis at 10× magnification in 28/30 cases. In two cases tumour was present on the tissue smear but not the frozen section (one case of recurrent astrocytoma, one case of meningeal carcinomatosis). In one case of lymphoma, tumour was present on frozen section only. These discrepancies were attributed to tissue sampling rather than image quality.

Examination of digitized slides at higher magnfication (20×) permitted confirmation of mitoses and Rosenthal fibers on tissue smear preparations, but did not change the primary diagnosis. Intra-slide variations in tissue thickness on smear preparations led to variable loss of focus in digitized images, but did not affect image quality in thinner areas of the smear or impede diagnosis.

Conclusion: Digitized tissue smears are suitable for intraoperative neurotelepathology and provide comparable information to digitized frozen sections at medium power magnification.
Histopathologic Patterns of Nervous System Tumors Based on Computer Vision Methods and Whole Slide Imaging (WSI)
Authors: Walkowski Slawomir , Szymas Janusz
Published: January 2015

Background: Making an automatic diagnosis based on virtual slides and whole slide imaging or even determining whether a case belongs to a single class, representing a specific disease, is a big challenge. In this work we focus on WHO Classification of Tumours of the Central Nervous System. We try to design a method which allows to automatically distinguish virtual slides which contain histopathologic patterns characteristic of glioblastoma – pseudopalisading necrosis and discriminate cases with neurinoma (schwannoma), which contain similar structures – palisading (Verocay bodies).

Methods: Our method is based on computer vision approaches like structural analysis and shape descriptors. We start with image segmentation in a virtual slide, find specific patterns and use a set of features which can describe pseudopalisading necrosis and distinguish it from palisades. Type of structures found in a slide decides about its classification.

Results: Described method is tested on a set of 49 virtual slides, captured using robotic microscope. Results show that 82% of glioblastoma cases and 90% of neurinoma cases were correctly identified by the proposed algorithm.

Conclusion: Our method is a promising approach to automatic detection of nervous system tumors using virtual slides.
Freegaming: Mobile, Collaborative, Adaptive and Augmented Exergaming
Authors: Görgü Levent , Campbell Abraham G. , McCusker Kealan , Dragone Mauro , O'Grady Michael J. , O'Connor Noel E. , O'Hare Gregory M. P.
Published: January 2015

Addressing the obesity epidemic that plagues many societies remains an outstanding public health issue. One innovative approach to addressing this problem is Exergaming. A combination of Exercise and Gaming, the objective is to motivate people participate in exercise regimes, usually in their home environment. In this article a more holistic interpretation of this exercise paradigm is proposed. Freegaming augments Exergaming in a number of key dimensions but especially through the promotion of games in outdoor mobile contexts and within a social environment. The design and implementation of a platform for Freegaming is described and illustrated through the description of a sample game.
A Routing Strategy for Non-Cooperation Wireless Multi-Hop Ad Hoc Networks
Authors: Tran Dung T. , Truong Trang T. M. , Le Thanh G.
Published: January 2015

Choosing routes such that the network lifetime is maximized in a wireless network with limited energy resources is a major routing problem in wireless multi-hop ad hoc networks. In this paper, we study the problem where participants are rationally selfish and non-cooperative. By selfish we designate the users who are ready to tamper with their source-routing (senders could choose intermediate nodes in the routing paths) or next hop selection strategies in order to increase the total number of packets transmitted, but do not try to harm or drop packets of the other nodes. The problem therefore amounts to a non-cooperative game. In the works [2,6,19,23], the authors show that the game admits Nash equilibria [1]. Along this line, we first show that if the cost function is linear, this game has pure-strategy equilibrium flow even though participants have different demands. However, finding a Nash equilibrium for a normal game is computationally hard [9]. In this work, inspired by mixed-strategy equilibrium, we propose a simple local routing algorithm called MIxed Path Routing protocol (MiPR). Using analysis and simulations, we show that MiPR drives the system to an equilibrium state where selfish participants do not have incentive to deviate. Moreover, MiPR significantly improves the network lifetime as compared to original routing protocols.
Reconfigurable and Parallelized Network Coding Decoder for VANETs
Authors: Kim Sunwoo , Ro Won W.
Published: January 2015

Network coding is a promising technique for data communications in wired and wireless networks. However, it places an additional computing overhead on the receiving node in exchange for the improved bandwidth. This paper proposes an FPGA-based reconfigurable and parallelized network coding decoder for embedded systems especially for vehicular ad hoc networks. In our design, rapid decoding process can be achieved by exploiting parallelism in the coefficient vector operations. The proposed decoder is implemented by using a modern Xilinx Virtex-5 device and its performance is evaluated considering the performance of the software decoding on various embedded processors. The performance on four different sizes of the coefficient matrix is measured and the decoding throughput of 18.3 Mbps for the size 16 × 16 and 6.5 Mbps for 128 × 128 has been achieved at the operating frequency of 64.5 MHz. Compared to the recent TEGRA 250 processor, the result obtained with128 × 128 coefficient matrix reaches up to 5.06 in terms of speedup.
Static Digital Telepathology: A Model for Diagnostic and Educational Support to Pathologists in the Developing World
Authors: Sohani Aliyah R. , Sohani Moez A.
Published: January 2015

Background: The practice of pathology in the developing world presents challenges in terms of limited resources, shortages of trained personnel, and lack of continuing education programs. Telepathology holds promise as a means of diagnostic and educational support.

Methods: We donated multiheaded teaching microscopes equipped with digital cameras to four hospitals in Eastern Africa and trained local pathologists on their use. Static images of challenging cases were posted on a web-based telepathology platform. A U.S.-based pathologist reviewed images in consultation with subspecialist colleagues.

Results: Over a period of 40 months, 109 cases were submitted for second opinion consultation, including 29 dermatopathology cases (26.6%), 14 hematopathology cases (12.8%), and 13 cases each (11.9%) in cytopathology and bone and soft tissue pathology. Static images enabled a complete or partial diagnosis in 100/109 cases (91.7%). Factors precluding a definitive diagnosis included absence of confirmatory immunophenotyping, technical issues, or lack of clinical history. Case responses included a diagnosis and discussion, including differential diagnosis, references, and treatment recommendations.

Conclusion: Static digital telepathology is a simple, cost-effective, reliable and efficient means to provide diagnostic and educational support to pathologists in the developing world. Additional training may help overcome technical factors precluding a definitive diagnosis in certain cases.
Storage Qos Provisioning for Execution Programming of Data-Intensive Applications
Authors: Słota Renata
Published: January 2015

In this paper a method for execution programming of data-intensive applications is presented. The method is based on storage Quality of Service (SQoS) provisioning. SQoS provisioning uses the semantic based storage monitoring based on a storage resources model and a storage performance management. Test results show the gain for the execution time when using the QStorMan toolkit which implements the presented method. Taking into account the SQoS provisioning opportunity on the one hand, and the increasingly growing user demands on the other hand, we believe that the execution programming of data-intensive applications can bring a new quality into the application execution.
Genetic Algorithms for Satellite Scheduling Problems
Authors: Xhafa Fatos , Sun Junzi , Barolli Admir , Biberaj Alexander , Barolli Leonard
Published: January 2015

Recently there has been a growing interest in mission operations scheduling problem. The problem, in a variety of formulations, arises in management of satellite/space missions requiring efficient allocation of user requests to make possible the communication between operations teams and spacecraft systems. Not only large space agencies, such as ESA (European Space Agency) and NASA, but also smaller research institutions and universities can establish nowadays their satellite mission, and thus need intelligent systems to automate the allocation of ground station services to space missions. In this paper, we present some relevant formulations of the satellite scheduling viewed as a family of problems and identify various forms of optimization objectives. The main complexities, due highly constrained nature, windows accessibility and visibility, multi-objectives and conflicting objectives are examined. Then, we discuss the resolution of the problem through different heuristic methods. In particular, we focus on the version of ground station scheduling, for which we present computational results obtained with Genetic Algorithms using the STK simulation toolkit.
Predictive Role of Telomerase Activity in the Clinical Outcome of Patients with Benign Lesions of the Uterine Cervix or CIN
Authors: Bravaccini Sara , Amadori Andrea , Scarpi Emanuela , Tumedei Maria Maddalena , Zoli Wainer , Silvestrini Rosella
Published: January 2015

Telomerase, a fundamental marker of neoplastic transformation, is widely expressed in both premalignant intraepithelial lesions and in most malignant lesions of the uterine cervix. We determined telomerase activity (TA) in uterine cervix by Repeat Amplification Protocol (TRAP) in a series of 62 cases, 44 with benign diseases (inflammation and/or metaplasia and/or acanthosis) and 18 with cervical intraepithelial neoplasia (CIN). No significant differences in TA were observed between benign lesions (median AEU value 36, range 0–119) and CIN (median AEU value 30, range 0–65). Conversely, TA was significantly higher in subjects who showed CIN evolution (65 range 45–119) than in disease-free individuals (34 range 0–95,p= 0.017) and in 1 patient with a CIN2 lesion who relapsed after 5 years. Our results suggest that TA of the uterine cervix is capable of predicting CIN evolution or relapse, thus indicating its potential usefulness as a prognostic marker in clinical surveillance programs.
The Challenges of Implementing a “Patient-Oriented” Telepathology Network; the Eastern Québec Telepathology Project Experience
Authors: Têtu Bernard , Fortin Jean-Paul , Gagnon Marie-Pierre , Louahlia Said
Published: January 2015

Background: The aim of the Eastern Québec telepathology project is to provide uniform diagnostic telepathology services across a huge geographic region with a low population density. This project is intended to provide surgeons and pathologists with frozen section and second opinion services anywhere and at any time across the entire region in order to avoid unnecessary patient transfer.

Methods: The project has been implemented in 21 sites, each equipped with a whole slide scanner, a macroscopy station, two videoconferencing devices and a viewer/case management and collaboration solution. Of the 21 sites, 6 are devoid of a pathology laboratory. Of the remaining 15 sites, two have no pathologists, 6 have one and 7 have two or more.

Results: The project has been successful and most appreciated by pathologists and surgeons. We report a number of challenges related to change management that we had to take into account in the course of implementation of this network. The challenges underscore the need for regular visits and active support to participating centers by the project team.

Conclusion: The Eastern Québec telepathology network is successful and improves medical care in this region. In the course of implementation, we encountered a number of challenges which required innovative solutions.
Modern Trends in Imaging IX: Biophotonics Techniques for Structural and Functional Imaging,In Vivo
Authors: Ardeshirpour Yasaman , Gandjbakhche Amir H. , Najafizadeh Laleh
Published: January 2015

In vivooptical imaging is being conducted in a variety of medical applications, including optical breast cancer imaging, functional brain imaging, endoscopy, exercise medicine, and monitoring the photodynamic therapy and progress of neoadjuvant chemotherapy. In the past three decades,in vivodiffuse optical breast cancer imaging has shown promising results in cancer detection, and monitoring the progress of neoadjuvant chemotherapy. The use of near infrared spectroscopy for functional brain imaging has been growing rapidly. In fluorescence imaging, the difference between autofluorescence of cancer lesions compared to normal tissues were used in endoscopy to distinguish malignant lesions from normal tissue or inflammation and in determining the boarders of cancer lesions in surgery. Recent advances in drugs targeting specific tumor receptors, such as AntiBodies (MAB), has created a new demand for developing non-invasivein vivoimaging techniques for detection of cancer biomarkers, and for monitoring their down regulations during therapy. Targeted treatments, combined with new imaging techniques, are expected to potentially result in new imaging and treatment paradigms in cancer therapy. Similar approaches can potentially be applied for the characterization of other disease-related biomarkers. In this chapter, we provide a review of diffuse optical and fluorescence imaging techniques with their application in functional brain imaging and cancer diagnosis.
Modern Trends in Imaging V: Optical Coherence Tomography for Rapid Tissue Screening and Directed Histological Sectioning
Authors: Jung Woonggyu , Boppart Stephen A.
Published: January 2015

In pathology, histological examination of the “gold standard” to diagnose various diseases. It has contributed significantly toward identifying the abnormalities in tissues and cells, but has inherent drawbacks when used for fast and accurate diagnosis. These limitations include the lack ofin vivoobservation in real time and sampling errors due to limited number and area coverage of tissue sections. Its diagnostic yield also varies depending on the ability of the physician and the effectiveness of any image guidance technique that may be used for tissue screening during excisional biopsy. In order to overcome these current limitations of histology-based diagnostics, there are significant needs for either complementary or alternative imaging techniques which perform non-destructive, high resolution, and rapid tissue screening. Optical coherence tomography (OCT) is an emerging imaging modality which allows real-time cross-sectional imaging with high resolutions that approach those of histology. OCT could be a very promising technique which has the potential to be used as an adjunct to histological tissue observation when it is not practical to take specimens for histological processing, when large areas of tissue need investigating, or when rapid microscopic imaging is needed. This review will describe the use of OCT as an image guidance tool for fast tissue screening and directed histological tissue sectioning in pathology.
Automating Embedded Analysis Capabilities and Managing Software Complexity in Multiphysics Simulation, Part II: Application to Partial Differential Equations
Authors: Pawlowski Roger P. , Phipps Eric T. , Salinger Andrew G. , Owen Steven J. , Siefert Christopher M. , Staten Matthew L.
Published: January 2015

A template-based generic programming approach was presented in Part I of this series of papers [Sci. Program. 20 (2012), 197–219] that separates the development effort of programming a physical model from that of computing additional quantities, such as derivatives, needed for embedded analysis algorithms. In this paper, we describe the implementation details for using the template-based generic programming approach for simulation and analysis of partial differential equations (PDEs). We detail several of the hurdles that we have encountered, and some of the software infrastructure developed to overcome them. We end with a demonstration where we present shape optimization and uncertainty quantification results for a 3D PDE application.
Glowbal IP: An Adaptive and Transparent IPv6 Integration in the Internet of Things
Authors: Jara Antonio J. , Zamora Miguel A. , Skarmeta Antonio
Published: January 2015

The Internet of Things (IoT) requires scalability, extensibility and a transparent integration of multi-technology in order to reach an efficient support for global communications, discovery and look-up, as well as access to services and information. To achieve these goals, it is necessary to enable a homogenous and seamless machine-to-machine (M2M) communication mechanism allowing global access to devices, sensors and smart objects. In this respect, the proposed answer to these technological requirements is called Glowbal IP, which is based on a homogeneous access to the devices/sensors offered by the IPv6 addressing and core network. Glowbal IP's main advantages with regard to 6LoWPAN/IPv6 are not only that it presents a low overhead to reach a higher performance on a regular basis, but also that it determines the session and identifies global access by means of a session layer defined over the application layer. Technologies without any native support for IP are thereby adaptable to IP e.g. IEEE 802.15.4 and Bluetooth Low Energy. This extension towards the IPv6 network opens access to the features and methods of the devices through a homogenous access based on WebServices (e.g. RESTFul/CoAP). In addition to this, Glowbal IP offers global interoperability among the different devices, and interoperability with external servers and users applications. All in all, it allows the storage of information related to the devices in the network through the extension of the Domain Name System (DNS) from the IPv6 core network, by adding the Service Directory extension (DNS-SD) to store information about the sensors, their properties and functionality. A step forward in network-based information systems is thereby reached, allowing a homogenous discovery, and access to the devices from the IoT. Thus, the IoT capabilities are exploited by allowing an easier and more transparent integration of the end users applications with sensors for the future evaluations and use cases.
Age Dependent Switching Role of Cyclin D1 in Breast Cancer
Authors: Rinaldi Carmela , Malara Natalia Maria , D’Angelo Rosalia , Sidoti Antonina , Leotta Attilio , Lio Santo , Caparello Basilio , Ruggeri Alessia , Mollace Vincenzo , Amato Aldo
Published: January 2015

Background: Cyclin D1 gene (CCND1) plays pivotal roles in the development of several human cancers, including breast cancer, functioning as an oncogene. The aim of this study was to better understand the molecular dynamics of ductal carcinomas with regard to proliferation and the ageing process.

Methods: 130 cases of ductal breast cancer in postmenopausal women, aged 52–96 in 3 age classes were selected. Tumoral tissues preserved in formaldehyde solution and subsequently embedded in paraffin were subjected to analysis Fluorescencein situHybridization (FISH), Reverse Transcription-Polymerase Chain Reaction (RT- PCR) and immuno-histochemical tests. The molecular variables studied were estimated in relation to the patients’ age.

Results: The results obtained suggest that the increment of the levels of cyclin D1 in intra-ductal breast tumors in older woman that we have examined is significantly associated with a lower proliferation rate.

Conclusion: Cyclin D1, which characterizes tumor in young women as molecular director involved in strengthening tumoral proliferation mechanisms, may be seen as a potential blocking molecular switch in corresponding tumours in old women.
Trilinos I/O Support (Trios)
Authors: Oldfield Ron A. , Sjaardema Gregory D. , Lofstead II Gerald F. , Kordenbrock Todd
Published: January 2015

Trilinos I/O Support (Trios) is a new capability area in Trilinos that serves two important roles: (1) it provides and supports I/O libraries used by in-production scientific codes; (2) it provides a research vehicle for the evaluation and distribution of new techniques to improve I/O on advanced platforms. This paper provides a brief overview of the production-grade I/O libraries in Trios as well as some of the ongoing research efforts that contribute to the experimental libraries in Trios.
Comprehensive Protection of Data-Partitioned Video for Broadband Wireless IPTV Streaming
Authors: Al-Jobouri Laith , Fleury Martin , Ghanbari Mohammed
Published: January 2015

This paper examines the threat to video streaming from slow and fast fading, traffic congestion, and channel packet drops. The proposed response is a combination of: rateless channel coding, which is adaptively applied; data-partitioned source coding to exploit prioritized packetization; and duplicate slice provision, which is the focus of the evaluation in this paper. The paper also considers the distribution of intra-refresh macroblocks as a means of avoiding sudden data rate increases. When error bursts occur, this paper shows that duplicate slices are certainly necessary but this provision is more effective for medium quality video than it is for high quality video. The percentage of intra-refresh macroblocks can be low and still reduce the impact of temporal error propagation.
How to Introduce Virtual Microscopy (VM) in Routine Diagnostic Pathology: Constraints, Ideas, and Solutions
Authors: Kayser Klaus , Borkenfeld Stephan , Kayser Gian
Published: January 2015

Context: Virtual microscopy which is the diagnostic work with digitized microscopic images in tissue – based diagnosis is in its childhood in being implemented in routine diagnosis. Until today, only a few pathology institutions take use of this new technology, although it is available since several years. Why?

Design: Virtual microscopy requires a new workflow organisation in the pathologist's diagnostic procedure. At a first view, the laboratory workflow seems to remain untouched to a high degree. However, the used laboratory information system (LIS), which is commonly built in a hierarchic order, has to be adjusted at its highest levels, i.e., diagnosis statement, quality evaluation, submission to the clinician (hospital information system), and feedback to the laboratory. Therefore, the laboratory's workflow is involved at all levels too, and the LIS has to be changed or adjusted to the requirements of VM. VM systems are usually equipped with a viewer that mimics the viewing of a conventional microscope, and do not offer access to sensitive nodes of the LIS. Similar, LIS are usually closed and fixed systems because of data security and certification demands. Thus, VM systems have to possess communication access at different LIS levels together with steering commands for the LIS in close association with the diagnostic quality and efficiency (for example demands for additional stains, immunohistochemical or quantitative image methods, etc.), as well as expert consultation, or panel discussion.

Outcome: An implementation of an open and active LIS – VM management system could significantly promote the introduction of VM into routine diagnostic surgical pathology. The management system has to coordinate and translate the demands of VM to LIS (and vice versa), and to assure the communication with HIS. Mandatory features include streaming of the laboratory workflow, feedback commands to LIS, as well as regulation of temporary priority levels.

Conclusion: A successful implementation of VM systems in routine tissue-based diagnosis requires communicative management systems as long as VM is considered to be a “stand alone system” that just mimics a conventional microscope.
Manycore Performance-Portability: Kokkos Multidimensional Array Library
Authors: Edwards H. Carter , Sunderland Daniel , Porter Vicki , Amsler Chris , Mish Sam
Published: January 2015

Large, complex scientific and engineering application code have a significant investment in computational kernels to implement their mathematical models. Porting these computational kernels to the collection of modern manycore accelerator devices is a major challenge in that these devices have diverse programming models, application programming interfaces (APIs), and performance requirements. The Kokkos Array programming model provides library-based approach to implement computational kernels that are performance-portable to CPU-multicore and GPGPU accelerator devices. This programming model is based upon three fundamental concepts: (1) manycore compute devices each with its own memory space, (2) data parallel kernels and (3) multidimensional arrays. Kernel execution performance is, especially for NVIDIA® devices, extremely dependent on data access patterns. Optimal data access pattern can be different for different manycore devices – potentially leading to different implementations of computational kernels specialized for different devices. The Kokkos Array programming model supports performance-portable kernels by (1) separating data access patterns from computational kernels through a multidimensional array API and (2) introduce device-specific data access mappings when a kernel is compiled. An implementation of Kokkos Array is available through Trilinos [Trilinos website, http://trilinos.sandia.gov/, August 2011].
Lung Cancer Survival Prediction using Ensemble Data Mining on Seer Data
Authors: Agrawal Ankit , Misra Sanchit , Narayanan Ramanathan , Polepeddi Lalith , Choudhary Alok
Published: January 2015

We analyze the lung cancer data available from the SEER program with the aim of developing accurate survival prediction models for lung cancer. Carefully designed preprocessing steps resulted in removal/modification/splitting of several attributes, and 2 of the 11 derived attributes were found to have significant predictive power. Several supervised classification methods were used on the preprocessed data along with various data mining optimizations and validations. In our experiments, ensemble voting of five decision tree based classifiers and meta-classifiers was found to result in the best prediction performance in terms of accuracy and area under the ROC curve. We have developed an on-line lung cancer outcome calculator for estimating the risk of mortality after 6 months, 9 months, 1 year, 2 year and 5 years of diagnosis, for which a smaller non-redundant subset of 13 attributes was carefully selected using attribute selection techniques, while trying to retain the predictive power of the original set of attributes. Further, ensemble voting models were also created for predicting conditional survival outcome for lung cancer (estimating risk of mortality after 5 years of diagnosis, given that the patient has already survived for a period of time), and included in the calculator. The on-line lung cancer outcome calculator developed as a result of this study is available at http://info.eecs.northwestern.edu:8080/LungCancerOutcomeCalculator/.
Balancing Image Quality and Compression Factor for Special Stains Whole Slide Images
Authors: Sharma Anurag , Bautista Pinky , Yagi Yukako
Published: January 2015

The objective is to find a practical balance between quality and performance for daily high volume whole slide imaging. We evaluated whole slide images created by various scanners at different compression factors to determine the best suitable quality factor (QF) needed for pathological images of special stains.

Method: We scanned two sets of eight special stains slides each at 0.50 μm/pixel resolution in Hamamatsu scanner at six and fiveQFlevels respectively to generate 72 images which were observed at a calibrated monitor by imaging specialists, a histo-technician, and a pathologist to find the most suitableQFlevel for special stains in digital slides.

Results: Most special stains images were acceptable at QF 30 except for the stain Reticulin where the lowest acceptableQFwas 50. The compression of images fromQF90 toQF50 reduced the size of the images by 62.73%.

Conclusion: 0.50 μm/pixel images atQF50 or above were found suitable 12 special stain.
A Localization Algorithm Based on AOA for Ad-Hoc Sensor Networks
Authors: Lee Yang Sun , Park Jang Woo , Barolli Leonard
Published: January 2015

Knowledge of positions of sensor nodes in Wireless Sensor Networks (WSNs) will make possible many applications such as asset monitoring, object tracking and routing. In WSNs, the errors may happen in the measurement of distances and angles between pairs of nodes in WSN and these errors will be propagated to different nodes, the estimation of positions of sensor nodes can be difficult and have huge errors. In this paper, we will propose localization algorithm based on both distance and angle to landmark. So, we introduce a method of incident angle to landmark and the algorithm to exchange physical data such as distances and incident angles and update the position of a node by utilizing multiple landmarks and multiple paths to landmarks.