ppxscal/embedding_network huggingface dataset:
Decrypting the shark text encryption scheme
Authors: Charles Ashbacher
Venue: Journal of Computing Sciences in Colleges (2008)

In his book, "The Raw Shark Texts", Steven Hall introduces an encryption scheme based on the QWERTY keyboard. By performing some simple rearrangements, the keyboard can be changed so that each letter key is surrounded by a combination of eight other letter keys. The encryption scheme is that when the key in the center of this nine key combination is pressed, one of the eight surrounding keys is randomly selected and printed instead. While messages encrypted this way can be decrypted using a lengthy brute-force method by applying a computer program, engaging in some computations using the fundamentals of conditional probability can speed up that search. This presentation will explain those techniques and how messages encrypted using this scheme can be decrypted. This assignment has applications to a course in encryption and data compression taught at Mount Mercy College.
Using MERIS on Envisat for land cover mapping in the Netherlands
Authors: J. G. P. W. Clevers, M. E. Schaepman, C. A. Mücher, A. J. W. de Wit, R. Zurita-Milla, H. M. Bartholomeus
Venue: International Journal of Remote Sensing (2007)

This paper describes the results of a feasibility study to test the usefulness of MERIS for land cover mapping. The Netherlands was used as a test site because of its highly fragmented landscape. Results showed that the geometric and radiometric properties of the studied MERIS images of the Netherlands are suitable for land applications. Calculation of principal components and correlation coefficients revealed that the 15 MERIS bands provided a lot of redundant spectral information. For land applications, information came from the visible part of the spectrum on the one hand and from the near-infrared part on the other hand. In addition, the red-edge slope of the reflectance curve (in particular MERIS band 9 at about 708 nm) provided supplementary information. The Dutch land use database LGN5 was used as a reference for classifications in this study after aggregation from 25 m to 300 m and recoding to 7 relevant land cover classes. For land cover classification best results in terms of classification accuracies were obtained for the image of 14 July 2003. For the seven land cover classes selected the overall classification accuracy was 67.2%. A multitemporal classification did not improve the overall classification accuracy.
Hacking Exposed Web 2.0: Web 2.0 Security Secrets and Solutions, 1 edition
Authors: Rich Cannings, Himanshu Dwivedi, Zane Lackey
Venue:  (2007)

Lock down next-generation Web services "This book concisely identifies the types of attacks which are faced daily by Web 2.0 sites, and the authors give solid, practical advice on how to identify and mitigate these threats." --Max Kelly, CISSP, CIPP, CFCE, Senior Director of Security, FacebookProtect your Web 2.0 architecture against the latest wave of cybercrime using expert tactics from Internet security professionals. Hacking Exposed Web 2.0 shows how hackers perform reconnaissance, choose their entry point, and attack Web 2.0-based services, and reveals detailed countermeasures and defense techniques. You'll learn how to avoid injection and buffer overflow attacks, fix browser and plug-in flaws, and secure AJAX, Flash, and XML-driven applications. Real-world case studies illustrate social networking site weaknesses, cross-site attack methods, migration vulnerabilities, and IE7 shortcomings.Plug security holes in Web 2.0 implementations the proven Hacking Exposed wayLearn how hackers target and abuse vulnerable Web 2.0 applications, browsers, plug-ins, online databases, user inputs, and HTML formsPrevent Web 2.0-based SQL, XPath, XQuery, LDAP, and command injection attacks Circumvent XXE, directory traversal, and buffer overflow exploits Learn XSS and Cross-Site Request Forgery methods attackers use to bypass browser security controls Fix vulnerabilities in Outlook Express and Acrobat Reader add-onsUse input validators and XML classes to reinforce ASP and .NET security Eliminate unintentional exposures in ASP.NET AJAX (Atlas), Direct Web Remoting, Sajax, and GWT Web applicationsMitigate ActiveX security exposures using SiteLock, code signing, and secure controlsFind and fix Adobe Flash vulnerabilities and DNS rebinding attacks Table of contentsForewordAcknowledgmentsIntroductionPart I: Attacking Web 2.0Chapter 1. Common Injection AttacksChapter 2. Cross-Site ScriptingPart II: Next Generation Web Application AttacksChapter 3. Cross-Domain AttacksChapter 4. Malicious JavaScript and AJAXChapter 5. .Net SecurityPart III: AJAXChapter 6. AJAX Types, Discovery, and Parameter ManipulationChapter 7. AJAX Framework ExposuresPart IV: Thick ClientsChapter 8. ActiveX SecurityChapter 9. Attacking Flash ApplicationsIndex
Water-mediated interactions in the CRP-cAMP-DNA complex: Does water mediate sequence-specific binding at the DNA primary-kink site?
Authors: Bryan M. B. VanSchouwen, Heather L. Gordon, Stuart M. Rothstein, Yuto Komeiji, Kaori Fukuzawa, Shigenori Tanaka
Venue: Computational Biology and Chemistry (2008)

The cyclic AMP receptor protein (CRP) of Escherichia coli binds preferentially to DNA sequences possessing a T:A base pair at position 6 (at which the DNA becomes kinked), but with which it does not form any direct interactions. It has been proposed that indirect readout is involved in CRP-DNA binding, in which specificity for this base pair is primarily related to sequence effects on the energetic susceptibility of the DNA to kink formation. In the current study, the possibility of contributions to indirect readout by water-mediated hydrogen bonding of CRP with the T:A base pair was investigated. A 1.0ns molecular dynamics simulation of the CRP-cAMP-DNA complex in explicit solvent was performed, and assessed for water-mediated CRP-DNA hydrogen bonds; results were compared to several X-ray crystal structures of comparable complexes. While several water-mediated CRP-DNA hydrogen bonds were identified, none of these involved the T:A base pair at position 6. Therefore, the sequence specificity for this base pair is not likely enhanced by water-mediated hydrogen bonding with the CRP.
Numerical implementation of the Adomian decomposition method for nonlinear Volterra integral equations of the second kind
Authors: SH. Javadi, A. Davari, E. Babolian
Venue: International Journal of Computer Mathematics (2007)

In this paper we propose new ideas for the implementation of the Adomian decomposition method to solve nonlinear Volterra integral equations. Numerical examples are presented to illustrate the method for nonlinear Volterra integral equations of the second kind.
Instruction Scheduling for Variation-Originated Variable Latencies
Authors: Toshinori Sato, Shingo Watanabe
Venue: Proceedings of the 9th international symposium on Quality Electronic Design (2008)

The advance in semiconductor technologies presents the serious problem of parameter variations. They affect threshold voltage of transistors and thus circuit delay also has variations. Recently, variable latency adders and long latency adders are proposed to manage the variation problem. Unfortunately, replacing a variation-affected adder with the long latency one has severe impact on processor performance. In order to maintain performance, the present paper proposes an instruction scheduling technique considering instruction criticality. By issuing and executing only uncritical instructions in the long latency ALU, we can maintain processor performance. From detailed simulations, we find that the proposed scheduling technique improves processor performance by 12.5% on average over the conventional scheduling and that performance degradation from a variation-free processor is only 4.0% on average, when 2 of 4 ALU’s are affected by variations.
Bayesian density estimation using skew student-t-normal mixtures
Authors: Celso Rômulo Barbosa Cabral, Heleno Bolfarine, José Raimundo Gomes Pereira
Venue: Computational Statistics Data Analysis (2008)

We present a Bayesian approach for modeling heterogeneous data and estimate multimodal densities using mixtures of Skew Student-t-Normal distributions [Gomez, H.W., Venegas, O., Bolfarine, H., 2007. Skew-symmetric distributions generated by the distribution function of the normal distribution. Environmetrics 18, 395-407]. A stochastic representation that is useful for implementing a MCMC-type algorithm and results about existence of posterior moments are obtained. Marginal likelihood approximations are obtained, in order to compare mixture models with different number of component densities. Data sets concerning the Gross Domestic Product per capita (Human Development Report) and body mass index (National Health and Nutrition Examination Survey), previously studied in the related literature, are analyzed.
slab: smart labeling of family photos through an interactive interface
Authors: Ehsan Fazl-Ersi, I. Scott MacKenzie, John K. Tsotsos
Venue: Proceedings of the 8th ACM/IEEE-CS joint conference on Digital libraries (2008)

A novel technique for semi-automatic photo annotation is proposed and evaluated. The technique, sLab, uses face processing algorithms and a simplified user interface for labeling family photos. A user study compared our system with two others. One was Adobe Photoshop Element. The other was an in-house implementation of a face clustering interface recently proposed in the research community. Nine participants performed an annotation task with each system on faces extracted from a set of 150 images from their own family photo albums. As the faces were all well known to participants, accuracy was near perfect with all three systems. On annotation time, sLab was 25% faster than Photoshop Element and 16% faster than the face clustering interface.
Art, design, education and research in pursuit of interactive experiences
Authors: Geoffrey Shea
Venue: Proceedings of the 7th ACM conference on Designing interactive systems (2008)

In the development of mobile and location-specific experience creation, artists, designers and researchers at the Ontario College of Art & Design are developing new approaches to creation and collaboration that take into account the realities of artistic, academic and technical cultures. These included iterative creation strategies, co-evolution of technical platforms and cultural content, and rapid prototyping through charettes. This paper will examine some of the strategies employed across several projects which all focused on creating new content and new types of content delivery for users of mobile devices, particularly cell phones. It will draw examples from games, sound compositions and virtual theatre experiences.
Exploring the collective actions of public servants in e-government development
Authors: Tzu-Chuan Chou, Jau-Rong Chen, Ching-Kuo Pu
Venue: Decision Support Systems (2008)

The importance of e-government has been widely recognized. However, the roles of public servants on e-government development have not yet been convincingly demonstrated. The main purpose of this paper is to explore the collective actions in the development of e-government in terms of public servants' information literacy. Drawing on a case study of Kaohsiung City, Taiwan, both the motivational and structural dimensions of collective actions are examined. Based on evidence from the case, this study proposes nine possible collective action problems and their effects that influence cooperative behaviors of public servants. The implications and future research directions are also discussed.
Professor Andy Clark on Natural-born Cyborgs
Authors: Andy Clark
Venue: Ubiquity (2008)

Bio of Dr. Clark: Dr. Andy Clark is a professor of philosophy and chair in logic and metaphysics at the University of Edinburgh in Scotland. Previously, he taught at Washington University at St. Louis and the University of Sussex in England. Clark is one of the founding members of the Contact collaborative research project, whose aim is to investigate the role environment plays in shaping the nature of conscious experience. Dr. Andy Clark research interests include philosophy of mind, artificial intelligence, including robotics, artificial life, embodied cognition, and mind, technology and culture. Dr. Clark's papers and books deal with the philosophy of mind and he is considered a leading scientist in mind extension. He has also written extensively on connectionism, robotics, and the role and nature of mental representation.
A thematic approach to emerging narrative structure
Authors: Charlie Hargood, David E. Millard, Mark J. Weal
Venue: Proceedings of the hypertext 2008 workshop on Collaboration and collective intelligence (2008)

In this paper we look at the possibility of using a thematic model of narrative to find emergent structure in tagged collections. We propose that a thematic underpinning could provide the narrative direction which can often be a problem with stories from existing narrative generation methods, and present a thematic model of narrative built of narrative atoms and their features, motifs and themes. We explore the feasibility of our approach by examining how collaborative tags in online collections match these properties, and find that while tags match across the model the majority are higher level (matching broader themes and motifs rather than more specific features) which may require further investigation into their utility.
Some special types of solutions of a class of the (N+1)-dimensional nonlinear wave equations
Authors: Deng-Shan Wang, Zhenya Yan, Hongbo Li
Venue: Computers Mathematics with Applications (2008)

Some special types of solutions with arbitrary functions for the (N+1)-dimensional sine-cosine-Gordon equation, the (N+1)-dimensional double sinh-Gordon equation, and the (N+1)-dimensional sinh-cosinh-Gordon equations are constructed by means of the separation transformation approach. As an illustrative sample, the properties of some solutions are shown by their figures.
Data-driven Networking Reveals 5-Genes Signature for Early Detection of Lung Cancer
Authors: Vladimir Kuznetsov, Sterling Thomas, Danail Bonchev
Venue: Proceedings of the 2008 International Conference on BioMedical Engineering and Informatics - Volume 01 (2008)

A new strategy is developed for a gene signature search proceeding from a biological basis in analyzing microarray databases. The procedure involves a combination of known and original methods for correlation, statistical, and network analysis. The application of the strategy to lung adenocarcinoma resulted in a 5-gene signature, which included four genes not associated earlier with lung adenocarcinoma. 93-96% accuracy of classification of cancer vs. normal was achieved. The final stage of our procedure included expanding of the gene signature network to a 43 gene/protein network, which showed that the five genes are in the cross-talk of 24 pathways, providing thus information for mechanistic analysis.
A Distributed Defense Framework for Flooding-Based DDoS Attacks
Authors: Yonghua You, Mohammad Zulkernine, Anwar Haque
Venue: Proceedings of the 2008 Third International Conference on Availability, Reliability and Security (2008)

A flooding-based Distributed Denial of Service (DDoS) attack sends a large amount of unwanted traffic to a victim machine. Existing network-level congestion control mechanisms are inadequate in preventing service quality from deteriorating because of these attacks. We propose a distributed framework to defend against DDoS attacks. It has three major components: detection, traceback, and traffic control. We present the traffic control component in detail in this paper. A distance-based rate limit mechanism is proposed to allow the traffic control component at the victim end request the defense systems at the source end to set up rate limits on the edge routers of the attack source ends. This rate limit mechanism efficiently reduces attack traffic from being forwarded to the victim. We evaluate the DDoS defense framework using the NS2 platform. The results demonstrate that the framework can effectively controlattack traffic to sustain quality of service for legitimate traffic compared to the pushback technique.
A quasistatic contact problem with normal compliance and damage involving viscoelastic materials with long memory
Authors: M. Campo, J. R. Fernández, Á. Rodríguez-Arós
Venue: Applied Numerical Mathematics (2008)

In this work, a model for the quasistatic frictionless contact between a viscoelastic body with long memory and a foundation is studied. The material constitutive relation is assumed to be nonlinear and the contact is modelled with the normal compliance condition, i.e., the obstacle is assumed deformable. The mechanical damage of the material, caused by excessive stress or strain, is described by the damage function, which is modelled by a nonlinear partial differential equation. We derive a variational formulation for the problem and prove the existence of its unique weak solution. Then, we introduce a fully discrete scheme for the numerical solutions of the problem, based on the finite element method to approximate the spatial variable and an Euler scheme to discretize the time derivatives, and we obtain error estimates on the approximate solutions. Finally, some numerical results are presented in the simulation of two-dimensional test problems.
P2PNS: A Secure Distributed Name Service for P2PSIP
Authors: Ingmar Baumgart
Venue: Proceedings of the 2008 Sixth Annual IEEE International Conference on Pervasive Computing and Communications (2008)

Decentralized Voice over IP networks are a promising alternative to classical server-based SIP networks especially in disaster areas or areas without centralized infrastructure. This paper presents P2PNS, a secure distributed name service for P2PSIP. P2PNS can be used to resolve SIP AoRs to Contact URIs without using DNS or centralized SIP servers. The name service provides several security mechanisms to efficiently prevent identity theft and to ensure the uniqueness of SIP AoRs in a completely decentralized and untrusted network. The proposed two-stage name resolution mechanism allows to efficiently handle frequent IP address changes. Because P2PNS provides a generic name service it is not limited to P2PSIP but can also be used e.g. to build a distributed DNS system.
Brief Communication: Why have serine/threonine/tyrosine kinases been evolutionarily selected in eukaryotic signaling cascades?
Authors: Hyung-Seok Choi, Jeong-Rae Kim, Sang-Woo Lee, Kwang-Hyun Cho
Venue: Computational Biology and Chemistry (2008)

The signal transduction systems of eukaryotes are different from those of prokaryotes with respect to their structures and mechanisms. The main signal transduction system of prokaryotes called the two-component system (TCS) is a one-step phosphorelay system composed of a histidine kinase (HK) while the central signal transduction system of eukaryotes called the mitogen-activated protein kinase (MAPK) cascade system (MCS) is a multi-step phosphorelay system composed of serine/threonine/tyrosine kinases (STYKs). The two signal transduction systems are also different in their transphosphorylation mechanisms. HK in the TCS transfers its own phosphate group to the response regulator protein while STYKs in the MCS phosphorylate other proteins using ATP. We were intrigued by the different dynamics resulting from such differences and wondered why STYKs instead of HKs have been evolutionarily selected in eukaryotic signaling cascades. In this paper, we compared the dynamical characteristics of two mathematical models which reflect such differences between the TCS and the MCS, and found that STYKs are more appropriate for cascade structures in eukaryotic signal transduction than HK with respect to the duration and settling time of response signals.
Case studies in model integration
Authors: M. Bigand, J. P. Bourey, N. Perry, M. Mauchand
Venue: International Journal of Computer Integrated Manufacturing (2007)

The current paper presents three case studies dealing with the integration of practical models, based on data-driven integration, model unification and use of the universal modified language (UML) language. The four steps of this approach are detailed, highlighted with three examples: a model-oriented problematic, an application in a small and medium-sized enterprise (SME) context, and a methodological approach in the car-manufacturing context. Finally, a comparison of these three studies is discussed.
New Chessboard (8×8) Representation of the Standard Genetic Code, and Its Application for Representing Primary Structures of Proteins
Authors: Alexandru T. Balaban, Milan Randic
Venue: Proceedings of the 2008 International Conference on Biocomputation, Bioinformatics, and Biomedical Technologies (2008)

In the new genetic code chessboard representation, the 1st nucleotide of triplet codons is assigned to each of the four quadrants; the 2nd nucleotide to each of the 16 subquadrants; and the 3rd nucleotide to the 8×8 = 64 cells of the chessboard, following in all cases the same clockwise ordering C-U-G-A. The result is an easily constructed and visualized representation of the genetic code that can be remembered by means of a mnemogram.
Issues in Australian ICT Education
Authors: Tony Koppi, Fazel Naghdy, Joe Chicharo
Venue: Proceedings of the 19th Australian Conference on Software Engineering (2008)

This session at the Australian Software Engineering Conference is concerned with ICT education from the holistic perspective of preparation in high schools, the university experience, transition to the workforce, and the contribution by industry, government, and professional bodies. The project to ascertain the issues and challenges facing the national ICT education sector is supported by the Carrick Institute as a Discipline-Based Initiative. Consultations to date with various stakeholders have revealed numerous concerns that include: the dispersed nature of the ICT sector; erroneous perceptions of ICT disciplines; decline in enrolments; gender imbalance; lack of industry involvement; and balancing knowledge with generic skills acquisition. This forum will involve the project team and invited participants to report on findings from consultations and research. Attendees will be invited to respond and to contribute their issues and challenges that are of particular concern to the software engineering community. The seven disciplines that comprise ICT are Electrical Engineering, Computer Engineering, Telecommunications Engineering, Software Engineering, Computer Science, Information Technology, and Information Systems.
Fast Gaussian process methods for point process intensity estimation
Authors: John P. Cunningham, Krishna V. Shenoy, Maneesh Sahani
Venue: Proceedings of the 25th international conference on Machine learning (2008)

Point processes are difficult to analyze because they provide only a sparse and noisy observation of the intensity function driving the process. Gaussian Processes offer an attractive framework within which to infer underlying intensity functions. The result of this inference is a continuous function defined across time that is typically more amenable to analytical efforts. However, a naive implementation will become computationally infeasible in any problem of reasonable size, both in memory and run time requirements. We demonstrate problem specific methods for a class of renewal processes that eliminate the memory burden and reduce the solve time by orders of magnitude.