TY - CONF TI - Systemic Issues in the Hart InterCivic and Premier Voting Systems: Reflections Following Project EVEREST AU - Butler, Kevin AU - Enck, William AU - Hursti, Harri AU - McLaughlin, Stephen AU - Traynor, Patrick AU - McDaniel, Patrick C2 - 2008/// C3 - Proceedings of the USENIX/ACCURATE Electronic Voting Technology (EVT) Workshop DA - 2008/// ER - TY - CONF TI - Realizing massive-scale conditional access systems through attribute-based cryptosystems AU - Traynor, Patrick AU - Butler, Kevin AU - Enck, William AU - McDaniel, Patrick C2 - 2008/// C3 - In Proceedings of the ISOC Network & Distributed System Security Symposium (NDSS) DA - 2008/// ER - TY - JOUR TI - Privacy Preserving Web-based Email AU - Butler, Kevin RB AU - Enck, William AU - Traynor, Patrick AU - Plasterr, Jennifer AU - McDaniel, Patrick D T2 - Algorithms, Architectures and Information Systems Security AB - Recent web-based applications offer users free service in exchange for access to personal communication, such as on-line email services and instant messaging. The inspection and retention of user communication is generally intended to enable targeted marketing. However, unless specifically stated otherwise by the collecting service’s privacy policy, such records have an indefinite lifetime and may be later used or sold without restriction. In this paper, we show that it is possible to protect a user’s privacy from these risks by exploiting mutually oblivious, competing communication channels. We create virtual channels over online services (e.g., Google’s Gmail, Microsoft’s Hotmail) through which messages and cryptographic keys are delivered. The message recipient uses a shared secret to identify the shares and ultimately recover the original plaintext. In so doing, we create a wired “spread-spectrum” mechanism for protecting the privacy of web-based communication. We discuss the design and implementation of our open-source Java applet, Aquinas, and consider ways that the myriad of communication channels present on the Internet can be exploited to preserve privacy. DA - 2008/// PY - 2008/// DO - 10.1007/11961635_8 VL - 3 SP - 349 ER - TY - CONF TI - Pinup: Pinning user files to known applications AU - Enck, William AU - McDaniel, Patrick AU - Jaeger, Trent T2 - IEEE C2 - 2008/// C3 - 2008 Annual Computer Security Applications Conference (ACSAC) DA - 2008/// SP - 55-64 ER - TY - JOUR TI - Mitigating Android software misuse before it happens AU - Enck, William AU - Ongtang, Machigar AU - McDaniel, Patrick T2 - Pennsylvania State University, Tech. Rep. NAS-TR-0094-2008 DA - 2008/// PY - 2008/// ER - TY - JOUR TI - Exploiting open functionality in SMS-capable cellular networks AU - Traynor, Patrick AU - Enck, William AU - Mcdaniel, Patrick AU - La Porta, Thomas T2 - Journal of Computer Security DA - 2008/// PY - 2008/// VL - 16 IS - 6 SP - 713-742 ER - TY - CONF TI - Defending against attacks on main memory persistence AU - Enck, William AU - Butler, Kevin AU - Richardson, Thomas AU - McDaniel, Patrick AU - Smith, Adam T2 - IEEE C2 - 2008/// C3 - 2008 Annual Computer Security Applications Conference (ACSAC) DA - 2008/// SP - 65-74 ER - TY - RPRT TI - A measurement framework of alert characteristics for false positive mitigation models AU - Heckman, Sarah Smith AU - Williams, Laurie Ann A3 - North Carolina State University. Dept. of Computer Science DA - 2008/// PY - 2008/// PB - North Carolina State University. Dept. of Computer Science ER - TY - CONF TI - On establishing a benchmark for evaluating static analysis alert prioritization and classification techniques AU - Heckman, Sarah AU - Williams, Laurie T2 - ACM C2 - 2008/// C3 - Proceedings of the Second ACM-IEEE international symposium on Empirical software engineering and measurement DA - 2008/// SP - 41-50 ER - TY - BOOK TI - Traffic Grooming for Optical Networks A3 - Dutta, Rudra A3 - Kamal, Ahmed E. A3 - Rouskas, George N. AB - The objective of this book is to provide timely and comprehensive coverage of the principles, technology, practice, and future of tra?c grooming in op- cal networks. Tra?c grooming considerations are DA - 2008/// PY - 2008/// DO - 10.1007/978-0-387-74518-3 PB - Springer US SN - 9780387745176 9780387745183 UR - http://dx.doi.org/10.1007/978-0-387-74518-3 ER - TY - CHAP TI - Hierarchical Traffic Grooming AU - Rouskas, George N. AU - Dutta, Rudra T2 - Optical Networks A2 - Dutta, Rudra A2 - Kamal, Ahmed E. A2 - Rouskas, George N. PY - 2008/// DO - 10.1007/978-0-387-74518-3_6 SP - 73-88 PB - Springer US SN - 9780387745176 9780387745183 UR - http://dx.doi.org/10.1007/978-0-387-74518-3_6 ER - TY - ER - TY - ER - TY - CONF TI - State extensions for java pathfinder AU - Gvero, Tihomir AU - Gligoric, Milos AU - Lauterburg, Steven AU - d’Amorim, Marcelo AU - Marinov, Darko AU - Khurshid, Sarfraz AB - Java PathFinder (JPF) is an explicit-state model checker for Java programs. JPF implements a backtrackable Java Virtual Machine (JVM) that provides non-deterministic choices and control over thread scheduling. JPF is itself implemented in Java and runs on top of a host JVM. JPF represents the JVM state of the program being checked and performs three main operations on this state representation: bytecode execution, state backtracking, and state comparison. This paper summarizes four extensions that we have developed to the JPF state representation and operations. One extension provides a new functionality to JPF, and three extensions improve performance of JPF in various scenarios. Some of our code has already been included in publicly available JPF. C2 - 2008/// C3 - 30th International Conference on Software Engineering (ICSE 2008), Leipzig, Germany, May 10-18, 2008 DA - 2008/// DO - 10.1145/1368088.1368224 SP - 863-866 UR - http://doi.acm.org/10.1145/1368088.1368224 ER - TY - JOUR TI - Delta Execution for Efficient State-Space Exploration of Object-Oriented Programs AU - d’Amorim, Marcelo AU - Lauterburg, Steven AU - Marinov, Darko T2 - IEEE Trans. Software Eng. AB - We present Delta execution, a technique that speeds up state-space exploration of object-oriented programs. State-space exploration is the essence of model checking and an increasingly popular approach for automating test generation. A key issue in exploration of object-oriented programs is handling the program state, in particular the heap. We exploit the fact that many execution paths in state-space exploration partially overlap. Delta execution simultaneously operates on several states/heaps and shares the common parts across the executions, separately executing only the "deltas" where the executions differ. We implemented Delta execution in two model checkers: JPF, a popular general-purpose model checker for Java programs, and BOX, a specialized model checker that we developed for efficient exploration of sequential Java programs. The results for bounded-exhaustive exploration of ten basic subject programs and one larger case study show that Delta execution reduces exploration time from 1.06x to 126.80x (with median 5.60x) in JPF and from 0.58x to 4.16x (with median 2.23x) in BOX. The results for a non-exhaustive exploration in JPF show that Delta execution reduces exploration time from 0.92x to 6.28x (with median 4.52x). DA - 2008/// PY - 2008/// DO - 10.1109/TSE.2008.37 VL - 34 IS - 5 SP - 597-613 UR - https://doi.org/10.1109/TSE.2008.37 ER - TY - CONF TI - 30th International Conference on Software Engineering (ICSE 2008), Leipzig, Germany, May 10-18, 2008 A2 - Sch\"a, Wilhelm C2 - 2008/// DA - 2008/// PB - ACM ER - TY - CHAP TI - On optimal sizing of tiered network services AU - Lv, Qian AU - Rouskas, George N. AU - IEEE T2 - 27th Ieee Conference on Computer Communications (Infocom), Vols 1-5 PY - 2008/// SP - 1-5 PB - SE - ER - TY - JOUR TI - Efficient resource management using advance reservations for heterogeneous Grids AU - Castillo, Claris AU - Rouskas, George N. AU - Harfoush, Khaled AU - IEEE T2 - 2008 Ieee International Symposium on Parallel & Distributed Processing, Vols 1-8 DA - 2008/// PY - 2008/// SP - 916-927 ER - TY - JOUR TI - Edge Reconfigurable Optical Network (ERON): Enabling Dynamic Sharing of Static Lightpaths AU - Karmous-Edwards, Gigi AU - Reeves, Douglas AU - Rouskas, George AU - Battestilli, Lina AU - Vegesna, Priyanka AU - Vishwanath, Arun AU - IEEE T2 - 2008 5th International Conference on Broadband Communications, Networks and Systems (Broadnets 2008) AB - In this paper, we propose an edge reconfigurable optical network as an intermediate step toward fully dynamic optical core network. ERON is an overlay-control network created by installing GMPLS-enabled MEMs optical switches at the edge of a core optical network composed of static lightpaths. We propose a network design algorithm that takes as input the key resource locations dispersed globally and a realistic traffic matrix from end-users and outputs a virtual topology comprised of the minimum required static lightpaths interconnected via ERON switches. This paper describes the key concepts involved in the design of an efficient ERON network combined with routing and reservation algorithms to assure low blocking probabilities. We also describe the management and control architecture and protocols required to provide end-user/application control of the dynamic lightpaths. DA - 2008/// PY - 2008/// DO - 10.1109/BROADNETS.2008.4769097 SP - 332-334 ER - TY - JOUR TI - A New Internet Architecture to Enable Software Defined Optics and Evolving Optical Switching Models AU - Rouskas, George N. AU - Dutta, Rudra AU - Baldine, Ilia AU - IEEE T2 - 2008 5th International Conference on Broadband Communications, Networks and Systems (Broadnets 2008) AB - The design of the SILO network architecture of fine-grain services was based on three fundamental principles. First, SILO generalizes the concept of layering and decouples layers from services, making it possible to introduce easily new functionality and innovations into the architecture. Second, cross-layer interactions are explicitly supported by extending the definition of a service to include control interfaces that can be tuned externally so as to modify the behavior of the service. The third principle is ldquodesign for change:ldquo the architecture does not dictate the services to be implemented, but provides mechanisms to introduce new services and compose them to perform specific communication tasks. In this paper, we provide an update on the current status of the architecture and the prototype software implementation. We also introduce the concept of ldquosoftware defined opticsrdquo (SDO) to refer to the emerging intelligent and programmable optical layer. We then explain how the SILO architecture may enable the rapid adoption of SDO functionality as well as evolving optical switching models, in particular, optical burst switching (OBS). DA - 2008/// PY - 2008/// DO - 10.1109/BROADNETS.2008.4769046 SP - 71-76 ER - TY - JOUR TI - A Hierarchical Model for Multigranular Optical Networks AU - Iyer, Mohan AU - Rouskas, George N. AU - Dutta, Rudra AU - IEEE T2 - 2008 5th International Conference on Broadband Communications, Networks and Systems (Broadnets 2008) AB - We present a hierarchical algorithm for grooming lightpaths into wavebands, and routing wavebands over a network of multigranular switching nodes. This algorithm focuses on lowering the number of wavelengths W and ports over the network while being conceptually simple, scalable, and consistent with the way networks are operated and controlled in practice. Our experiments indicate that this algorithm easily scales across different waveband and network sizes. DA - 2008/// PY - 2008/// DO - 10.1109/BROADNETS.2008.4769124 SP - 444-451 ER - TY - RPRT TI - THU and ICRC at TRECVID 2008 AU - Liang, Yingyu AU - Liu, Xiaobing AU - Wang, Zhikun AU - Li, Jiammin AU - Cao, Binbin AU - Cao, Zhichao AU - Dai, Zhenlong AU - Guo, Zhishan AU - Li, Wen AU - Luo, Leigang AU - Meng, Zhaoshi AU - Qin, Yinfeng AU - Qiu, Shi AU - Tian, Arbo AU - Wang, Dong AU - Wang, Qiuping AU - Zhu, Chenguang AU - Hu, Xiaolin AU - Yuan, Jinhui AU - Yuan, Peijiang AU - Zhang, Bo AU - Chen, Shi AU - Li, JianGuo AU - Wang, Tao AU - Zhang, Yimin A3 - National Institute of Standards and Technology DA - 2008/// PY - 2008/// PB - National Institute of Standards and Technology ER - TY - CONF TI - Longboard: A sketch based intelligent storyboarding tool for creating machinima AU - Jhala, A. AU - Rawls, C. AU - Munilla, S. AU - Young, R.M. C2 - 2008/// C3 - Proceedings of the 21th International Florida Artificial Intelligence Research Society Conference, FLAIRS-21 DA - 2008/// SP - 386-391 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-55849084267&partnerID=MN8TOARS ER - TY - CONF TI - Automatically generating summary visualizations from game logs AU - Cheong, Y.-G. AU - Jhala, A. AU - Bae, B.-C. AU - Young, R.M. C2 - 2008/// C3 - Proceedings of the 4th Artificial Intelligence and Interactive Digital Entertainment Conference, AIIDE 2008 DA - 2008/// SP - 167-172 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84858960339&partnerID=MN8TOARS ER - TY - JOUR TI - Special issue: QoS, control, and security in next generation networks AU - Pujolle, Guy AU - Perros, Harry T2 - Telecommunication Systems DA - 2008/9/19/ PY - 2008/9/19/ DO - 10.1007/S11235-008-9121-1 VL - 39 IS - 3-4 SP - 169-169 J2 - Telecommun Syst LA - en OP - SN - 1018-4864 1572-9451 UR - http://dx.doi.org/10.1007/S11235-008-9121-1 DB - Crossref ER - TY - CONF TI - Advance Reservation and Dynamic Scheduling of Point to Multipoint Lightpaths AU - Arshad, Faraz AU - Ramay, Sarfraz Rasheed AU - Tanwir, Savera AU - Battestilli, Lina AU - Zaidi, S. M. H T2 - 2008 International Symposium on High Capacity Optical Networks and Enabling Technologies (HONET) AB - Advance reservation is a technique employed so that a request is guaranteed 100% availability of the resource it applied for sometimes earlier. In this paper we introduce the concept of advance reservation of lightpaths for a certain request characterized by some source and multiple destinations and also the time when network resources are demanded. We first present a point to multipoint adaptive routing algorithm that forms the basis of establishing lightpaths. Then the lightpaths are in fixed on the route through a wavelength assignment technique that works along with an advance reservation scheme to ensure conflict resolution among incoming requests. Based on our algorithm, we run our simulation model to generate results and exemplify the fact that advance reservation outruns on-demand reservation as far as the blocking probability is concerned. C2 - 2008/11// C3 - 2008 International Symposium on High Capacity Optical Networks and Enabling Technologies DA - 2008/11// DO - 10.1109/honet.2008.4810211 PB - IEEE SN - 9781424429608 UR - http://dx.doi.org/10.1109/honet.2008.4810211 DB - Crossref ER - TY - RPRT TI - Cross-Input Learning and Discriminative Prediction in Evolvable Virtual Machines AU - Mao, Feng AU - Shen, Xipeng A3 - Computer Science Department, The College of William and Mary DA - 2008/// PY - 2008/// M1 - WM-CS-2008-06 PB - Computer Science Department, The College of William and Mary SN - WM-CS-2008-06 ER - TY - RPRT TI - A Cross-Input Adaptive Framework for GPU Program Optimization AU - Liu, Yixun AU - Zhang, Eddy Z. AU - Shen, Xipeng A3 - Computer Science Department, The College of William and Mary DA - 2008/// PY - 2008/// M1 - WM-CS-2008-09 PB - Computer Science Department, The College of William and Mary SN - WM-CS-2008-09 ER - TY - RPRT TI - LU Decomposition on Cell Broadband Engine AU - Mao, Feng AU - Shen, Xipeng A3 - Computer Science Department, The College of William and Mary DA - 2008/// PY - 2008/// M1 - WM-CS-2008-08 M3 - Technical Report PB - Computer Science Department, The College of William and Mary SN - WM-CS-2008-08 ER - TY - CONF TI - Trust in Agent Societies: 11th International Workshop, TRUST 2008, Estoril, Portugal, May 12 -13, 2008. Revised Selected and Invited Papers A2 - Falcone, Rino A2 - Barber, Suzanne A2 - Sabater-Mir, Jordi A2 - Singh, Munindar P. T3 - Lecture Notes in Computer Science AB - This special issue is the result of the selection and re-submission of advanced and revised versions of papers from the workshop on "Trust in Agent Societies" (11th edition), held in Estoril (Portugal C2 - 2008/// DA - 2008/// DO - 10.1007/978-3-540-92803-4 PB - Springer ER - TY - CONF TI - Proceedings of the 3rd International Workshop on Normative Multiagent Systems (NorMAS) A2 - Boella, Guido A2 - Pigozzi, Gabriella A2 - Singh, Munindar P. A2 - Verhagen, Harko C2 - 2008/7// DA - 2008/7// ER - TY - JOUR TI - Editorial, special issue, repeatable experiments in software engineering AU - Menzies, Tim T2 - Empirical Software Engineering DA - 2008/9/5/ PY - 2008/9/5/ DO - 10.1007/s10664-008-9087-3 VL - 13 IS - 5 SP - 469-471 J2 - Empir Software Eng LA - en OP - SN - 1382-3256 1573-7616 UR - http://dx.doi.org/10.1007/s10664-008-9087-3 DB - Crossref ER - TY - JOUR TI - Special issue on information retrieval for program comprehension AU - Etzkorn, Letha AU - Menzies, Tim T2 - Empirical Software Engineering AB - Welcome to the special issue on information retrieval for program comprehension (IR4PC). IR4PC employs various interdisciplinary information search techniques to examine the properties of both existing (legacy) and newly created software. IR4PC is important for software reuse, software maintenance and evolution, and reverse engineering, just to mention a few areas. Back in the 1980s and early 1990s, much program comprehension involved representing program code as control and data flow graphs. Recognizing program constructs was performed by comparing flow graphs to a plan library of known constructs (e.g. Rich and Waters 1989). However, formal non-heuristic approaches to program comprehension have been shown to be NP-hard and their success was often illustrated only in toy domains (Woods and Yang 1996). For this reason, heuristic approaches acquired new importance. In the 21st century, much program comprehension research has focused on applying various information retrieval techniques (e.g. text mining, LSI, knowledge-based NL understanding) to software. These new IR4PC semantic measures examine informal information in the tokens within the software itself (e.g. identifier names, function names and variable names, code comments) as well as the natural language content in external documentation such as software requirements documents or software design documents. In the past, IR4PC techniques have been successfully applied to (among other areas) static concept location (using information derived from informal tokens together with structural information such as call graphs to locate code sections that are related to given concepts), to determining whether a particular software component is reusable, to dynamic search or software reconnaissance (examining informal tokens along execution traces of program executed with and without a particular feature), to developer identification (determining which developer is the best one to perform a particular task), to bug location Empir Software Eng DOI 10.1007/s10664-008-9097-1 DA - 2008/10/21/ PY - 2008/10/21/ DO - 10.1007/s10664-008-9097-1 VL - 14 IS - 1 SP - 1-4 J2 - Empir Software Eng LA - en OP - SN - 1382-3256 1573-7616 UR - http://dx.doi.org/10.1007/s10664-008-9097-1 DB - Crossref ER - TY - CHAP TI - Exploiting Structure and Conventions of Movie Scripts for Information Retrieval and Text Mining AU - Jhala, Arnav T2 - Interactive Storytelling AB - Movie scripts are documents that describe the story, stage direction for actors and camera, and dialogue. Script writers, directors, and cinematographers have standardized the format and language that is used in script writing. Scripts contain a wealth of information about narrative patterns, character direction, blocking, and camera control that can be extracted for various applications in interactive storytelling. In this short paper, we propose the creation of an automatically annotated corpus of movie scripts and describe our initial efforts in automating script annotation. We first describe the parts of a movie script that can be automatically annotated and then describe the use of an existing language processing toolkit to automatically annotate specific parts of a movie script. PY - 2008/// DO - 10.1007/978-3-540-89454-4_27 VL - 5334 LNCS SP - 210-213 OP - PB - Springer Berlin Heidelberg SN - 9783540894247 9783540894544 UR - http://dx.doi.org/10.1007/978-3-540-89454-4_27 DB - Crossref ER - TY - CONF TI - Adaptive Software Speculation for Enhancing the Cost-Efficiency of Behavior-Oriented Parallelization AU - Jiang, Yunlian AU - Shen, Xipeng T2 - 2008 37th International Conference on Parallel Processing (ICPP) AB - Recently, software speculation has shown promising results in parallelizing complex sequential programs by exploiting dynamic high-level parallelism. The speculation however is cost-inefficient. Failed speculations may cause unnecessary shared resource contention, power consumption, and interference to co-running applications. In this work, we propose adaptive speculation and design two algorithms to predict the profitability of a speculation and dynamically disable and enable the speculation of a region. Experimental results demonstrate significant improvement of computation efficiency without performance degradation. The adaptive speculation can also enhance the usability of behavior-oriented parallelization by allowing more flexibility in labeling possibly parallel regions. C2 - 2008/9// C3 - 2008 37th International Conference on Parallel Processing DA - 2008/9// DO - 10.1109/icpp.2008.50 PB - IEEE UR - http://dx.doi.org/10.1109/icpp.2008.50 DB - Crossref ER - TY - CONF TI - Analysis and approximation of optimal co-scheduling on chip multiprocessors AU - Jiang, Yunlian AU - Shen, Xipeng AU - Chen, Jie AU - Tripathi, Rahul T2 - the 17th international conference AB - Cache sharing among processors is important for Chip Multiprocessors to reduce inter-thread latency, but also brings cache contention, degrading program performance considerably. Recent studies have shown that job co-scheduling can effectively alleviate the contention, but it remains an open question how to efficiently find optimal co-schedules. Solving the question is critical for determining the potential of a co-scheduling system. This paper presents a theoretical analysis of the complexity of co-scheduling, proving its NP-completeness. Furthermore, for a special case when there are two sharers per chip, we propose an algorithm that finds the optimal co-schedules in polynomial time. For more complex cases, we design and evaluate a sequence of approximation algorithms, among which, the hierarchical matching algorithm produces near-optimal schedules and shows good scalability. This study facilitates the evaluation of co-scheduling systems, as well as offers some techniques directly usable in proactive job co-scheduling. C2 - 2008/// C3 - Proceedings of the 17th international conference on Parallel architectures and compilation techniques - PACT '08 DA - 2008/// DO - 10.1145/1454115.1454146 PB - ACM Press SN - 9781605582825 UR - http://dx.doi.org/10.1145/1454115.1454146 DB - Crossref KW - co-scheduling KW - CMP scheduling KW - cache contention KW - perfect matching ER - TY - CHAP TI - Graph Summaries for Subgraph Frequency Estimation AU - Maduko, Angela AU - Anyanwu, Kemafor AU - Sheth, Amit AU - Schliekelman, Paul T2 - The Semantic Web: Research and Applications. ESWC 2008. A2 - Bechhofer, S. A2 - Hauswirth, M. A2 - Hoffmann, J. A2 - Koubarakis, M. T3 - Lecture Notes in Computer Science AB - A fundamental problem related to graph structured databases is searching for substructures. One issue with respect to optimizing such searches is the ability to estimate the frequency of substructures within a query graph. In this work, we present and evaluate two techniques for estimating the frequency of subgraphs from a summary of the data graph. In the first technique, we assume that edge occurrences on edge sequences are position independent and summarize only the most informative dependencies. In the second technique, we prune small subgraphs using a valuation scheme that blends information about their importance and estimation power. In both techniques, we assume conditional independence to estimate the frequencies of larger subgraphs. We validate the effectiveness of our techniques through experiments on real and synthetic datasets. PY - 2008/5/23/ DO - 10.1007/978-3-540-68234-9_38 SP - 508–523 PB - Springer SN - 9783540682332 9783540682349 SV - 5021 UR - http://dx.doi.org/10.1007/978-3-540-68234-9_38 ER - TY - CONF TI - Linear-size meshes AU - Miller, Gary L. AU - Phillips, Todd AU - Sheehy, Donald R. T2 - Canadian Conference in Computational Geometry C2 - 2008/// C3 - CCCG: The Canadian Conference in Computational Geometry CY - Montreal, Quebec, Canada DA - 2008/// PY - 2008/8/13/ ER - TY - CONF TI - Achieving Spatial Adaptivity while Finding Approximate Nearest Neighbors AU - Derryberry, Jonathan AU - Sleator, Daniel D. AU - Sheehy, Donald R. AU - Woo, Maverick T2 - Canadian Conference in Computational Geometry C2 - 2008/// C3 - CCCG: The Canadian Conference in Computational Geometry CY - Montreal, Quebec, Canada DA - 2008/// PY - 2008/8/13/ ER - TY - JOUR TI - Dynamic scheduling of network resources with advance reservations in optical grids AU - Tanwir, Savera AU - Battestilli, Lina AU - Perros, Harry AU - Karmous-Edwards, Gigi T2 - International Journal of Network Management AB - Abstract Advance reservation of lightpaths in grid environments is necessary to guarantee QoS and reliability. In this paper, we have evaluated and compared several algorithms for dynamic scheduling of lightpaths using a flexible advance reservation model. The main aim is to find the best scheduling policy for a grid network resource manager that improves network utilization and minimizes blocking. The scheduling of lightpaths involves both routing and wavelength assignment. Our simulation results show that minimum‐cost adaptive routing where link costs are determined by the current and future usage of the link provides the minimum blocking. For wavelength assignment, we have used a scheme that reduces fragmentation by minimizing unused gaps. We have also analyzed approaches for failure recovery and resource optimization. Copyright © 2008 John Wiley & Sons, Ltd. DA - 2008/3// PY - 2008/3// DO - 10.1002/nem.680 VL - 18 IS - 2 SP - 79-105 J2 - Int. J. Network Mgmt. LA - en OP - SN - 1055-7148 1099-1190 UR - http://dx.doi.org/10.1002/nem.680 DB - Crossref ER - TY - CHAP TI - Scalable Implementation of Efficient Locality Approximation AU - Shen, Xipeng AU - Shaw, Jonathan T2 - Languages and Compilers for Parallel Computing AB - As memory hierarchy becomes deeper and shared by more processors, locality increasingly determines system performance. As a rigorous and precise locality model, reuse distance has been used in program optimizations, performance prediction, memory disambiguation, and locality phase prediction. However, the high cost of measurement has been severely impeding its uses in scenarios requiring high efficiency, such as product compilers, performance debugging, run-time optimizations. We recently discovered the statistical connection between time and reuse distance, which led to an efficient way to approximate reuse distance using time. However, not exposed are some algorithmic and implementation techniques that are vital for the efficiency and scalability of the approximation model. This paper presents these techniques. It describes an algorithm that approximates reuse distance on arbitrary scales; it explains a portable scheme that employs memory controller to accelerate the measure of time distance; it uncovers the algorithm and proof of a trace generator that can facilitate various locality studies. PY - 2008/// DO - 10.1007/978-3-540-89740-8_14 SP - 202-216 OP - PB - Springer Berlin Heidelberg SN - 9783540897392 9783540897408 UR - http://dx.doi.org/10.1007/978-3-540-89740-8_14 DB - Crossref ER - TY - CHAP TI - A Learning Scheme for Recognizing Sub-classes from Model Trained on Aggregate Classes AU - Vatsavai, Ranga Raju AU - Shekhar, Shashi AU - Bhaduri, Budhendra T2 - Lecture Notes in Computer Science AB - In many practical situations it is not feasible to collect labeled samples for all available classes in a domain. Especially in supervised classification of remotely sensed images it is impossible to collect ground truth information over large geographic regions for all thematic classes. As a result often analysts collect labels for aggregate classes. In this paper we present a novel learning scheme that automatically learns sub-classes from the user given aggregate classes. We model each aggregate class as finite Gaussian mixture instead of classical assumption of unimodal Gaussian per class. The number of components in each finite Gaussian mixture are automatically estimated. Experimental results on real remotely sensed image classification showed not only improved accuracy in aggregate class classification but the proposed method also recognized sub-classes. PY - 2008/// DO - 10.1007/978-3-540-89689-0_100 SP - 967-976 OP - PB - Springer Berlin Heidelberg SN - 9783540896883 9783540896890 UR - http://dx.doi.org/10.1007/978-3-540-89689-0_100 DB - Crossref ER - TY - CHAP TI - Exploration of the Influence of Program Inputs on CMP Co-scheduling AU - Jiang, Yunlian AU - Shen, Xipeng T2 - Lecture Notes in Computer Science AB - Recent studies have showed the effectiveness of job co-scheduling in alleviating shared-cache contention on Chip Multiprocessors. Although program inputs affect cache usage and thus cache contention significantly, their influence on co-scheduling remains unexplored. In this work, we measure that influence and show that the ability to adapt to program inputs is important for a co-scheduler to work effectively on Chip Multiprocessors. We then conduct an exploration in addressing the influence by constructing cross-input predictive models for some memory behaviors that are critical for a recently proposed co-scheduler. The exploration compares the effectiveness of both linear and non-linear regression techniques in the model building. Finally, we conduct a systematic measurement of the sensitivity of co-scheduling on the errors of the predictive behavior models. The results demonstrate the potential of the predictive models in guiding contention-aware co-scheduling. PY - 2008/8/19/ DO - 10.1007/978-3-540-85451-7_29 SP - 263-273 OP - PB - Springer Berlin Heidelberg SN - 9783540854500 9783540854517 UR - http://dx.doi.org/10.1007/978-3-540-85451-7_29 DB - Crossref ER - TY - CHAP TI - A Scalable Formal Framework for Analyzing the Behavior of Nature-Inspired Routing Protocols AU - Shahzad, Muhammad AU - Zahid, Saira AU - Farooq, Muddassar T2 - Parallel Problem Solving from Nature – PPSN X AB - Nature-inspired routing algorithms for fixed networks is an active area of research. In these algorithms, ant- or bee-agents are deployed for collecting the state of a network and providing them to autonomous and fully distributed controllers at each network node. In these routing systems the agents, through local interactions, self-organize to produce system-level behaviors which show adaptivity to changes and perturbations in the network environment. The formal modeling of such fully self-organizing, distributed and adaptive routing systems is a difficult task. In this paper, we propose a scalable formal framework that has following desirable features: (1) it models important performance metrics: throughput, delay and goodness of links, (2) it is scalable to any size of topology, (3) it is robust to changing network traffic conditions. The proposed framework is utilized to model a well-known BeeHive protocol which is further validated on NTTNeT (a 57 node topology). To the best of our knowledge, this is the first formal framework that has been validated on such a large topology. PY - 2008/// DO - 10.1007/978-3-540-87700-4_112 SP - 1130-1139 OP - PB - Springer Berlin Heidelberg SN - 9783540876991 9783540877004 UR - http://dx.doi.org/10.1007/978-3-540-87700-4_112 DB - Crossref ER - TY - JOUR TI - Learning better IV&V practices AU - Menzies, Tim AU - Benson, Markland AU - Costello, Ken AU - Moats, Christina AU - Northey, Melissa AU - Richardson, Julian T2 - Innovations in Systems and Software Engineering DA - 2008/2/22/ PY - 2008/2/22/ DO - 10.1007/S11334-008-0046-3 VL - 4 IS - 2 SP - 169-183 J2 - Innovations Syst Softw Eng LA - en OP - SN - 1614-5046 1614-5054 UR - http://dx.doi.org/10.1007/S11334-008-0046-3 DB - Crossref KW - IV&V KW - Data mining KW - Early life cycle defect prediction KW - NASA ER - TY - CHAP TI - Accurate Estimates without Calibration? AU - Menzies, Tim AU - Elrawas, Oussama AU - Boehm, Barry AU - Madachy, Raymond AU - Hihn, Jairus AU - Baker, Daniel AU - Lum, Karen T2 - Making Globally Distributed Software Development a Success Story PY - 2008/5/5/ DO - 10.1007/978-3-540-79588-9_19 SP - 210-221 OP - PB - Springer Berlin Heidelberg SN - 9783540795872 9783540795889 UR - http://dx.doi.org/10.1007/978-3-540-79588-9_19 DB - Crossref ER - TY - CHAP TI - Re-evaluating LARGO in the Classroom: Are Diagrams Better Than Text for Teaching Argumentation Skills? AU - Pinkwart, Niels AU - Lynch, Collin AU - Ashley, Kevin AU - Aleven, Vincent T2 - Intelligent Tutoring Systems AB - Diagrams appear to be a convenient vehicle for teaching argumentation skills in ill-defined domains, but can an ITS provide useful feedback on students’ argument diagrams without assuming a well-defined procedure for objectively evaluating argument? LARGO is an ITS for legal argumentation that supports students as they diagram transcripts of US Supreme Court oral argument. It provides on-demand advice by identifying small, interesting or incomplete patterns within students’ graphs. We conducted a study in which LARGO was used as mandatory part of a first-year law school class. In contrast to prior findings in lab studies with voluntary participants, the use of LARGO did not lead to superior learning as compared to a text-based note-taking tool. These results can be partially attributed to low use of the graphical tools and advice by the students as well as (and possibly due to) a different motivational focus. Some evidence was found that higher engagement with the system led to better learning, leaving open the tantalizing possibility of helping especially lower-aptitude students through use of LARGO. PY - 2008/8/12/ DO - 10.1007/978-3-540-69132-7_14 SP - 90-100 OP - PB - Springer Berlin Heidelberg SN - 9783540691303 9783540691327 UR - http://dx.doi.org/10.1007/978-3-540-69132-7_14 DB - Crossref ER - TY - CHAP TI - Eliminating the Gap between the High and Low Students through Meta-cognitive Strategy Instruction AU - Chi, Min AU - VanLehn, Kurt T2 - Intelligent Tutoring Systems AB - One important goal of Intelligent Tutoring Systems (ITSs) is to bring students up to the same level of mastery. We showed that an ITS teaching a domain-independent problem-solving strategy indeed closed the gap between High and Low learners, not only in the domain where it was taught (probability) but also in a second domain where it was not taught (physics). The strategy includes two main components: one is solving problems via Backward-Chaining (BC) from goals to givens, named the BC-strategy, and the other is drawing students’ attention on the characteristics of each individual domain principle, named the principle-emphasis skill. Evidence suggests that the Low learners transferred the principle-emphasis skill to physics while the High learners seemingly already had such skill and thus mainly transferred the other skill, the BC-strategy. Surprisingly, the former learned just as effectively as the latter in physics. We concluded that the effective element of the taught strategy seemed not to be the BC-Strategy, but the principle-emphasis skill. PY - 2008/8/12/ DO - 10.1007/978-3-540-69132-7_63 SP - 603-613 OP - PB - Springer Berlin Heidelberg SN - 9783540691303 9783540691327 UR - http://dx.doi.org/10.1007/978-3-540-69132-7_63 DB - Crossref ER - TY - JOUR TI - Locating sensors in paths and cycles: The case of 2-identifying codes AU - Roberts, David L. AU - Roberts, Fred S. T2 - European Journal of Combinatorics AB - For a graph G and a set D⊆V(G), define Nr[x]={xi∈V(G):d(x,xi)≤r} (where d(x,y) is graph theoretic distance) and Dr(x)=Nr[x]∩D. D is known as an r-identifying code if for every vertex x,Dr(x)≠0̸, and for every pair of vertices x and y, x≠y⇒Dr(x)≠Dr(y). The various applications of these codes include attack sensor placement in networks and fault detection/localization in multiprocessor or distributed systems. Bertrand et al. [N. Bertrand, I. Charon, O. Hudry, A. Lobstein, Identifying and locating–dominating codes on chains and cycles, European Journal of Combinatorics 25 (2004) 969–987] and Gravier et al. [S. Gravier, J. Moncel, A. Semri, Identifying codes of cycles, European Journal of Combinatorics 27 (2006) 767–776] provide partial results about the minimum size of D for r-identifying codes for paths and cycles and present complete closed form solutions for the case r=1, based in part on Daniel [M. Daniel, Codes identifiants, Rapport pour le DEA ROCO, Grenoble, June 2003]. We provide complete solutions for the case r=2. DA - 2008/1// PY - 2008/1// DO - 10.1016/j.ejc.2006.12.006 VL - 29 IS - 1 SP - 72-82 J2 - European Journal of Combinatorics LA - en OP - SN - 0195-6698 UR - http://dx.doi.org/10.1016/j.ejc.2006.12.006 DB - Crossref ER - TY - JOUR TI - Optimization problems involving collections of dependent objects AU - Roberts, David L. AU - Isbell, Charles L., Jr. AU - Littman, Michael L. T2 - Annals of Operations Research DA - 2008/4/24/ PY - 2008/4/24/ DO - 10.1007/S10479-008-0350-1 VL - 163 IS - 1 SP - 255-270 J2 - Ann Oper Res LA - en OP - SN - 0254-5330 1572-9338 UR - http://dx.doi.org/10.1007/S10479-008-0350-1 DB - Crossref ER - TY - CHAP TI - On the Use of Computational Models of Influence for Managing Interactive Virtual Experiences AU - Roberts, David L. AU - Isbell, Charles AU - Riedl, Mark AU - Bogost, Ian AU - Furst, Merrick L. T2 - Interactive Storytelling AB - We highlight some of the characteristics of existing technical approaches to the management of interactive experiences and motivate computational models of influence, a technique we are developing to aid drama managers in the persuasion of players to make decisions that are consistent with an author’s goals. Many of the existing approaches to managing interactive experiences have focused on the physical manipulation of the environment, but we argue instead for the use of theories from social psychology and behavioral economics to affect the adoption of specific goals by the player. PY - 2008/// DO - 10.1007/978-3-540-89454-4_34 SP - 268-272 OP - PB - Springer Berlin Heidelberg SN - 9783540894247 9783540894544 UR - http://dx.doi.org/10.1007/978-3-540-89454-4_34 DB - Crossref ER - TY - CHAP TI - Adaptive Request Scheduling for Parallel Scientific Web Services AU - Lin, Heshan AU - Ma, Xiaosong AU - Li, Jiangtian AU - Yu, Ting AU - Samatova, Nagiza T2 - Lecture Notes in Computer Science AB - Scientific web services often possess data models and query workloads quite different from commercial ones and are much less studied. Individual queries have to be processed in parallel by multiple server nodes, due to the computation- and data-intensiveness of the processing. Meanwhile, each query is performed against portions of a large, common dataset. Existing scheduling policies from traditional environments (namely cluster web servers and supercomputers) consider only the data or the computation aspect alone and are therefore inadequate for this new type of workload. In this paper, we systematically investigate adaptive scheduling for scientific web services, by taking into account parallel computation scalability, data locality, and load balancing. Our case study focuses on high-throughput query processing on biological sequence databases, a fundamental task performed daily by millions of scientists, who increasingly prefer to use web services powered by parallel servers. Our research indicates that intelligent resource allocation and scheduling are crucial in improving the overall performance of a parallel sequence database search server. Failure to consider either the parallel computation scalability or the data locality issues can significantly hurt the system throughput and query response time. Also, no single static strategy works best for all request workloads or all resources settings. In response, we present several dynamic scheduling techniques that automatically adapt to the request workload and system configuration in making scheduling decisions. Experiments on a cluster using 32 processors show the combination of these techniques delivers a several-fold improvement in average query response time across various workloads. PY - 2008/8/12/ DO - 10.1007/978-3-540-69497-7_19 SP - 276-294 OP - PB - Springer Berlin Heidelberg SN - 9783540694762 9783540694977 UR - http://dx.doi.org/10.1007/978-3-540-69497-7_19 DB - Crossref ER - TY - CHAP TI - The Buffered Work-Pool Approach for Search-Tree Based Optimization Algorithms AU - Abu-Khzam, Faisal N. AU - Rizk, Mohamad A. AU - Abdallah, Deema A. AU - Samatova, Nagiza F. T2 - Parallel Processing and Applied Mathematics PY - 2008/5/28/ DO - 10.1007/978-3-540-68111-3_19 SP - 170-179 OP - PB - Springer Berlin Heidelberg SN - 9783540681052 9783540681113 UR - http://dx.doi.org/10.1007/978-3-540-68111-3_19 DB - Crossref ER - TY - CHAP TI - Archetype-Driven Character Dialogue Generation for Interactive Narrative AU - Rowe, Jonathan P. AU - Ha, Eun Young AU - Lester, James C. T2 - Intelligent Virtual Agents AB - Recent years have seen a growing interest in creating virtual agents to populate the cast of characters for interactive narrative. A key challenge posed by interactive characters for narrative environments is devising expressive dialogue generators. To be effective, character dialogue generators must be able to simultaneously take into account multiple sources of information that bear on dialogue, including character attributes, plot development, and communicative goals. Building on the narrative theory of character archetypes, we propose an archetype-driven character dialogue generator that uses a probabilistic unification framework to generate dialogue motivated by character personality and narrative history to achieve communicative goals. The generator’s behavior is illustrated with character dialogue generation in a narrative-centered learning environment, Crystal Island. PY - 2008/8/23/ DO - 10.1007/978-3-540-85483-8_5 SP - 45-58 OP - PB - Springer Berlin Heidelberg SN - 9783540854821 9783540854838 UR - http://dx.doi.org/10.1007/978-3-540-85483-8_5 DB - Crossref ER - TY - CHAP TI - Story-Based Learning: The Impact of Narrative on Learning Experiences and Outcomes AU - McQuiggan, Scott W. AU - Rowe, Jonathan P. AU - Lee, Sunyoung AU - Lester, James C. T2 - Intelligent Tutoring Systems AB - Within the intelligent tutoring systems community, narrative is emerging as an effective medium for contextualizing learning. To date, relatively few empirical studies have been conducted to assess learning in narrative-centered learning environments. In this paper, we investigate the effect of narrative on learning experiences and outcomes. We present results from an experiment conducted with eighth-grade middle school students interacting with a narrative-centered learning environment in the domain of microbiology. The study found that students do exhibit learning gains, that those gains are less than those produced by traditional instructional approaches, but that the motivational benefits of narrative-centered learning with regard to self-efficacy, presence, interest, and perception of control are substantial. PY - 2008/8/12/ DO - 10.1007/978-3-540-69132-7_56 SP - 530-539 OP - PB - Springer Berlin Heidelberg SN - 9783540691303 9783540691327 UR - http://dx.doi.org/10.1007/978-3-540-69132-7_56 DB - Crossref ER - TY - CHAP TI - Student Note-Taking in Narrative-Centered Learning Environments: Individual Differences and Learning Effects AU - McQuiggan, Scott W. AU - Goth, Julius AU - Ha, Eunyoung AU - Rowe, Jonathan P. AU - Lester, James C. T2 - Intelligent Tutoring Systems AB - Note-taking has a long history in educational settings. Previous research has shown that note-taking leads to improved learning and performance on assessment. It was therefore hypothesized that note-taking could play an important role in narrative-centered learning. To investigate this question, a note-taking facility was introduced into a narrative-centered learning environment. Students were able to use the facility to take and review notes while solving a science mystery. In this paper we explore the individual differences of note-takers and the notes they take. Finally, we use machine learning techniques to model the content of student notes to support future pedagogical adaptation in narrative-centered learning environments. PY - 2008/8/12/ DO - 10.1007/978-3-540-69132-7_54 SP - 510-519 OP - PB - Springer Berlin Heidelberg SN - 9783540691303 9783540691327 UR - http://dx.doi.org/10.1007/978-3-540-69132-7_54 DB - Crossref ER - TY - CHAP TI - Affective Transitions in Narrative-Centered Learning Environments AU - McQuiggan, Scott W. AU - Robison, Jennifer L. AU - Lester, James C. T2 - Intelligent Tutoring Systems AB - Affect has been the subject of increasing attention in cognitive accounts of learning. Many intelligent tutoring systems now seek to adapt pedagogy to student affective and motivational processes in an effort to increase the effectiveness of tutorial interaction and improve learning outcomes. To this end, recent work has begun to investigate the emotions experienced during learning in a variety of environments. In this paper we extend this line of research by investigating the affective transitions that occur throughout narrative-centered learning experiences. Further analysis differentiates the likelihood of affective transitions stemming from pedagogical agent empathetic responses to student affect. PY - 2008/8/12/ DO - 10.1007/978-3-540-69132-7_52 SP - 490-499 OP - PB - Springer Berlin Heidelberg SN - 9783540691303 9783540691327 UR - http://dx.doi.org/10.1007/978-3-540-69132-7_52 DB - Crossref ER - TY - CONF TI - Planning-integrated story graph for interactive narratives AU - Min, W.-H. AU - Shim, E.-S. AU - Kim, Y.-J. AU - Cheong, Y.-G. AB - The advances in the interactive contents enable users to have a variety of experiences on diverse devices. In particular, two main approaches have been researched to construct digital interactive contents: a) conditional branch techniques and b) planning techniques. Each approach offers its own benefits; the conditional branch techniques allow the user to create tightly-plotted interactive contents; the planning techniques reduce the author's burden to specify every possible connection between contents considering the user input. As an attempt to combine these advantages provided by each technique, this paper discusses an interactive story structure incorporating the planning technique into the conditional branch techniques. Also, we briefly describe PRISM, a framework capable of creating and playing our story structure. We expect that the author can compose well-woven stories which can respond to a wide range of user interaction. C2 - 2008/// C3 - MM'08 - Proceedings of the 2008 ACM International Conference on Multimedia, with co-located Symposium and Workshops DA - 2008/// DO - 10.1145/1462014.1462021 SP - 27-32 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-72449210908&partnerID=MN8TOARS ER - TY - BOOK TI - PRISM: A framework for authoring interactive narratives AU - Cheong, Y.-G. AU - Kim, Y.-J. AU - Min, W.-H. AU - Shim, E.-S. AU - Kim, J.-Y. AB - The advances in computing technologies enable the computer users to create and share their own stories to the community at large. However, it is still regarded as complicated and laborious to author interactive narratives, where a story adapts as the user interacts with it. In authoring interactive narratives, two main approaches—branching graphs and AI planning—have been significantly used to augment interactivity into conventional linear narratives. Although each approach offers its own possibilities and limitations, few efforts have been made to blend these approaches. This paper describes a framework for authoring interactive narratives that employs an adapted branching narrative structure that also uses planning formalism to enable automated association between nodes. We expect that our work is valuable for non-expert users as well as AI researchers in interactive storytelling who need to create a large quantity of story contents for varied endings for a story. DA - 2008/// PY - 2008/// DO - 10.1007/978-3-540-89454-4_37 VL - 5334 LNCS SE - 297-308 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-58449129103&partnerID=MN8TOARS ER - TY - CONF TI - Structure Discovery Queries in Disk-Based Semantic Web Databases AU - Anyanwu, K. AU - Murukannaiah, P. K. AU - Maduko, A. AB - Link analysis tasks are fundamental to analytical applications in scientific research, business, national security, etc. Such tasks involve finding associations or interactions between entities e.g. people, chemical or genes. In graph theoretic terms, this amounts to finding arbitrary sub-graph structures that link a given set of entities. On the other hand, the traditional graph pattern matching query paradigm focuses on finding sub-graphs that match the structure given in a query. Consequently, an important problem is developing methods for evaluating such queries, particularly, when data resides on disk. In such cases, query processing techniques must avoid loading the whole database graph into memory and must utilize indexing and query processing techniques that mitigate the inherently I/O bound nature of navigating disk based graphs. In this paper, we present a computational framework for efficiently evaluating a class of structure discovery queries. It is based on an algebraic approach to solving path problems that leads to a natural disk storage model for graph data using traditional B+ tree index structures. We present some very promising preliminary evaluation results which show a very significant improvement in query performance over other approaches. C2 - 2008/// C3 - 2008 Fourth International Conference on Semantics, Knowledge and Grid DA - 2008/// DO - 10.1109/SKG.2008.108 VL - SP - 336-342 M1 - ER - TY - CHAP TI - Toward Automatic Hint Generation for Logic Proof Tutoring Using Historical Student Data AU - Barnes, Tiffany AU - Stamper, John T2 - Intelligent Tutoring Systems AB - We have proposed a novel application of Markov decision processes (MDPs), a reinforcement learning technique, to automatically generate hints for an intelligent tutor that learns. We demonstrate the feasibility of this approach by extracting MDPs from four semesters of student solutions in a logic proof tutor, and calculating the probability that we will be able to generate hints at any point in a given problem. Our results indicate that extracted MDPs and our proposed hint-generating functions will be able to provide hints over 80% of the time. Our results also indicate that we can provide valuable tradeoffs between hint specificity and the amount of data used to create an MDP. PY - 2008/8/12/ DO - 10.1007/978-3-540-69132-7_41 SP - 373-382 OP - PB - Springer Berlin Heidelberg SN - 9783540691303 9783540691327 UR - http://dx.doi.org/10.1007/978-3-540-69132-7_41 DB - Crossref ER - TY - CHAP TI - A Model for Sharing of Confidential Provenance Information in a Query Based System AU - Nagappan, Meiyappan AU - Vouk, Mladen A. T2 - Lecture Notes in Computer Science AB - Workflow management systems are increasingly being used to automate scientific discovery. Provenance meta-data is collected about scientific workflows, processes, simulations and data to add value. There is a variety of workflow management tools that cater to this. The provenance information may have as much value as the raw data. Typically, sensitive information produced by a computational processes or experiments is well guarded. However, this may not necessarily be true when it comes to provenance information. The issue is how to share confidential provenance information. We present a model for sharing provenance information when the confidentiality level is decided by the user dynamically. The key feature of this model is the Query Sharing concept. We illustrate the model for workflows implemented using provenance enabled Kepler system. PY - 2008/// DO - 10.1007/978-3-540-89965-5_8 SP - 62-69 OP - PB - Springer Berlin Heidelberg SN - 9783540899648 9783540899655 UR - http://dx.doi.org/10.1007/978-3-540-89965-5_8 DB - Crossref ER - TY - CHAP TI - Balancing Cognitive and Motivational Scaffolding in Tutorial Dialogue AU - Boyer, Kristy Elizabeth AU - Phillips, Robert AU - Wallis, Michael AU - Vouk, Mladen AU - Lester, James T2 - Intelligent Tutoring Systems AB - A key challenge in the design of tutorial dialogue systems is identifying tutorial strategies that can effectively balance the tradeoffs between cognitive and affective student outcomes. This balance is problematic because the precise nature of the interdependence between cognitive and affective strategies is not well understood. Furthermore, previous studies suggest that some cognitive and motivational goals are at odds with one another because a tutorial strategy designed to maximize one may negatively impact the other. This paper reports on a tutorial dialogue study that investigates motivational strategies and cognitive feedback. It was found that the choice of corrective tutorial strategy makes a significant difference in the outcomes of both student learning gains and self-efficacy gains. PY - 2008/8/12/ DO - 10.1007/978-3-540-69132-7_28 SP - 239-249 OP - PB - Springer Berlin Heidelberg SN - 9783540691303 9783540691327 UR - http://dx.doi.org/10.1007/978-3-540-69132-7_28 DB - Crossref ER - TY - BOOK TI - Why tutored problem solving may be better than example study: Theoretical implications from a simulated-student study AU - Matsuda, N. AU - Cohen, W.W. AU - Sewall, J. AU - Lacerda, G. AU - Koedinger, K.R. DA - 2008/// PY - 2008/// DO - 10.1007/978-3-540-69132-7-16 VL - 5091 LNCS SE - 111-121 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-70349865310&partnerID=MN8TOARS ER - TY - JOUR TI - Cycles in dense digraphs AU - Chudnovsky, Maria AU - Seymour, Paul AU - Sullivan, Blair T2 - Combinatorica DA - 2008/1// PY - 2008/1// DO - 10.1007/S00493-008-2331-Z VL - 28 IS - 1 SP - 1-18 J2 - Combinatorica LA - en OP - SN - 0209-9683 1439-6912 UR - http://dx.doi.org/10.1007/S00493-008-2331-Z DB - Crossref ER - TY - JOUR TI - Shape deformation in continuous map generalization AU - Danciger, Jeff AU - Devadoss, Satyan L. AU - Mugno, John AU - Sheehy, Don AU - Ward, Rachel T2 - GeoInformatica DA - 2008/5/10/ PY - 2008/5/10/ DO - 10.1007/s10707-008-0049-0 VL - 13 IS - 2 SP - 203-221 J2 - Geoinformatica LA - en OP - SN - 1384-6175 1573-7624 UR - http://dx.doi.org/10.1007/s10707-008-0049-0 DB - Crossref KW - Continuous generalization KW - Scale change KW - Homotopy KW - Cartograms ER - TY - JOUR TI - Adaptive speculation in behavior-oriented parallelization AU - Jiang, Yunlian AU - Shen, Xipeng T2 - 2008 IEEE International Symposium on Parallel and Distributed Processing AB - Behavior-oriented parallelization is a technique for parallelizing complex sequential programs that have dynamic parallelism. Although the technique shows promising results, the software speculation mechanism it uses is not cost-efficient. Failed speculations may waste computing resource and severely degrade system efficiency. In this work, we propose adaptive speculation to predict the profitability of a speculation and dynamically enable or disable the speculation of a region. Experimental results demonstrate the effectiveness of the scheme in improving the efficiency of software speculation. In addition, the adaptive speculation can also enhance the usability of behavior-oriented parallelization by allowing users to label potential parallel regions more flexibly. DA - 2008/4// PY - 2008/4// DO - 10.1109/ipdps.2008.4536403 ER - TY - CONF TI - Semantical considerations on dialectical and practical commitments AU - Singh, M.P. C2 - 2008/// C3 - Proceedings of the National Conference on Artificial Intelligence DA - 2008/// VL - 1 SP - 176-181 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-57749190779&partnerID=MN8TOARS ER - TY - CONF TI - Checking Correctness of Business Contracts via Commitments AU - Desai, Nirmit AU - Narendra, Nanjangud C. AU - Singh, Munindar P. C2 - 2008/5// C3 - Proceedings of the 7th International Conference on Autonomous Agents and MultiAgent Systems (AAMAS) DA - 2008/5// VL - 2 SP - 787–794 PB - IFAAMAS UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84899949549&partnerID=MN8TOARS ER - TY - CONF TI - On the enactability of business protocols AU - Desai, N. AU - Singh, M.P. C2 - 2008/// C3 - Proceedings of the National Conference on Artificial Intelligence DA - 2008/// VL - 2 SP - 1126-1131 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-57749188042&partnerID=MN8TOARS ER - TY - CONF TI - ICWS 2008: Message from the program chairs AU - Huai, J. AU - Shan, M.C. AU - Singh, M.P. AU - Zhang, J. AU - Casati, F. AU - Hsu, M. C2 - 2008/// C3 - Proceedings of the IEEE International Conference on Web Services, ICWS 2008 DA - 2008/// DO - 10.1109/ICWS.2008.5 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-57749196149&partnerID=MN8TOARS ER - TY - CONF TI - Design patterns for policy-based service engagements AU - Udupi, Y.B. AU - Singh, M.P. AB - Service engagements arise commonly in business and scientific computing. A service engagement is characterized by autonomous parties coming together in a contractual arrangement to share resources or carry out tasks for one another. Recent work shows how to model service engagements in an interactive manner and at a high level. This work formalizes the atoms of a service engagement as commitments among the participants, to be created and manipulated as the engagement progresses. Further, it scopes the commitments of an engagement in a (virtual) organization, and specifies how the policies of the participants affect their interactions. This paper contributes design patterns for service engagements formulated in terms of roles, commitments, and allied concepts. Each pattern reflects a distinct element of a service engagement from a business perspective and highlights exactly where policies apply. This enables the perspicuous, reusable specification of service engagements. C2 - 2008/// C3 - Proceedings - 2008 IEEE Workshop on Policies for Distributed Systems and Networks, POLICY 2008 DA - 2008/// DO - 10.1109/POLICY.2008.38 SP - 97-100 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-51849132583&partnerID=MN8TOARS ER - TY - CONF TI - Constitutive Interoperability AU - Chopra, Amit K. AU - Singh, Munindar P. C2 - 2008/5// C3 - Proceedings of the 7th International Conference on Autonomous Agents and MultiAgent Systems (AAMAS) DA - 2008/5// VL - 2 SP - 797–804 PB - IFAAMAS UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84899983406&partnerID=MN8TOARS ER - TY - BOOK TI - Interoperation in protocol enactment AU - Chopra, A.K. AU - Singh, M.P. AB - Interoperability has been broadly conceptualized as the ability of agents to work together. In open systems, the interoperability of agents is an important concern. A common way of achieving interoperability is by requiring agents to follow prescribed protocols in their interactions with others. In existing systems, agents must follow any protocol to the letter; in other words, they should exchange messages exactly as prescribed by the protocol. This is an overly restrictive constraint; it results in rigid, fragile implementations and curbs the autonomy of agents. For example, a customer agent may send a reminder to a merchant agent to deliver the promised goods. However, if reminders are not supported explicitly in the protocol they are enacting, then the reminder would be considered illegal and the transaction may potentially fail. This paper studies the interoperation of agents, dealing with their autonomy and heterogeneity in computational terms. DA - 2008/// PY - 2008/// DO - 10.1007/978-3-540-77564-5_3 VL - 4897 LNAI SE - 36-49 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-49949113616&partnerID=MN8TOARS ER - TY - CONF TI - An adaptive probabilistic trust model and its evaluation AU - Hang, C.-W. AU - Wang, Y. AU - Singh, M.P. C2 - 2008/// C3 - Proceedings of the International Joint Conference on Autonomous Agents and Multiagent Systems, AAMAS DA - 2008/// VL - 3 SP - 1449-1452 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84899977303&partnerID=MN8TOARS ER - TY - CONF TI - Comparing preferences expressed by cp-networks (extended abstract) AU - Wicker, A.W. AU - Doyle, J. C2 - 2008/// C3 - AAAI Workshop - Technical Report DA - 2008/// VL - WS-08-09 SP - 128-133 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-66149165890&partnerID=MN8TOARS ER - TY - CONF TI - Cognitive mechanics: Natural intelligence beyond biology and computation AU - Doyle, J. C2 - 2008/// C3 - AAAI Fall Symposium - Technical Report DA - 2008/// VL - FS-08-06 SP - 35-37 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-77952157352&partnerID=MN8TOARS ER - TY - RPRT TI - Visualizing very large layered graphs with quilts AU - Watson, Benjamin AU - Brink, David AU - Lograsso, Thomas A AU - Devajaran, D AU - Rhyne, Theresa-Marie AU - Patel, Himesh A3 - North Carolina State University. Dept. of Computer Science DA - 2008/// PY - 2008/// PB - North Carolina State University. Dept. of Computer Science ER - TY - RPRT TI - Matrix depictions for large layered graphs AU - Watson, BA AU - Brink, David AU - Stallmann, Matthias AU - Devajaran, Ravinder AU - Rakow, Matt AU - Rhyne, Theresa-Marie AU - Patel, Himesh A3 - Dept. Computer Science, North Carolina State University DA - 2008/// PY - 2008/// M1 - TR-2008-17 PB - Dept. Computer Science, North Carolina State University SN - TR-2008-17 ER - TY - CONF TI - View and index selection for query-performance improvement: quality-centered algorithms and heuristics AU - Kormilitsin, Maxim AU - Chirkova, Rada AU - Fathi, Yahya AU - Stallmann, Matthias T2 - ACM C2 - 2008/// C3 - Proceedings of the 17th ACM conference on Information and knowledge management DA - 2008/// SP - 1329-1330 ER - TY - CONF TI - Exact and inexact methods for selecting views and indexes for OLAP performance improvement AU - Talebi, Zohreh Asgharzadeh AU - Chirkova, Rada AU - Fathi, Yahya AU - Stallmann, Matthias T2 - ACM C2 - 2008/// C3 - Proceedings of the 11th international conference on Extending database technology: Advances in database technology DA - 2008/// SP - 311-322 ER - TY - CONF TI - Expressing a fraction of two determinants as a determinant AU - Kaltofen, Erich AU - Koiran, Pascal T2 - the twenty-first international symposium AB - Suppose the polynomials f and g in K[x1,...,xr] over the field K are determinants of non-singular m x m and n x n matrices, respectively, whose entries are in K ∪ x1,...,xr. Furthermore, suppose h = f/g is a polynomial in K[x1,..., xr]. We construct an s x s matrix C whose entries are in K ∪ x1,...,xr, such that h = det(C) and s = γ (m+n)6, where γ = O(1) if K is an infinite field or if for the finite field K = F{q} with q elements we have m = O(q), and where γ = (logq m)1+o(1) if q = o(m). Our construction utilizes the notion of skew circuits by Toda and WSK circuits by Malod and Portier. Our problem was motivated by resultant formulas derived from Chow forms. C2 - 2008/// C3 - Proceedings of the twenty-first international symposium on Symbolic and algebraic computation - ISSAC '08 DA - 2008/// DO - 10.1145/1390768.1390790 PB - ACM Press SN - 9781595939043 UR - http://dx.doi.org/10.1145/1390768.1390790 DB - Crossref ER - TY - CONF TI - Exact certification of global optimality of approximate factorizations via rationalizing sums-of-squares with floating point scalars AU - Kaltofen, Erich AU - Li, Bin AU - Yang, Zhengfeng AU - Zhi, Lihong T2 - the twenty-first international symposium AB - We generalize the technique by Peyrl and Parillo [Proc. SNC 2007] to computing lower bound certificates for several well-known factorization problems in hybrid symbolic-numeric computation. The idea is to transform a numerical sum-of-squares (SOS) representation of a positive polynomial into an exact rational identity. Our algorithms successfully certify accurate rational lower bounds near the irrational global optima for benchmark approximate polynomial greatest common divisors and multivariate polynomial irreducibility radii from the literature, and factor coefficient bounds in the setting of a model problem by Rump (up to n = 14, factor degree = 13. C2 - 2008/// C3 - Proceedings of the twenty-first international symposium on Symbolic and algebraic computation - ISSAC '08 DA - 2008/// DO - 10.1145/1390768.1390792 PB - ACM Press SN - 9781595939043 UR - http://dx.doi.org/10.1145/1390768.1390792 DB - Crossref ER - TY - CONF TI - Understanding and relating to your international students AU - Gehringer, Edward F. T2 - 2008 ASEE Annual Conference and Exposition C2 - 2008/// C3 - Proceedings of the 2008 ASEE Annual Conference and Exposition CY - Pittsburgh, PA DA - 2008/// PY - 2008/6/22/ PB - American Society for Engineering Education ER - TY - CONF TI - Damage control: What to do when things don’t work AU - Gehringer, Edward F. T2 - 2008 ASEE Annual Conference and Exposition C2 - 2008/// C3 - Proceedings of the 2008 ASEE Annual Conference and Exposition CY - Pittsburgh, PA DA - 2008/// PY - 2008/6/22/ PB - American Society for Engineering Education ER - TY - CONF TI - Assessing students’ wiki contributions AU - Gehringer, Edward F. T2 - 2008 ASEE Annual Conference and Exposition C2 - 2008/// C3 - Proceedings of the 2008 ASEE Annual Conference and Exposition CY - Pittsburgh, PA DA - 2008/// PY - 2008/6/22/ PB - American Society for Engineering Education ER - TY - CONF TI - Rose: A repository of education-friendly open-source projects AU - Meneely, Andrew AU - Williams, Laurie AU - Gehringer, Edward F. T2 - ITiCSE '08 AB - Open-source project artifacts can be used to inject realism into software engineering courses or lessons on open-source software development. However, the use of open-source projects presents challenges for both educators and for students. Educators must search for projects that meet the constraints of their classes, and often must negotiate the scope and terms of the project with project managers. For students, many available open-source projects have a steep learning curve that inhibits them from making significant contributions to the project and benefiting from a "realistic" experience. To alleviate these problems and to encourage cross-institution collaboration, we have created the Repository for Open Software Education (ROSE) and have contributed three open-source projects intended for an undergraduate computer science or software engineering course. The projects in ROSE are education-friendly in terms of a manageable size and scope, and are intended to be evolved over many semesters. All projects have a set of artifacts covering all aspects of the development process, from requirements, design, code, and test. We invite other educators to contribute to ROSE and to use projects found on ROSE in their own courses. C2 - 2008/// C3 - Proceedings of the 13th annual conference on Innovation and technology in computer science education - ITiCSE '08 CY - Madrid, Spain DA - 2008/// PY - 2008/6/30/ DO - 10.1145/1384271.1384276 PB - ACM Press SN - 9781605580784 UR - http://dx.doi.org/10.1145/1384271.1384276 ER - TY - JOUR TI - Extraction of natural-language dates and comparison of dates in hypothesis and text to identify negative textual entailment AU - Orphanides, Andreas K T2 - University of North Carolina at Chapel Hill DA - 2008/4/25/ PY - 2008/4/25/ UR - https://ils.unc.edu/MSpapers/3403.pdf ER - TY - CONF TI - Massively parallel genomic sequence search on the Blue Gene/P architecture AU - Lin, H. S. AU - Balaji, P. AU - Poole, R. AU - Sosa, C. AU - Ma, X. S. AU - Feng, W. C. C2 - 2008/// C3 - International Conference for High Performance Computing, Networking, Storage and Analysis DA - 2008/// SP - 522-532 ER - TY - JOUR TI - Shortest-path routing in randomized DHT-based Peer-to-Peer systems AU - Wang, Chih-Chiang AU - Harfoush, Khaled T2 - COMPUTER NETWORKS AB - Randomized DHT-based Peer-to-Peer (P2P) systems grant nodes certain flexibility in selecting their overlay neighbors, leading to irregular overlay structures but to better overall performance in terms of path latency, static resilience and local convergence. However, routing in the presence of overlay irregularity is challenging. In this paper, we propose a novel routing protocol, RASTER, that approximates shortest overlay routes between nodes in randomized DHTs. Unlike previously proposed routing protocols, RASTER encodes and aggregates routing information. Its simple bitmap-encoding scheme together with the proposed RASTER routing algorithm enable a performance edge over current overlay routing protocols. RASTER provides a forwarding overhead of merely a small constant number of bitwise operations, a routing performance close to optimal, and a better resilience to churn. RASTER also provides nodes with the flexibility to adjust the size of the maintained routing information based on their storage/processing capabilities. The cost of storing and exchanging encoded routing information is manageable and grows logarithmically with the number of nodes in the system. DA - 2008/12/22/ PY - 2008/12/22/ DO - 10.1016/j.comnet.2008.07.014 VL - 52 IS - 18 SP - 3307-3317 SN - 1872-7069 KW - Distributed hash tables KW - Randomized networks KW - Shortest-path routing ER - TY - JOUR TI - Semantic Parameterization: A Process for Modeling Domain Descriptions AU - Breaux, Travis D. AU - Anton, Annie I. AU - Doyle, Jon T2 - ACM TRANSACTIONS ON SOFTWARE ENGINEERING AND METHODOLOGY AB - Software engineers must systematically account for the broad scope of environmental behavior, including nonfunctional requirements, intended to coordinate the actions of stakeholders and software systems. The Inquiry Cycle Model (ICM) provides engineers with a strategy to acquire and refine these requirements by having domain experts answer six questions: who, what, where, when, how, and why. Goal-based requirements engineering has led to the formalization of requirements to answer the ICM questions about when , how , and why goals are achieved, maintained, or avoided. In this article, we present a systematic process called Semantic Parameterization for expressing natural language domain descriptions of goals as specifications in description logic. The formalization of goals in description logic allows engineers to automate inquiries using who , what , and where questions, completing the formalization of the ICM questions. The contributions of this approach include new theory to conceptually compare and disambiguate goal specifications that enables querying goals and organizing goals into specialization hierarchies. The artifacts in the process include a dictionary that aligns the domain lexicon with unique concepts, distinguishing between synonyms and polysemes, and several natural language patterns that aid engineers in mapping common domain descriptions to formal specifications. Semantic Parameterization has been empirically validated in three case studies on policy and regulatory descriptions that govern information systems in the finance and health-care domains. DA - 2008/11// PY - 2008/11// DO - 10.1145/1416563.1416565 VL - 18 IS - 2 SP - SN - 1557-7392 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-56149121201&partnerID=MN8TOARS KW - Documentation KW - Standardization KW - Human Factors KW - Natural language KW - domain knowledge KW - formal specification KW - description logic ER - TY - JOUR TI - Use of a nitinol gooseneck snare catheter for removal of adult Dirofilaria immitis in two cats AU - Small, Merrilee T. AU - Atkins, Clarke E. AU - Gordon, Sonya G. AU - Birkenheuer, Adam J. AU - Booth-Sayer, Margaret A. AU - Keene, Bruce W. AU - Fujii, Yoko AU - Miller, Matthew W. T2 - JAVMA-JOURNAL OF THE AMERICAN VETERINARY MEDICAL ASSOCIATION AB - Abstract Case Description —2 cats were examined because of congestive heart failure secondary to heartworm infection. Clinical Findings —One cat had severe abdominal distention and the other had dyspnea secondary to chylothorax. Both had loud right-sided heart murmurs, precordial thrills, and jugular distension. Thoracic radiography revealed cardiomegaly and enlarged caudal pulmonary arteries. Echocardiography revealed tricuspid regurgitation and multiple hyperechoic structures consistent with adult Dirofilaria immitis within the right atrium, right ventricle, and main pulmonary artery. Pulmonary hypertension was documented by means of Doppler echocardiography in 1 cat. Treatment and Outcome —Cats were anesthetized, and a nitinol gooseneck snare catheter was introduced into the right side of the heart via a jugular venotomy. In the first cat, the snare was used to retrieve 5 female and 2 male adult D immitis. The catheter was then passed into the main pulmonary artery in an unsuccessful attempt to retrieve remaining heartworms. In the second cat, 2 adult female D immitis were removed from the right atrium with the nitinol snare. In both cats, clinical signs resolved within 4 weeks after the procedure. Clinical Relevance —Findings suggested that use of a nitinol gooseneck snare catheter may be a safe and effective technique for removing adult D immitis from the right atrium and ventricle in cats and that successful removal of adult heartworms in infected cats may resolve clinical signs of right-sided congestive heart failure and chylothorax. In addition, findings in 1 cat suggested that removal of all adult heartworms may not be necessary for clinical signs to resolve. DA - 2008/11/1/ PY - 2008/11/1/ DO - 10.2460/javma.233.9.1441 VL - 233 IS - 9 SP - 1441-1445 SN - 0003-1488 ER - TY - JOUR TI - Trustworthy Web services provisioning for differentiated customer services AU - Xiong, Kaiqi AU - Perros, Harry T2 - TELECOMMUNICATION SYSTEMS DA - 2008/12// PY - 2008/12// DO - 10.1007/s11235-008-9126-9 VL - 39 IS - 3-4 SP - 171-185 SN - 1572-9451 KW - Web services KW - Security KW - Trustworthiness KW - Percentile response time KW - Service availability ER - TY - JOUR TI - Geometric modeling of rigid and non-rigid 3D shapes using the global geodesic function AU - Aouada, D. AU - Dreisigmeyer, D. W. AU - Krim, H. T2 - Pattern Recognition AB - In this paper, we present a novel intrinsic geometric representation of 3D objects. We add the proposed modeling of objects to their topological graphs to ensure a full and compact description necessary for shape-based retrieval, recognition and analysis of 3D models. In our approach, we address the challenges due to pose variability, computational complexity and noisy data by intrinsically and simply describing a 3D object by a global geodesic function. We exploit the geometric features contained in the dense set of iso-levels of this function. Using Whitney easy embedding theorem, we embed the manifold of the geodesic iso-levels in Ropf 3 and obtain a single space curve as our geometry descriptor. 3D shape comparison is then reduced to comparing the resulting modeling curves. To quantify the dissimilarities between them we simply compute an L 2 distance between classical Euclidian invariants applied to space curves. The experimental results show that in addition to being straightforward and easy to compute, our modeling technique achieves a high level of discrimination, and appears to be robust to both noise and decimation. DA - 2008/// PY - 2008/// DO - 10.1109/cvprw.2008.4563075 SP - 935-942 ER - TY - JOUR TI - An algebraic condition for product form in stochastic automata networks without synchronizations AU - Fourneau, J. M. AU - Plateau, B. AU - Stewart, W. J. T2 - Performance Evaluation AB - We consider Stochastic Automata Networks (SANs) in continuous time and we prove a sufficient condition for the steady-state distribution to have product form. We consider synchronization-free SANs in which the transitions of one automaton may depend upon the states of the other automata. This model can represent efficiently multidimensional Markov chains whose transitions are limited to one component but whose rates may depend on the state of the chain. The sufficient condition we obtain is quite simple and our theorem generalizes former results on SANs as well as results on modulated Markovian queues, such as Boucherie’s theory on competing Markov chain, on reversible queues considered by Kelly and on modulated Jackson queueing networks studied by Zhu. The sufficient condition and the proof are purely algebraic and are based on the intersection of kernels for a certain set of matrices. DA - 2008/// PY - 2008/// DO - 10.1016/j.peva.2008.04.007 VL - 65 IS - 11-12 SP - 854-868 ER - TY - JOUR TI - On Hierarchical Traffic Grooming in WDM Networks AU - Chen, Bensong AU - Rouskas, George N. AU - Dutta, Rudra T2 - IEEE-ACM TRANSACTIONS ON NETWORKING AB - The traffic grooming problem is of high practical importance in emerging wide-area wavelength division multiplexing (WDM) optical networks, yet it is intractable for any but trivial network topologies. In this work, we present an effective and efficient hierarchical traffic grooming framework for WDM networks of general topology, with the objective of minimizing the total number of electronic ports. At the first level of hierarchy, we decompose the network into clusters and designate one node in each cluster as the hub for grooming traffic. At the second level, the hubs form another cluster for grooming intercluster traffic. We view each (first- or second-level) cluster as a virtual star , and we present an efficient near-optimal algorithm for determining the logical topology of lightpaths to carry the traffic within each cluster. Routing and wavelength assignment is then performed directly on the underlying physical topology. We demonstrate the effectiveness of our approach by applying it to two networks of realistic size, a 32-node, 53-link topology and a 47-node, 96-link network. Comparisons to lower bounds indicate that hierarchical grooming is efficient in its use of the network resources of interest, namely, electronic ports and wavelengths. In addition to scaling to large network sizes, our hierarchical approach also facilitates the control and management of multigranular networks. DA - 2008/10// PY - 2008/10// DO - 10.1109/TNET.2007.906655 VL - 16 IS - 5 SP - 1226-1238 SN - 1558-2566 KW - Hierarchical traffic grooming KW - K-center KW - optical networks KW - wavelength division multiplexing (WDM) ER - TY - JOUR TI - Addressing diverse needs through a balance of agile and plan-driven software development methodologies in the core software engineering course AU - Layman, L. AU - Williams, L. AU - Slaten, K. AU - Berenson, S. AU - Vouk, M. T2 - International Journal of Engineering Education DA - 2008/// PY - 2008/// VL - 24 IS - 4 SP - 659-670 ER - TY - CONF TI - On the Levy-walk nature of human mobility AU - Rhee, L. AU - Shin, M. AU - Hong, S. AU - Lee, K. AU - Chong, S. C2 - 2008/// C3 - 27th IEEE Conference on Computer Communications (Infocom), vols 1-5 DA - 2008/// SP - 1597-1605 ER - TY - CONF TI - Countering persistent kernel rootkits through systematic hook discovery AU - Wang, Z. AU - Jiang, X. X. AU - Cui, W. D. AU - Wang, X. Y. C2 - 2008/// C3 - Recent advances in intrusion detection, raid 2008 DA - 2008/// VL - 5230 SP - 21-38 ER - TY - JOUR TI - Attack-resistant location estimation in wireless sensor networks AU - Liu, Donggang AU - Ning, Peng AU - Liu, An AU - Wang, Cliff AU - Du, Wenliang Kevin T2 - ACM TRANSACTIONS ON INFORMATION AND SYSTEM SECURITY AB - Many sensor network applications require sensors' locations to function correctly. Despite the recent advances, location discovery for sensor networks in hostile environments has been mostly overlooked. Most of the existing localization protocols for sensor networks are vulnerable in hostile environments. The security of location discovery can certainly be enhanced by authentication. However, the possible node compromises and the fact that location determination uses certain physical features (e.g., received signal strength) of radio signals make authentication not as effective as in traditional security applications. This article presents two methods to tolerate malicious attacks against range-based location discovery in sensor networks. The first method filters out malicious beacon signals on the basis of the “consistency” among multiple beacon signals, while the second method tolerates malicious beacon signals by adopting an iteratively refined voting scheme. Both methods can survive malicious attacks even if the attacks bypass authentication, provided that the benign beacon signals constitute the majority of the beacon signals. This article also presents the implementation and experimental evaluation (through both field experiments and simulation) of all the secure and resilient location estimation schemes that can be used on the current generation of sensor platforms (e.g., MICA series of motes), including the techniques proposed in this article, in a network of MICAz motes. The experimental results demonstrate the effectiveness of the proposed methods, and also give the secure and resilient location estimation scheme most suitable for the current generation of sensor networks. DA - 2008/7// PY - 2008/7// DO - 10.1145/1380564.1380570 VL - 11 IS - 4 SP - SN - 1557-7406 KW - security KW - design KW - algorithms KW - sensor networks KW - security KW - localization ER - TY - JOUR TI - Just-in-time dynamic voltage scaling: Exploiting inter-node slack to save energy in MPI programs AU - Freeh, Vincent W. AU - Kappiah, Nandini AU - Lowenthal, David K. AU - Bletsch, Tyler K. T2 - JOURNAL OF PARALLEL AND DISTRIBUTED COMPUTING AB - Although users of high-performance computing are most interested in raw performance, both energy and power consumption have become critical concerns. As a result, improving energy efficiency of nodes on HPC machines has become important, and the prevalence of power-scalable clusters, where the frequency and voltage can be dynamically modified, has increased. On power-scalable clusters, one opportunity for saving energy with little or no loss of performance exists when the computational load is not perfectly balanced. This situation occurs frequently, as keeping the load balanced between nodes is one of the long-standing fundamental problems in parallel and distributed computing. Indeed, despite the large body of research aimed at balancing load both statically and dynamically, this problem is quite difficult to solve. This paper presents a system called Jitter that reduces the frequency and voltage on nodes that are assigned less computation and, therefore, have idle or slack time. This saves energy on these nodes, and the goal of Jitter is to attempt to ensure that they arrive “just in time” so that they avoid increasing overall execution time. Specifically, we dynamically determine which nodes have enough slack time such that they can execute at a reduced frequency with little performance cost—which will greatly reduce the consumed energy on that node. In particular, Jitter saves 12.8% energy with 0.4% time increase–which is essentially the same as a hand-tuned solution–on the Aztec benchmark. DA - 2008/9// PY - 2008/9// DO - 10.1016/j.jpdc.2008.04.007 VL - 68 IS - 9 SP - 1175-1185 SN - 1096-0848 KW - power-aware KW - distributed computing KW - message passing interface (MPI) ER - TY - JOUR TI - Mitigating DoS attacks against broadcast authentication in wireless sensor networks AU - Ning, Peng AU - Liu, An AU - Du, Wenliang T2 - ACM TRANSACTIONS ON SENSOR NETWORKS AB - Broadcast authentication is a critical security service in wireless sensor networks. There are two general approaches for broadcast authentication in wireless sensor networks: digital signatures and μTESLA-based techniques. However, both signature-based and μTESLA-based broadcast authentication are vulnerable to Denial of Services (DoS) attacks: An attacker can inject bogus broadcast packets to force sensor nodes to perform expensive signature verifications (in case of signature-based broadcast authentication) or packet forwarding (in case of μTESLA-based broadcast authentication), thus exhausting their limited battery power. This paper presents an efficient mechanism called message-specific puzzle to mitigate such DoS attacks. In addition to signature-based or μTESLA-based broadcast authentication, this approach adds a weak authenticator in each broadcast packet, which can be efficiently verified by a regular sensor node, but takes a computationally powerful attacker a substantial amount of time to forge. Upon receiving a broadcast packet, each sensor node first verifies the weak authenticator, and performs the expensive signature verification (in signature-based broadcast authentication) or packet forwarding (in μTESLA-based broadcast authentication) only when the weak authenticator is valid. A weak authenticator cannot be precomputed without a non-reusable (or short-lived) key disclosed only in a valid packet. Even if an attacker has intensive computational resources to forge one or more weak authenticators, it is difficult to reuse these forged weak authenticators. Thus, this weak authentication mechanism substantially increases the difficulty of launching successful DoS attacks against signature-based or μTESLA-based broadcast authentication. A limitation of this approach is that it requires a powerful sender and introduces sender-side delay. This article also reports an implementation of the proposed techniques on TinyOS, as well as initial experimental evaluation in a network of MICAz motes. DA - 2008/1// PY - 2008/1// DO - 10.1145/1325651.1325652 VL - 4 IS - 1 SP - SN - 1550-4867 KW - security KW - design KW - algorithms KW - sensor networks KW - security KW - broadcast authentication KW - DoS attacks ER - TY - JOUR TI - The worst-case execution-time problem - Overview of methods and survey of tools AU - Wilhelm, R. AU - Engblom, J. AU - Ermedahl, A. AU - Holsti, N. AU - Thesing, S. AU - Whalley, D. AU - Bernat, G. AU - Ferdinand, C. AU - Heckmann, R. AU - Mitra, T. AU - Mueller, F. AU - Puaut, I. AU - Puschner, P. AU - Staschulat, J. AU - Stenstrom, P. T2 - ACM Transactions on Embedded Computing Systems DA - 2008/// PY - 2008/// VL - 7 IS - 3 ER - TY - JOUR TI - A differential HBT power cell and its model AU - Lee, Dong Ho AU - Chen, Yue AU - Lee, Kyung-Ai AU - Hong, Songcheol T2 - MICROWAVE AND OPTICAL TECHNOLOGY LETTERS AB - Abstract A differential heterojunction bipolar transistor (HBT) power cell has been designed and modeled with additional model extraction patterns. The differential power cell, which is composed of a unit differential amplifier with a common emitter ballast resistor, has no gain degradation by the ballast resistors and has been implemented in InGaP/GaAs HBT technology. DC and AC characteristics are extracted from a half circuit of the differential power cell and thermal characteristics are extracted from a common‐mode circuit of that. Using the extracted model, a 5‐GHz differential power amplifier has been designed and fabricated with on‐chip output networks. The 5‐GHz differential power amplifier delivers 26 dBm of P 1dB with 30% collector efficiency. © 2008 Wiley Periodicals, Inc. Microwave Opt Technol Lett 50: 2262–2268, 2008; Published online in Wiley InterScience (www.interscience.wiley.com).DOI 10.1002/mop.23684 DA - 2008/9// PY - 2008/9// DO - 10.1002/mop.23684 VL - 50 IS - 9 SP - 2262-2268 SN - 1098-2760 KW - heterojunction bipolar transistor (HBT) KW - differential amplifiers KW - large-signal model KW - MMIC power amplifiers KW - semiconductor device modeling ER - TY - JOUR TI - Comparison of static and switching characteristics of 1200 V 4H-SiCBJT and 1200 V Si-IGBT AU - Gao, Yan AU - Huang, Alex Q. AU - Krishnaswami, Sumi AU - Richmond, Jim AU - Agarwal, Anant K. T2 - IEEE TRANSACTIONS ON INDUSTRY APPLICATIONS AB - In this paper, static and switching characteristics of a 1200 V 4H-silicon carbide (SiC) bipolar junction transistor (BJT) at a bus voltage of 600 V are reported for the first time. Comparison was made between the SiC BJT and a 1200 V Si insulated gate bipolar transistor (IGBT). The experimental data show that the SiC BJT has much smaller conduction and switching losses than the Si IGBT. The SiC BJT also shows an extremely large reverse bias safe operation area, and no second breakdown was observed. This removes one of the most unattractive aspects of the BJT. The results prove that, unlike Si BJTs, BJTs in 4H-SiC are good competitors for Si IGBTs. DA - 2008/// PY - 2008/// DO - 10.1109/TIA.2008.921408 VL - 44 IS - 3 SP - 887-893 SN - 1939-9367 KW - loss KW - reverse-biased safe operating area (RBSOA) KW - Si insulated gate bipolar transistor (IGBT) KW - silicon carbide bipolar junction transistor (SiC BJT) ER - TY - JOUR TI - Z-MAC: A hybrid MAC for wireless sensor networks AU - Rhee, Injong AU - Warrier, Ajit AU - Aia, Mahesh AU - Min, Jeongki AU - Sichitiu, Mihail L. T2 - IEEE-ACM TRANSACTIONS ON NETWORKING AB - This paper presents the design, implementation and performance evaluation of a hybrid MAC protocol, called Z-MAC, for wireless sensor networks that combines the strengths of TDMA and CSMA while offsetting their weaknesses. Like CSMA, Z-MAC achieves high channel utilization and low latency under low contention and like TDMA, achieves high channel utilization under high contention and reduces collision among two-hop neighbors at a low cost. A distinctive feature of Z-MAC is that its performance is robust to synchronization errors, slot assignment failures, and time-varying channel conditions; in the worst case, its performance always falls back to that of CSMA. Z-MAC is implemented in TinyOS. DA - 2008/6// PY - 2008/6// DO - 10.1109/TNET.2007.900704 VL - 16 IS - 3 SP - 511-524 SN - 1558-2566 KW - CSMA KW - MAC KW - TDMA KW - wireless sensor networks ER - TY - JOUR TI - Realizing quality improvement through test driven development: results and experiences of four industrial teams AU - Nagappan, Nachiappan AU - Maximilien, E. Michael AU - Bhat, Thirumalesh AU - Williams, Laurie T2 - EMPIRICAL SOFTWARE ENGINEERING DA - 2008/6// PY - 2008/6// DO - 10.1007/s10664-008-9062-z VL - 13 IS - 3 SP - 289-302 SN - 1573-7616 KW - test driven development KW - empirical study KW - defects/faults KW - development time ER - TY - JOUR TI - Procedural urban modeling in practice AU - Watson, Benjamin AU - Mueller, Pascal AU - Wonka, Peter AU - Sexton, Chris AU - Veryovka, Oleg AU - Fuller, Andy T2 - IEEE COMPUTER GRAPHICS AND APPLICATIONS AB - Film and game studios can no longer meet audience demand for visual content by increasing production budgets. Instead they are turning to procedural modeling, particularly for modeling cities. The authors review procedural modeling, examine the CityEngine tool, and study the use of procedural urban modeling in Electronic Arts' Need for Speed games. DA - 2008/// PY - 2008/// DO - 10.1109/MCG.2008.58 VL - 28 IS - 3 SP - 18-26 SN - 1558-1756 ER - TY - JOUR TI - Procedural methods for urban modeling AU - Watson, Benjamin AU - Wonka, Peter T2 - IEEE COMPUTER GRAPHICS AND APPLICATIONS AB - Simulation of our man-made environment, especially cities, is becoming an increasingly important research problem in computer graphics. This special issue captures a good snapshot of work in this emerging area. DA - 2008/// PY - 2008/// DO - 10.1109/mcg.2008.57 VL - 28 IS - 3 SP - 16-17 SN - 0272-1716 ER - TY - JOUR TI - Exploiting synchronous and asynchronous DVS for feedback EDF scheduling on an embedded platform AU - Zhu, Yifan AU - Mueller, Frank T2 - ACM TRANSACTIONS ON EMBEDDED COMPUTING SYSTEMS AB - Contemporary processors support dynamic voltage scaling (DVS) to reduce power consumption by varying processor voltage/frequency dynamically. We develop power-aware feedback--DVS algorithms for hard real-time systems that adapt to dynamically changing workloads. The algorithms lower execution speed while guaranteeing timing constraints. We study energy consumption for synchronous and asynchronous DVS switching on a PowerPC board. Energy, measured via data acquisition, is reduced up to 70% over naïve DVS for our feedback scheme with 24% peak savings over previous algorithms. These results, albeit differing in quantity, confirm trends observed under simulation. They are the first of their kind on an embedded board. DA - 2008/// PY - 2008/// DO - 10.1145/1324969.1324972 VL - 7 IS - 1 SP - SN - 1558-3465 KW - algorithms KW - experimentation KW - real-time systems KW - scheduling KW - dynamic voltage scaling KW - feedback control ER - TY - JOUR TI - Euler's partition theorem and the combinatorics of l-sequences AU - Savage, Carla D. AU - Yee, Ae Ja T2 - JOURNAL OF COMBINATORIAL THEORY SERIES A AB - Euler's partition theorem states that the number of partitions of an integer N into odd parts is equal to the number of partitions of N in which the ratio of successive parts is greater than 1. It was shown by Bousquet-Mélou and Eriksson in [M. Bousquet-Mélou, K. Eriksson, Lecture hall partitions II, Ramanujan J. 1 (2) (1997) 165–185] that a similar result holds when “odd parts” is replaced by “parts that are sums of successive terms of an ℓ -sequence” and the ratio “1” is replaced by a root of the characteristic polynomial of the ℓ -sequence. This generalization of Euler's theorem is intrinsically different from the many others that have appeared, as it involves a family of partitions constrained by the ratio of successive parts. In this paper, we provide a surprisingly simple bijection for this result, a question suggested by Richard Stanley. In fact, we give a parametrized family of bijections, that include, as special cases, Sylvester's bijection and a bijection for the lecture hall theorem. We introduce Sylvester diagrams as a way to visualize these bijections and deduce their properties. In proving the bijections, we uncover the intrinsic role played by the combinatorics of ℓ -sequences and use this structure to give a combinatorial characterization of the partitions defined by the ratio constraint. Several open questions suggested by this work are described. DA - 2008/8// PY - 2008/8// DO - 10.1016/j.jcta.2007.11.006 VL - 115 IS - 6 SP - 967-996 SN - 0097-3165 KW - integer partitions KW - lecture hall partitions KW - Euler's partition theorem KW - Sylvester's bijection KW - partition bijections ER - TY - JOUR TI - DSD-Crasher: A hybrid analysis tool for bug finding AU - Csallner, Christoph AU - Smaragdakis, Yannis AU - Xie, Tao T2 - ACM TRANSACTIONS ON SOFTWARE ENGINEERING AND METHODOLOGY AB - DSD-Crasher is a bug finding tool that follows a three-step approach to program analysis: D. Capture the program's intended execution behavior with dynamic invariant detection. The derived invariants exclude many unwanted values from the program's input domain. S. Statically analyze the program within the restricted input domain to explore many paths. D. Automatically generate test cases that focus on reproducing the predictions of the static analysis. Thereby confirmed results are feasible. This three-step approach yields benefits compared to past two-step combinations in the literature. In our evaluation with third-party applications, we demonstrate higher precision over tools that lack a dynamic step and higher efficiency over tools that lack a static step. DA - 2008/// PY - 2008/// DO - 10.1145/1348250.1348254 VL - 17 IS - 2 SP - SN - 1557-7392 KW - reliability KW - verification KW - automatic testing KW - bug finding KW - dynamic analysis KW - dynamic invariant detection KW - extended static checking KW - false positives KW - static analysis KW - test case generation KW - usability ER - TY - JOUR TI - Characterization of anaerobic catabolism of p-coumarate in Rhodopseudomonas palustris by integrating transcriptomics and quantitative proteomics AU - Pan, Chongle AU - Oda, Yasuhiro AU - Lankford, Patricia K. AU - Zhang, Bing AU - Samatova, Nagiza F. AU - Pelletier, Dale A. AU - Harwood, Caroline S. AU - Hettich, Robert L. T2 - MOLECULAR & CELLULAR PROTEOMICS AB - In this study, the pathway for anaerobic catabolism of p-coumarate by a model bacterium, Rhodopseudomonas palustris, was characterized by comparing the gene expression profiles of cultures grown in the presence of p-coumarate, benzoate, or succinate as the sole carbon sources. Gene expression was quantified at the mRNA level with transcriptomics and at the protein level with quantitative proteomics using 15N metabolic labeling. Protein relative abundances, along with their confidence intervals for statistical significance evaluation, were estimated with the software ProRata. Both -omics measurements were used as the transcriptomics provided near-full genome coverage of gene expression profiles and the quantitative proteomics ascertained abundance changes of over 1600 proteins. The integrated gene expression data are consistent with the hypothesis that p-coumarate is converted to benzoyl-CoA, which is then degraded via a known aromatic ring reduction pathway. For the metabolism of p-coumarate to benzoyl-CoA, two alternative routes, a β-oxidation route and a non-β-oxidation route, are possible. The integrated gene expression data provided strong support for the non-β-oxidation route in R. palustris. A putative gene was proposed for every step in the non-β-oxidation route. In this study, the pathway for anaerobic catabolism of p-coumarate by a model bacterium, Rhodopseudomonas palustris, was characterized by comparing the gene expression profiles of cultures grown in the presence of p-coumarate, benzoate, or succinate as the sole carbon sources. Gene expression was quantified at the mRNA level with transcriptomics and at the protein level with quantitative proteomics using 15N metabolic labeling. Protein relative abundances, along with their confidence intervals for statistical significance evaluation, were estimated with the software ProRata. Both -omics measurements were used as the transcriptomics provided near-full genome coverage of gene expression profiles and the quantitative proteomics ascertained abundance changes of over 1600 proteins. The integrated gene expression data are consistent with the hypothesis that p-coumarate is converted to benzoyl-CoA, which is then degraded via a known aromatic ring reduction pathway. For the metabolism of p-coumarate to benzoyl-CoA, two alternative routes, a β-oxidation route and a non-β-oxidation route, are possible. The integrated gene expression data provided strong support for the non-β-oxidation route in R. palustris. A putative gene was proposed for every step in the non-β-oxidation route. Lignin constitutes almost one-third of all plant dry mass, making it the second most abundant organic compound on earth after cellulose. Biodegradation of lignin during the decay of plant residues in natural environments is a massive biological process within the global carbon cycle (1Kirk T.K. Degradation of lignin.in: Gibson D.T. Microbial Degradation of Organic Compounds. Marcel Dekker, Inc., New York1984: 399-437Google Scholar). Lignin biodegradation is also of great practical significance because of its potential application to biological treatment and the reuse of agricultural wastes. Lignin is a polymer of phenylpropanoid units, and its biodegradation involves depolymerization and subsequent catabolism of the derived aromatic monomers (2Sarkanen K.V. Ludwig C.H. Definition and nomenclature.in: Lignins: Occurrence, Formation, Structure and Reactions. John Wiley and Sons, New York1971: 1-18Google Scholar). p-Coumarate, or 4-hydroxycinnamic acid, is one of the main aromatic monomers (3Hartley R.D. Ford C.W. Phenolic constituents of plant cell walls and wall biodegradability.in: Lewis N.G. Paice M.G. Plant Cell Wall Polymers: Biogenesis and Biodegradation. American Chemical Society, Washington, D. C.1989: 137-145Crossref Google Scholar). The biodegradation of p-coumarate can take place not only under oxygen-rich environments but also under anoxic environments as in aquifers, aquatic sediments, and submerged soils.The purple, non-sulfur phototrophic bacterium Rhodopseudomonas palustris has served as a model organism for studies of anaerobic aromatic compound degradation (4Diaz E. Bacterial degradation of aromatic pollutants: a paradigm of metabolic versatility.Int. Microbiol. 2004; 7: 173-180PubMed Google Scholar, 5Egland P.G. Pelletier D.A. Dispensa M. Gibson J. Harwood C.S. A cluster of bacterial genes for anaerobic benzene ring biodegradation.Proc. Natl. Acad. Sci. U. S. A. 1997; 94: 6484-6489Crossref PubMed Scopus (141) Google Scholar). R. palustris can grow aerobically by respiration or anaerobically using photophosphorylation. Under anaerobic conditions R. palustris generates energy from light and uses organic compounds, including aliphatic and aromatic compounds, as its source of carbon for growth. Structurally diverse single aromatic ring compounds, such as p-coumarate and p-hydroxybenzoate, are proposed to be degraded to a central intermediate, benzoyl-CoA, via various peripheral pathways (6Harwood C.S. Burchhardt G. Herrmann H. Fuchs G. Anaerobic metabolism of aromatic compounds via the benzoyl-CoA pathway.FEMS Microbiol. Rev. 1999; 22: 439-458Crossref Google Scholar, 7Gibson J. Harwood C.S. Metabolic diversity in aromatic compound utilization by anaerobic microbes.Annu. Rev. Microbiol. 2002; 56: 345-369Crossref PubMed Scopus (174) Google Scholar). Then benzoyl-CoA is degraded to acetyl-CoA through a central pathway in the steps of ring reduction, ring cleavage, and β-oxidation (see Fig. 1) (6Harwood C.S. Burchhardt G. Herrmann H. Fuchs G. Anaerobic metabolism of aromatic compounds via the benzoyl-CoA pathway.FEMS Microbiol. Rev. 1999; 22: 439-458Crossref Google Scholar). Most enzymes in the benzoyl-CoA pathway have been identified and characterized. However, the peripheral pathway used by R. palustris to anaerobically convert p-coumarate to benzoyl-CoA has not been elucidated.Different metabolic routes have been discovered for catabolizing ferulate, (4-hydroxy-3-methoxycinnamic acid), which differs from p-coumarate by an additional methoxyl group on the aromatic ring. The two major routes are 1) a β-oxidation route found in Pseudomonas acidovorans (8Toms A. Wood J.M. Degradation of trans-ferulic acid by Pseudomonas acidovorans.Biochemistry. 1970; 9: 337-343Crossref PubMed Scopus (116) Google Scholar) and Rhodotorula rubra (9Huang Z.X. Dostal L. Rosazza J.P.N. Mechanisms of ferulic acid conversions to vanillic acid and guaiacol by Rhodotorula rubra.J. Biol. Chem. 1993; 268: 23954-23958Abstract Full Text PDF PubMed Google Scholar) and 2) a non-β-oxidation route found in Pseudomonas fluorescens (10Narbad A. Gasson M.J. Metabolism of ferulic acid via vanillin using a novel CoA-dependent pathway in a newly-isolated strain of Pseudomonas fluorescens.Microbiology (Read.). 1998; 144: 1397-1405Crossref PubMed Scopus (148) Google Scholar, 11Gasson M.J. Kitamura Y. McLauchlan W.R. Narbad A. Parr A.J. Lindsay E. Parsons H. Payne J. Rhodes M.J.C. Walton N.J. Metabolism of ferulic acid to vanillin. A bacterial gene of the enoyl-SCoA hydratase/isomerase superfamily encodes an enzyme for the hydration and cleavage of a hydroxycinnamic acid SCoA thioester.J. Biol. Chem. 1998; 273: 4163-4170Abstract Full Text Full Text PDF PubMed Scopus (186) Google Scholar), Delftia acidovorans (12Plaggenborg R. Steinbuchel A. Priefert H. The coenzyme A-dependent, non-beta-oxidation pathway and not direct deacetylation is the major route for ferulic acid degradation in Delftia acidovorans.FEMS Microbiol. Lett. 2001; 205: 9-16PubMed Google Scholar), and Pseudomonas sp. strain HR199 (13Overhage J. Priefert H. Steinbuchel A. Biochemical and genetic analyses of ferulic acid catabolism in Pseudomonas sp strain HR199.Appl. Environ. Microbiol. 1999; 65: 4837-4847Crossref PubMed Google Scholar). Fig. 1 illustrates the two probable routes for p-coumarate catabolism in R. palustris. Both routes convert the intermediate p-coumaroyl-CoA to 4-hydroxybenzoyl-CoA, yielding an acetyl-CoA. However, the β-oxidation route uses a β-oxidation sequence of reactions for the conversion, whereas the non-β-oxidation route directly cleaves an acetyl-CoA from p-coumaroyl-CoA to generate 4-hydroxybenzaldehyde, which is then oxidized to 4-hydroxybenzoate in a CoA-independent manner. Both routes could easily function under anaerobic conditions. Furthermore the genome sequence of R. palustris indicates the genetic potential for both routes. There are many β-oxidation genes in the R. palustris genome. Similarly there are several candidate genes for the enoyl-CoA hydratase/lyase and aldehyde dehydrogenase needed for the non-β-oxidation route. In this study, we aimed to determine which of the two routes is likely used for anaerobic p-coumarate catabolism and furthermore to identify the probable genes for every step of this catabolic pathway. To this end, the global gene expression profile of R. palustris grown with p-coumarate as the sole organic carbon source was compared with those of R. palustris grown with succinate or benzoate (Figs. 1 and 2).Fig. 2Experimental scheme for the integrated gene expression profiling. The p-coumarate, succinate, and benzoate cultures were prepared in biological duplicate with 15N metabolic labeling. Each culture was divided for transcriptomics and quantitative proteomics measurements. The experimental steps are shown with solid arrows, and the data analysis steps are shown with dashed arrows.View Large Image Figure ViewerDownload Hi-res image Download (PPT)Gene expression activity can be measured at the mRNA level with transcriptomics and at the protein level with proteomics. In many of the past studies, proteomics measurements have largely been qualitative with the aim of detecting the presence of as many proteins as possible from a proteome (14Washburn M.P. Yates III, J.R. Analysis of the microbial proteome.Curr. Opin. Microbiol. 2000; 3: 292-297Crossref PubMed Scopus (122) Google Scholar). However, it is not straightforward to correlate the presence of proteins detected by qualitative proteomics with the relative abundances of mRNAs quantified by transcriptomics (15Brown S.D. Thompson M.R. VerBerkmoes N.C. Chourey K. Shah M. Zhou J.Z. Hettich R.L. Thompson D.K. Molecular dynamics of the Shewanella oneidensis response to chromate stress.Mol. Cell. Proteomics. 2006; 5: 1054-1071Abstract Full Text Full Text PDF PubMed Scopus (145) Google Scholar). With the development of quantitative proteomics using stable isotope labeling, the relative protein abundances can now be quantitatively measured for thousands of genes (16Ong S.E. Mann M. Mass spectrometry-based proteomics turns quantitative.Nat. Chem. Biol. 2005; 1: 252-262Crossref PubMed Scopus (1305) Google Scholar). In this study, transcriptomics and quantitative proteomics were integrated for global gene expression profiling. The comparison of the p-coumarate growth condition with the succinate growth condition yielded the relative expression level for 1680 genes at both the mRNA level and the protein level. 1324 genes had no significant expression change at both levels. 58 genes were up-regulated significantly at both levels; some of these genes are known to be involved in aromatic compound degradation. Interestingly 41 genes were up-regulated significantly at the protein level but not at the mRNA level, warranting further investigation for post-transcriptional regulations and experimental artifacts. Similar trends were also observed in the other comparisons in this study.ConclusionsQuantitative proteomics measurements were conducted to provide a global view of the cellular pathways involved in p-coumarate catabolism for R. palustris by using metabolic stable isotope labeling, MudPIT analysis, and the ProRata data analysis program. By characterizing technical and biological replicates, over 1600 proteins were confidently quantified from R. palustris cultures grown with succinate, benzoate, or p-coumarate as the sole carbon sources. The same R. palustris cultures were also examined by transcriptomics. The transcriptomics results and the quantitative proteomics results were integrated to reconstruct global gene expression profiles of R. palustris at the mRNA level and the protein level. This integrated gene expression data set provided evidence that the anaerobic degradation of p-coumarate proceeds through a non-β-oxidation route, rather than an alternative β-oxidation route, and then through the central benzoyl-CoA pathway. RPA1787, RPA1786, and RPA1206 were hypothesized to be the probable p-coumarate-CoA ligase, p-coumaroyl-CoA hydratase/lyase, and 4-hydroxybenzaldehyde dehydrogenase, respectively, in the non-β-oxidation route. Lignin constitutes almost one-third of all plant dry mass, making it the second most abundant organic compound on earth after cellulose. Biodegradation of lignin during the decay of plant residues in natural environments is a massive biological process within the global carbon cycle (1Kirk T.K. Degradation of lignin.in: Gibson D.T. Microbial Degradation of Organic Compounds. Marcel Dekker, Inc., New York1984: 399-437Google Scholar). Lignin biodegradation is also of great practical significance because of its potential application to biological treatment and the reuse of agricultural wastes. Lignin is a polymer of phenylpropanoid units, and its biodegradation involves depolymerization and subsequent catabolism of the derived aromatic monomers (2Sarkanen K.V. Ludwig C.H. Definition and nomenclature.in: Lignins: Occurrence, Formation, Structure and Reactions. John Wiley and Sons, New York1971: 1-18Google Scholar). p-Coumarate, or 4-hydroxycinnamic acid, is one of the main aromatic monomers (3Hartley R.D. Ford C.W. Phenolic constituents of plant cell walls and wall biodegradability.in: Lewis N.G. Paice M.G. Plant Cell Wall Polymers: Biogenesis and Biodegradation. American Chemical Society, Washington, D. C.1989: 137-145Crossref Google Scholar). The biodegradation of p-coumarate can take place not only under oxygen-rich environments but also under anoxic environments as in aquifers, aquatic sediments, and submerged soils. The purple, non-sulfur phototrophic bacterium Rhodopseudomonas palustris has served as a model organism for studies of anaerobic aromatic compound degradation (4Diaz E. Bacterial degradation of aromatic pollutants: a paradigm of metabolic versatility.Int. Microbiol. 2004; 7: 173-180PubMed Google Scholar, 5Egland P.G. Pelletier D.A. Dispensa M. Gibson J. Harwood C.S. A cluster of bacterial genes for anaerobic benzene ring biodegradation.Proc. Natl. Acad. Sci. U. S. A. 1997; 94: 6484-6489Crossref PubMed Scopus (141) Google Scholar). R. palustris can grow aerobically by respiration or anaerobically using photophosphorylation. Under anaerobic conditions R. palustris generates energy from light and uses organic compounds, including aliphatic and aromatic compounds, as its source of carbon for growth. Structurally diverse single aromatic ring compounds, such as p-coumarate and p-hydroxybenzoate, are proposed to be degraded to a central intermediate, benzoyl-CoA, via various peripheral pathways (6Harwood C.S. Burchhardt G. Herrmann H. Fuchs G. Anaerobic metabolism of aromatic compounds via the benzoyl-CoA pathway.FEMS Microbiol. Rev. 1999; 22: 439-458Crossref Google Scholar, 7Gibson J. Harwood C.S. Metabolic diversity in aromatic compound utilization by anaerobic microbes.Annu. Rev. Microbiol. 2002; 56: 345-369Crossref PubMed Scopus (174) Google Scholar). Then benzoyl-CoA is degraded to acetyl-CoA through a central pathway in the steps of ring reduction, ring cleavage, and β-oxidation (see Fig. 1) (6Harwood C.S. Burchhardt G. Herrmann H. Fuchs G. Anaerobic metabolism of aromatic compounds via the benzoyl-CoA pathway.FEMS Microbiol. Rev. 1999; 22: 439-458Crossref Google Scholar). Most enzymes in the benzoyl-CoA pathway have been identified and characterized. However, the peripheral pathway used by R. palustris to anaerobically convert p-coumarate to benzoyl-CoA has not been elucidated. Different metabolic routes have been discovered for catabolizing ferulate, (4-hydroxy-3-methoxycinnamic acid), which differs from p-coumarate by an additional methoxyl group on the aromatic ring. The two major routes are 1) a β-oxidation route found in Pseudomonas acidovorans (8Toms A. Wood J.M. Degradation of trans-ferulic acid by Pseudomonas acidovorans.Biochemistry. 1970; 9: 337-343Crossref PubMed Scopus (116) Google Scholar) and Rhodotorula rubra (9Huang Z.X. Dostal L. Rosazza J.P.N. Mechanisms of ferulic acid conversions to vanillic acid and guaiacol by Rhodotorula rubra.J. Biol. Chem. 1993; 268: 23954-23958Abstract Full Text PDF PubMed Google Scholar) and 2) a non-β-oxidation route found in Pseudomonas fluorescens (10Narbad A. Gasson M.J. Metabolism of ferulic acid via vanillin using a novel CoA-dependent pathway in a newly-isolated strain of Pseudomonas fluorescens.Microbiology (Read.). 1998; 144: 1397-1405Crossref PubMed Scopus (148) Google Scholar, 11Gasson M.J. Kitamura Y. McLauchlan W.R. Narbad A. Parr A.J. Lindsay E. Parsons H. Payne J. Rhodes M.J.C. Walton N.J. Metabolism of ferulic acid to vanillin. A bacterial gene of the enoyl-SCoA hydratase/isomerase superfamily encodes an enzyme for the hydration and cleavage of a hydroxycinnamic acid SCoA thioester.J. Biol. Chem. 1998; 273: 4163-4170Abstract Full Text Full Text PDF PubMed Scopus (186) Google Scholar), Delftia acidovorans (12Plaggenborg R. Steinbuchel A. Priefert H. The coenzyme A-dependent, non-beta-oxidation pathway and not direct deacetylation is the major route for ferulic acid degradation in Delftia acidovorans.FEMS Microbiol. Lett. 2001; 205: 9-16PubMed Google Scholar), and Pseudomonas sp. strain HR199 (13Overhage J. Priefert H. Steinbuchel A. Biochemical and genetic analyses of ferulic acid catabolism in Pseudomonas sp strain HR199.Appl. Environ. Microbiol. 1999; 65: 4837-4847Crossref PubMed Google Scholar). Fig. 1 illustrates the two probable routes for p-coumarate catabolism in R. palustris. Both routes convert the intermediate p-coumaroyl-CoA to 4-hydroxybenzoyl-CoA, yielding an acetyl-CoA. However, the β-oxidation route uses a β-oxidation sequence of reactions for the conversion, whereas the non-β-oxidation route directly cleaves an acetyl-CoA from p-coumaroyl-CoA to generate 4-hydroxybenzaldehyde, which is then oxidized to 4-hydroxybenzoate in a CoA-independent manner. Both routes could easily function under anaerobic conditions. Furthermore the genome sequence of R. palustris indicates the genetic potential for both routes. There are many β-oxidation genes in the R. palustris genome. Similarly there are several candidate genes for the enoyl-CoA hydratase/lyase and aldehyde dehydrogenase needed for the non-β-oxidation route. In this study, we aimed to determine which of the two routes is likely used for anaerobic p-coumarate catabolism and furthermore to identify the probable genes for every step of this catabolic pathway. To this end, the global gene expression profile of R. palustris grown with p-coumarate as the sole organic carbon source was compared with those of R. palustris grown with succinate or benzoate (Figs. 1 and 2). Gene expression activity can be measured at the mRNA level with transcriptomics and at the protein level with proteomics. In many of the past studies, proteomics measurements have largely been qualitative with the aim of detecting the presence of as many proteins as possible from a proteome (14Washburn M.P. Yates III, J.R. Analysis of the microbial proteome.Curr. Opin. Microbiol. 2000; 3: 292-297Crossref PubMed Scopus (122) Google Scholar). However, it is not straightforward to correlate the presence of proteins detected by qualitative proteomics with the relative abundances of mRNAs quantified by transcriptomics (15Brown S.D. Thompson M.R. VerBerkmoes N.C. Chourey K. Shah M. Zhou J.Z. Hettich R.L. Thompson D.K. Molecular dynamics of the Shewanella oneidensis response to chromate stress.Mol. Cell. Proteomics. 2006; 5: 1054-1071Abstract Full Text Full Text PDF PubMed Scopus (145) Google Scholar). With the development of quantitative proteomics using stable isotope labeling, the relative protein abundances can now be quantitatively measured for thousands of genes (16Ong S.E. Mann M. Mass spectrometry-based proteomics turns quantitative.Nat. Chem. Biol. 2005; 1: 252-262Crossref PubMed Scopus (1305) Google Scholar). In this study, transcriptomics and quantitative proteomics were integrated for global gene expression profiling. The comparison of the p-coumarate growth condition with the succinate growth condition yielded the relative expression level for 1680 genes at both the mRNA level and the protein level. 1324 genes had no significant expression change at both levels. 58 genes were up-regulated significantly at both levels; some of these genes are known to be involved in aromatic compound degradation. Interestingly 41 genes were up-regulated significantly at the protein level but not at the mRNA level, warranting further investigation for post-transcriptional regulations and experimental artifacts. Similar trends were also observed in the other comparisons in this study. ConclusionsQuantitative proteomics measurements were conducted to provide a global view of the cellular pathways involved in p-coumarate catabolism for R. palustris by using metabolic stable isotope labeling, MudPIT analysis, and the ProRata data analysis program. By characterizing technical and biological replicates, over 1600 proteins were confidently quantified from R. palustris cultures grown with succinate, benzoate, or p-coumarate as the sole carbon sources. The same R. palustris cultures were also examined by transcriptomics. The transcriptomics results and the quantitative proteomics results were integrated to reconstruct global gene expression profiles of R. palustris at the mRNA level and the protein level. This integrated gene expression data set provided evidence that the anaerobic degradation of p-coumarate proceeds through a non-β-oxidation route, rather than an alternative β-oxidation route, and then through the central benzoyl-CoA pathway. RPA1787, RPA1786, and RPA1206 were hypothesized to be the probable p-coumarate-CoA ligase, p-coumaroyl-CoA hydratase/lyase, and 4-hydroxybenzaldehyde dehydrogenase, respectively, in the non-β-oxidation route. Quantitative proteomics measurements were conducted to provide a global view of the cellular pathways involved in p-coumarate catabolism for R. palustris by using metabolic stable isotope labeling, MudPIT analysis, and the ProRata data analysis program. By characterizing technical and biological replicates, over 1600 proteins were confidently quantified from R. palustris cultures grown with succinate, benzoate, or p-coumarate as the sole carbon sources. The same R. palustris cultures were also examined by transcriptomics. The transcriptomics results and the quantitative proteomics results were integrated to reconstruct global gene expression profiles of R. palustris at the mRNA level and the protein level. This integrated gene expression data set provided evidence that the anaerobic degradation of p-coumarate proceeds through a non-β-oxidation route, rather than an alternative β-oxidation route, and then through the central benzoyl-CoA pathway. RPA1787, RPA1786, and RPA1206 were hypothesized to be the probable p-coumarate-CoA ligase, p-coumaroyl-CoA hydratase/lyase, and 4-hydroxybenzaldehyde dehydrogenase, respectively, in the non-β-oxidation route. DA - 2008/5// PY - 2008/5// DO - 10.1074/mcp.M700147-MCP200 VL - 7 IS - 5 SP - 938-948 SN - 1535-9484 ER - TY - JOUR TI - Theoretical and experimental analyses of safe operating area (SOA) of 1200-V 4H-SiC BJT AU - Gao, Yan AU - Huang, Alex Q. AU - Agarwal, Anant K. AU - Zhang, Qingchun T2 - IEEE TRANSACTIONS ON ELECTRON DEVICES AB - The safe operating area (SOA) of 1200-V SiC bipolar junction transistor (BJT) is investigated by experiments and simulations. The SiC BJT is free of the second breakdown even under the turn-off power density of 3.7 MW/cm 2 . The theoretical boundary of reverse-biased SOA caused by the false turn-on is obtained by simulations. The short-circuit capability of the 1200-V SiC BJT is also investigated theoretically and experimentally. Self-heating is considered by the nonisothermal simulation, and 1800-K maximum local temperature is the simulated critical temperature of device failure. The surface condition is very critical for short-circuit capability. From simulations, when the interface trap density increases, the critical temperature decreases. This is believed to be the reason why the experimental results show much shorter short-circuit withstand time than the simulation showed. DA - 2008/8// PY - 2008/8// DO - 10.1109/TED.2008.926682 VL - 55 IS - 8 SP - 1887-1893 SN - 1557-9646 KW - safe operating area (SOA) KW - short-circuit KW - SiC bipolar junction transistor (BJT) ER - TY - JOUR TI - Group-based key predistribution for wireless sensor networks AU - Liu, Donggang AU - Ning, Peng AU - Du, Wenliang T2 - ACM TRANSACTIONS ON SENSOR NETWORKS AB - Many key predistribution techniques have been developed recently to establish pairwise keys between sensor nodes in wireless sensor networks. To further improve these schemes, researchers have also proposed to take advantage of the sensors' expected locations and discovered locations to help the predistribution of the keying materials. However, in many cases, it is very difficult to deploy sensor nodes at their expected locations or guarantee the correct location discovery at sensor nodes in hostile environments. In this article, a group-based deployment model is developed to improve key predistribution. In this model, sensor nodes are only required to be deployed in groups. The critical observation in the article is that the sensor nodes in the same group are usually close to each other after deployment . This deployment model is practical; it greatly simplifies the deployment of sensor nodes, while still providing an opportunity to improve key predistribution. Specifically, the article presents a novel framework for improving key predistribution using the group-based deployment knowledge. This framework does not require the knowledge of the sensors' expected or discovered locations and is thus suitable for applications where it is difficult to deploy the sensor nodes at their expected locations or correctly estimate the sensors' locations after deployment. To seek practical key predistribution schemes, the article presents two efficient instantiations of this framework, a hash key-based scheme and a polynomial-based scheme . The evaluation shows that these two schemes are efficient and effective for pairwise key establishment in sensor networks; they can achieve much better performance than the previous key predistribution schemes when the sensor nodes are deployed in groups. DA - 2008/3// PY - 2008/3// DO - 10.1145/1340771.1340777 VL - 4 IS - 2 SP - SN - 1550-4867 KW - security KW - design KW - algorithms KW - sensor networks KW - security KW - pairwise key establishment KW - key predistribution KW - group-based deployment ER - TY - JOUR TI - A smart stochastic approach for manifolds smoothing AU - El Ouafdi, A. F. AU - Ziou, D. AU - Krim, H. T2 - COMPUTER GRAPHICS FORUM AB - Abstract In this paper, we present a probabilistic approach for 3D object's smoothing. The core idea behind the proposed method is to relate the problem of smoothing objects to that of tracking the transition probability density functions of an underlying random process. We show that such an approach allows for additional insight and sufficient flexibility compared with existing standard smoothing techniques. In particular, we are able to propose a newer, faster, and simpler smoothing approach that retains and enhances important manifold features. Furthermore, it is demonstrated to improve performance over existing smoothing techniques. DA - 2008/7// PY - 2008/7// DO - 10.1111/j.1467-8659.2008.01275.x VL - 27 IS - 5 SP - 1357-1364 SN - 1467-8659 ER - TY - JOUR TI - Revisiting the definition of animal tool use AU - St Amant, Robert AU - Horton, Thomas E. T2 - Animal Behaviour AB - Benjamin Beck's definition of tool use has served the field of animal cognition well for over 25 years (Beck 1980, Animal Tool Behavior: the Use and Manufacture of Tools, New York, Garland STPM). This article proposes a new, more explanatory definition that accounts for tool use in terms of two complementary subcategories of behaviours: behaviours aimed at altering a target object by mechanical means and behaviours that mediate the flow of information between the tool user and the environment or other organisms in the environment. The conceptual foundation and implications of the new definition are contrasted with those of existing definitions, particularly Beck's. The new definition is informally evaluated with respect to a set of scenarios that highlights differences from Beck's definition as well as those of others in the literature. DA - 2008/4// PY - 2008/4// DO - 10.1016/j.anbehav.2007.09.028 VL - 75 IS - 4 SP - 1199-1208 J2 - Animal Behaviour LA - en OP - SN - 0003-3472 UR - http://dx.doi.org/10.1016/j.anbehav.2007.09.028 DB - Crossref KW - cognition KW - tool use ER - TY - JOUR TI - Performance analysis of IEEE 802.11e EDCA with a virtual collision handier AU - Hwang, Ho Young AU - Kim, Seong Joon AU - Sung, Dan Keun AU - Song, Nah-Oak T2 - IEEE TRANSACTIONS ON VEHICULAR TECHNOLOGY AB - This paper presents an analytical model of IEEE 802.11e enhanced distributed channel access (EDCA) with a virtual collision handler (VCH). The proposed analytical model provides different access categories (ACs) for supporting the quality of service (QoS) of differentiated services by using different contention window (CW) sizes and arbitration interframe space (AIFS) values in EDCA. The proposed model considers a network of stations, each of which has multiple queues and a VCH for different ACs. Based on the proposed model, we analyze the throughput and delay performance of the EDCA with four different ACs and investigate the effect of the VCH by considering two VCH schemes. The analytical and simulation results show that the proposed analytical model is very accurate for various CW sizes and AIFS values. DA - 2008/3// PY - 2008/3// DO - 10.1109/TVT.2007.911611 VL - 57 IS - 2 SP - 1293-1297 SN - 1939-9359 KW - enhanced distributed channel access (EDCA) KW - IEEE 802.11e KW - virtual collision handler (VCH) ER - TY - JOUR TI - Microarray data mining using landmark gene-guided clustering AU - Chopra, P. AU - Kang, J. AU - Yang, J. AU - Cho, H. AU - Kim, H. S. AU - Lee, M. G. T2 - BMC Bioinformatics DA - 2008/// PY - 2008/// VL - 9 ER - TY - JOUR TI - Multipoint-to-point lightpaths in all-optical networks: Dimensioning and cost analysis AU - Bouabdallah, Nizar AU - Pujolle, Guy AU - Perros, Haffy T2 - PERFORMANCE EVALUATION AB - One of the major concerns in optical networks is the bandwidth underutilization problem. In fact, as WDM technology keeps maturing, there is a bandwidth gap between the transmission speed of a wavelength channel (over a Gb/s) and the capacity requirement of customers’ connections. In this regard, building cost-efficient optical networks requires an efficient traffic grooming solution at the high speed optical access nodes. In this paper, we propose and evaluate a new concept of traffic aggregation in wavelength-division multiplexing (WDM) optical networks. Our objective is to reduce the network cost while preserving the benefits of all-optical wavelength-routed networks. In order to assess the efficiency of our proposal, all underlying network costs are compared. These costs include that of the transceivers required at node level as well as the number of wavelengths. Our results show that the proposed aggregation technique can significantly improve the network throughput while reducing its cost. DA - 2008/3// PY - 2008/3// DO - 10.1016/j.peva.2007.06.021 VL - 65 IS - 3-4 SP - 262-285 SN - 1872-745X KW - optical networking KW - traffic grooming KW - network dimensioning KW - cost evaluation ER - TY - JOUR TI - Approximate factorization of multivariate polynomials using singular value decomposition AU - Kaltofen, Erich AU - May, John P. AU - Yang, Zhengfeng AU - Zhi, Lihong T2 - JOURNAL OF SYMBOLIC COMPUTATION AB - We describe the design, implementation and experimental evaluation of new algorithms for computing the approximate factorization of multivariate polynomials with complex coefficients that contain numerical noise. Our algorithms are based on a generalization of the differential forms introduced by W. Ruppert and S. Gao to many variables, and use singular value decomposition or structured total least squares approximation and Gauss–Newton optimization to numerically compute the approximate multivariate factors. We demonstrate on a large set of benchmark polynomials that our algorithms efficiently yield approximate factorizations within the coefficient noise even when the relative error in the input is substantial (10−3). DA - 2008/5// PY - 2008/5// DO - 10.1016/j.jsc.2007.11.005 VL - 43 IS - 5 SP - 359-376 SN - 0747-7171 KW - multivariate polynomial factorization KW - approximate factorization KW - singular value decomposition KW - numerical algebra KW - Gauss-Newton optimization ER - TY - JOUR TI - A framework for identifying compromised nodes in wireless sensor networks AU - Zhang, Qing AU - Yu, Ting AU - Ning, Peng T2 - ACM TRANSACTIONS ON INFORMATION AND SYSTEM SECURITY AB - Sensor networks are often subject to physical attacks. Once a node's cryptographic key is compromised, an attacker may completely impersonate it and introduce arbitrary false information into the network. Basic cryptographic mechanisms are often not effective in this situation. Most techniques to address this problem focus on detecting and tolerating false information introduced by compromised nodes. They cannot pinpoint exactly where the false information is introduced and who is responsible for it. In this article, we propose an application-independent framework for accurately identifying compromised sensor nodes. The framework provides an appropriate abstraction of application-specific detection mechanisms and models the unique properties of sensor networks. Based on the framework, we develop alert reasoning algorithms to identify compromised nodes. The algorithm assumes that compromised nodes may collude at will. We show that our algorithm is optimal in the sense that it identifies the largest number of compromised nodes without introducing false positives. We evaluate the effectiveness of the designed algorithm through comprehensive experiments. DA - 2008/3// PY - 2008/3// DO - 10.1145/1341731.1341733 VL - 11 IS - 3 SP - SN - 1557-7406 KW - algorithms KW - security KW - sensor networks KW - intrusion detection ER - TY - PAT TI - Method of manufacturing gallium nitride based high-electron mobility devices AU - Harris, C. AU - Gehrke, T. AU - Weeks, T. W. AU - Basceri, C. C2 - 2008/// DA - 2008/// PY - 2008/// ER - TY - PAT TI - Gallium nitride based high-electron mobility devices AU - Harris, C. AU - Gehrke, T. AU - Weeks, T. W. AU - Basceri, C. C2 - 2008/// DA - 2008/// PY - 2008/// ER - TY - JOUR TI - Dual-resource TCP/AQM for processing-constrained networks AU - Shin, Minsu AU - Chong, Song AU - Rhee, Injong T2 - IEEE-ACM TRANSACTIONS ON NETWORKING AB - This paper examines congestion control issues for TCP flows that require in-network processing on the fly in network elements such as gateways, proxies, firewalls and even routers. Applications of these flows are increasingly abundant in the future as the Internet evolves. Since these flows require use of CPUs in network elements, both bandwidth and CPU resources can be a bottleneck and thus congestion control must deal with ldquocongestionrdquo on both of these resources. In this paper, we show that conventional TCP/AQM schemes can significantly lose throughput and suffer harmful unfairness in this environment, particularly when CPU cycles become more scarce (which is likely the trend given the recent explosive growth rate of bandwidth). As a solution to this problem, we establish a notion of dual-resource proportional fairness and propose an AQM scheme, called Dual-Resource Queue (DRQ), that can closely approximate proportional fairness for TCP Reno sources with in-network processing requirements. DRQ is scalable because it does not maintain per-flow states while minimizing communication among different resource queues, and is also incrementally deployable because of no required change in TCP stacks. The simulation study shows that DRQ approximates proportional fairness without much implementation cost and even an incremental deployment of DRQ at the edge of the Internet improves the fairness and throughput of these TCP flows. Our work is at its early stage and might lead to an interesting development in congestion control research. DA - 2008/4// PY - 2008/4// DO - 10.1109/TNET.2007.900415 VL - 16 IS - 2 SP - 435-449 SN - 1558-2566 KW - CPU capacity KW - efficiency KW - fairness KW - proportional fairness KW - TCP-AQM KW - transmission link capacity ER - TY - JOUR TI - Coordinating hundreds of cooperative, autonomous vehicles in warehouses AU - Wurman, P. R. AU - D'Andrea, R. AU - Mountz, M. T2 - AI Magazine DA - 2008/// PY - 2008/// VL - 29 IS - 1 SP - 9-19 ER - TY - JOUR TI - From pull-down data to protein interaction networks and complexes with biological relevance AU - Zhang, Bing AU - Park, Byung-Hoon AU - Karpinets, Tatiana AU - Samatova, Nagiza F. T2 - BIOINFORMATICS AB - Recent improvements in high-throughput Mass Spectrometry (MS) technology have expedited genome-wide discovery of protein-protein interactions by providing a capability of detecting protein complexes in a physiological setting. Computational inference of protein interaction networks and protein complexes from MS data are challenging. Advances are required in developing robust and seamlessly integrated procedures for assessment of protein-protein interaction affinities, mathematical representation of protein interaction networks, discovery of protein complexes and evaluation of their biological relevance.A multi-step but easy-to-follow framework for identifying protein complexes from MS pull-down data is introduced. It assesses interaction affinity between two proteins based on similarity of their co-purification patterns derived from MS data. It constructs a protein interaction network by adopting a knowledge-guided threshold selection method. Based on the network, it identifies protein complexes and infers their core components using a graph-theoretical approach. It deploys a statistical evaluation procedure to assess biological relevance of each found complex. On Saccharomyces cerevisiae pull-down data, the framework outperformed other more complicated schemes by at least 10% in F(1)-measure and identified 610 protein complexes with high-functional homogeneity based on the enrichment in Gene Ontology (GO) annotation. Manual examination of the complexes brought forward the hypotheses on cause of false identifications. Namely, co-purification of different protein complexes as mediated by a common non-protein molecule, such as DNA, might be a source of false positives. Protein identification bias in pull-down technology, such as the hydrophilic bias could result in false negatives. DA - 2008/4/1/ PY - 2008/4/1/ DO - 10.1093/bioinformatics/btn036 VL - 24 IS - 7 SP - 979-986 SN - 1460-2059 ER - TY - JOUR TI - Phase-type distributions in stochastic automata networks AU - Sbeity, I. AU - Brenner, L. AU - Plateau, B. AU - Stewart, W. J. T2 - EUROPEAN JOURNAL OF OPERATIONAL RESEARCH AB - Stochastic automata networks (Sans) are high-level formalisms for modeling very large and complex Markov chains in a compact and structured manner. To date, the exponential distribution has been the only distribution used to model the passage of time in the evolution of the different San components. In this paper we show how phase-type distributions may be incorporated into Sans thereby providing the wherewithal by which arbitrary distributions can be used which in turn leads to an improved ability for more accurately modeling numerous real phenomena. The approach we develop is to take a San model containing phase-type distributions and to translate it into another, stochastically equivalent, San model having only exponential distributions. In the San formalism, it is the events that are responsible for firing transitions and our procedure is to associate a stochastic automaton with each event having a phase-type distribution. This automaton models the distribution of time until the event occurs. In this way, the size of the elementary matrices remain small, because the size of the automata are small: the automata are either those of the original San, or are those associated with the phase-type events and are of size k, the number of phases in the representation of the distribution. DA - 2008/5/1/ PY - 2008/5/1/ DO - 10.1016/j.ejor.2007.02.019 VL - 186 IS - 3 SP - 1008-1028 SN - 1872-6860 KW - stochastic automata networks KW - phase-type distributions ER - TY - JOUR TI - Scenario support for effective requirements AU - Alspaugh, Thomas A. AU - Anton, Annie I. T2 - INFORMATION AND SOFTWARE TECHNOLOGY AB - Scenarios are widely used as requirements, and the quality of requirements is an important factor in the efficiency and success of a development project. The informal nature of scenarios requires that analysts do much manual work with them, and much tedious and detailed effort is needed to make a collection of scenarios well-defined, relatively complete, minimal, and coherent. We discuss six aspects of scenarios having inherent structure on which automated support may be based, and the results of using such support. This automated support frees analysts to concentrate on tasks requiring human intelligence, resulting in higher-quality scenarios for better system requirements. Two studies validating the work are presented. DA - 2008/2// PY - 2008/2// DO - 10.1016/j.infsof.2006.12.003 VL - 50 IS - 3 SP - 198-220 SN - 1873-6025 KW - requirements engineering KW - scenario analysis KW - scenario management ER - TY - JOUR TI - Modeling self-efficacy in intelligent tutoring systems: An inductive approach AU - McQuiggan, Scott W. AU - Mott, Bradford W. AU - Lester, James C. T2 - USER MODELING AND USER-ADAPTED INTERACTION DA - 2008/2// PY - 2008/2// DO - 10.1007/s11257-007-9040-y VL - 18 IS - 1-2 SP - 81-123 SN - 1573-1391 KW - affective user modeling KW - affective student modeling KW - self-efficacy KW - intelligent tutoring systems KW - inductive learning KW - human-computer interaction ER - TY - JOUR TI - Bright, low voltage europium doped gallium oxide thin film electroluminescent devices AU - Wellenius, P. AU - Suresh, A. AU - Muth, J. F. T2 - APPLIED PHYSICS LETTERS AB - Europium doped gallium oxide thin film electroluminescent devices with bright, red emission (611nm) and relatively low threshold voltages of 60V were produced using pulsed laser deposition. The use of transparent conducting electrodes of amorphous InGaZnO on transparent aluminum titanium oxide/indium tin oxide/7059 Corning glass substrates resulted in a device that is transparent throughout the visible spectrum. At 100V, with 1kHz excitation, the luminance was 221cd∕m2. The Sawyer-Tower circuit analysis and time dependent emission measurements suggest that the charge trapping at the aluminum titanium oxide/Ga2O3:Eu interface plays an important role in producing efficient emission. DA - 2008/1/14/ PY - 2008/1/14/ DO - 10.1063/1.2824846 VL - 92 IS - 2 SP - SN - 0003-6951 ER - TY - JOUR TI - peerTalk: A peer-to-peer multiparty voice-over-IP system AU - Gu, Xiaohui AU - Wen, Zhen AU - Yu, Philip S. AU - Shae, Zon-Yin T2 - IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS AB - Multiparty voice-over-IP (MVolP) services allow a group of people to freely communicate with each other via the Internet, which have many important applications such as online gaming and teleconferencing. In this paper, we present a peer-to-peer MVolP system called peerTalk. Compared to traditional approaches such as server-based mixing, peerTalk achieves better scalability and failure resilience by dynamically distributing the stream processing workload among different peers. Particularly, peerTalk decouples the MVolP service delivery into two phases: mixing phase and distribution phase. The decoupled model allows us to explore the asymmetric property of MVolP services (for example, distinct speaking/listening activities and unequal inbound/outbound bandwidths) so that the system can better adapt to distinct stream mixing and distribution requirements. To overcome arbitrary peer departures/ failures, peerTalk provides lightweight backup schemes to achieve fast failure recovery. We have implemented a prototype of the peerTalk system and evaluated its performance using both a large-scale simulation testbed and a real Internet environment. Our initial implementation demonstrates the feasibility of our approach and shows promising results: peerTalk can outperform existing approaches such as P2P overlay multicast and coupled distributed processing for providing MVolP services. DA - 2008/4// PY - 2008/4// DO - 10.1109/TPDS.2007.70766 VL - 19 IS - 4 SP - 515-528 SN - 1558-2183 KW - peer-to-peer streaming KW - voice-over-IP KW - adaptive system KW - service overlay network KW - quality-of-service KW - failure resilience ER - TY - JOUR TI - Visual perception and mixed-initiative interaction for assisted visualization design AU - Healey, Christopher G. AU - Kocherlakota, Sarat AU - Rao, Vivek AU - Mehta, Reshma AU - Amant, Robert St. T2 - IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS AB - This paper describes the integration of perceptual guidelines from human vision with an AI-based mixed-initiative search strategy. The result is a visualization assistant called ViA, a system that collaborates with its users to identify perceptually salient visualizations for large, multidimensional datasets. ViA applies knowledge of low-level human vision to: (1) evaluate the effectiveness of a particular visualization for a given dataset and analysis tasks; and (2) rapidly direct its search towards new visualizations that are most likely to offer improvements over those seen to date. Context, domain expertise, and a high-level understanding of a dataset are critical to identifying effective visualizations. We apply a mixed-initiative strategy that allows ViA and its users to share their different strengths and continually improve ViA's understanding of a user's preferences. We visualize historical weather conditions to compare ViA's search strategy to exhaustive analysis, simulated annealing, and reactive tabu search, and to measure the improvement provided by mixed-initiative interaction. We also visualize intelligent agents competing in a simulated online auction to evaluate ViA's perceptual guidelines. Results from each study are positive, suggesting that ViA can construct high-quality visualizations for a range of real-world datasets. DA - 2008/// PY - 2008/// DO - 10.1109/TVCG.2007.70436 VL - 14 IS - 2 SP - 396-411 SN - 1941-0506 KW - computer graphics KW - perception KW - search KW - user interfaces KW - visualization ER - TY - JOUR TI - Virtual organizations AU - Ripeanu, Matei AU - Singh, Munindar P. AU - Vazhkudai, Sudharshan S. T2 - IEEE INTERNET COMPUTING AB - Today's organizations are no longer constrained by traditional time and place barriers. Instead, information technology supports virtual organizations: flexible networks of independent, globally distributed entities that share knowledge and resources and work toward a common goal. Resources aren't limited to computing power, but include elements as diverse as storage, network links, data sets, analysis tools, sensors, and scientific instruments. Sharing policies are highly diverse, given that sharing must be controlled, secure, flexible, and limited in time. DA - 2008/// PY - 2008/// DO - 10.1109/mic.2008.48 VL - 12 IS - 2 SP - 10-12 SN - 1089-7801 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-41649089050&partnerID=MN8TOARS ER - TY - JOUR TI - Incorporating events into cross-organizational business processes AU - Chakravarty, Payal AU - Singh, Munindar P. T2 - IEEE INTERNET COMPUTING AB - Because Web-scale processes are inherently cross-organizational, they require the robust enactment of interactions among autonomous parties. However, specifying the processes involved is difficult. To overcome this obstacle, the authors use a business protocol that lets the applicable events and responses vary based on where the process is deployed and the infrastructure and IT applications installed therein. Treating events and business logic as separate concerns also yields clearer models and improves reusability. The authors describe the architecture and tools and outline a methodology by which each participant in a process can define, detect, and respond to events. DA - 2008/// PY - 2008/// DO - 10.1109/MIC.2008.35 VL - 12 IS - 2 SP - 46-53 SN - 1941-0131 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-41649118788&partnerID=MN8TOARS ER - TY - JOUR TI - Analyzing regulatory rules for privacy and security requirements AU - Breaux, Travis D. AU - Anton, Annie I. T2 - IEEE TRANSACTIONS ON SOFTWARE ENGINEERING AB - Information practices that use personal, financial and health-related information are governed by U.S. laws and regulations to prevent unauthorized use and disclosure. To ensure compliance under the law, the security and privacy requirements of relevant software systems must be properly aligned with these regulations. However, these regulations describe stakeholder rules, called rights and obligations, in complex and sometimes ambiguous legal language. These "rules" are often precursors to software requirements that must undergo considerable refinement and analysis before they are implementable. To support the software engineering effort to derive security requirements from regulations, we present a methodology to extract access rights and obligations directly from regulation texts. The methodology provides statement-level coverage for an entire regulatory document to consistently identify and infer six types of data access constraints, handle complex cross-references, resolve ambiguities, and assign required priorities between access rights and obligations to avoid unlawful information disclosures. We present results from applying this methodology to the entire regulation text of the U.S. Health Insurance Portability and Accountability Act (HIPAA) Privacy Rule. DA - 2008/// PY - 2008/// DO - 10.1109/TSE.2007.70746 VL - 34 IS - 1 SP - 5-20 SN - 1939-3520 KW - data security and privacy KW - laws and regulations KW - compliance KW - accountability KW - requirements engineering ER - TY - JOUR TI - Search-based inference of dialect grammars AU - Di Penta, M. AU - Lombardi, P. AU - Taneja, K. AU - Troiano, L. T2 - Soft Computing (Berlin, Germany) DA - 2008/// PY - 2008/// VL - 12 IS - 1 SP - 51-66 ER -