ppxscal/embedding_network huggingface dataset:
Research Article: In silico analyses of a new group of fungal and plant RecQ4-homologous proteins
Authors: Fernanda Barea, Simone Tessaro, Diego Bonatto
Venue: Computational Biology and Chemistry (2008)

Bacterial and eukaryotic RecQ helicases comprise a family of homologous proteins necessary for maintaining genomic integrity during the cell cycle and DNA repair. There is one known bacterial RecQ helicase, and five eukaryotic RecQ helicases that have been described: RecQ1p, RecQ4p, RecQ5p, Bloom, and Werner. While the biochemical functions of Bloom and Werner helicases are well understood, the same is not true for RecQ4p helicase. RecQ4p mutations lead to pathologies like Rothmund-Thompson syndrome (RTS), RAPADILINO, and Baller-Gerold syndrome (BGS). Until now, RecQ4p helicases had only been described in metazoans, and their presence in organisms like fungi and plants were not known. Thus far only one RecQ-homologous protein (Sgs1p), similar to Bloom helicase, has been described in fungal genomes. In the present study we employed an in silico approach, and successfully identified and characterized a second RecQ helicase from the genomes of different fungal and two plant species that shows similarity to metazoan RecQ4 proteins. An in-depth phylogenetic analysis of these new fungal and plant RecQ4-like sequences (termed Hrq1p) indicated that they are orthologous to the metazoan RecQ4p. We employed hydrophobic cluster analysis (HCA) and three-dimensional modeling of selected Hrq1p sequences to compare conserved regions among Hrq1p, human RecQ4p and bacterial RecQp. The results indicated that Hrq1p sequences, as previously observed for metazoan RecQ4 proteins, probably act in genomic maintenance and/or chromatin remodeling in fungal and plant cells.
CLL: A Cryptographic Link Layer for Local Area Networks
Authors: Yves Igor Jerschow, Christian Lochert, Björn Scheuermann, Martin Mauve
Venue: Proceedings of the 6th international conference on Security and Cryptography for Networks (2008)

Ethernet and IP form the basis of the vast majority of LAN installations. But these protocols do not provide comprehensive security mechanisms, and thus give way for a plethora of attack scenarios. In this paper, we introduce a layer 2/3 security extension for LANs, the Cryptographic Link Layer (CLL). CLL provides authentication and confidentiality to the hosts in the LAN by safeguarding all layer 2 traffic including ARP and DHCP handshakes. It is transparent to existing protocol implementations, especially to the ARP module and to DHCP clients and servers. Beyond fending off external attackers, CLL also protects from malicious behavior of authenticated clients. We discuss the CLL protocol, motivate the underlying design decisions, and finally present implementations of CLL for both Windows and Linux. Their performance is demonstrated through real-world measurement results.
Some New Modes of Competence-Based Derivations in CD Grammar Systems
Authors: Erzsébet Csuhaj-Varjú, Jürgen Dassow, György Vaszil
Venue: Proceedings of the 12th international conference on Developments in Language Theory (2008)

We introduce some new cooperation protocols for cooperating distributed (CD) grammar systems. They depend on the number of different nonterminals present in the sentential form if a component has finished its work, i.e. on the final competence or efficiency of the grammar on the string (the competence is large if the number of the different nonterminals is small). We prove that if the underlying derivation mode is the t-mode derivation, then some variants of these systems determine the class of random context ET0L languages. If these CD grammar systems use the k step limited derivations (for k ¿ 3) as underlying derivations, they are able to generate any recursively enumerable language.
Application Briefs
Authors: W. Myers
Venue: IEEE Computer Graphics and Applications (1982)

Continental Graphics opened a new facility last March in central Los Angeles to provide computer-aided design and drafting services to the area's architects and engineers. " The system gives architects and engineers the freedom to practice their profession rather than being involved in repetitious work which a computer can perform in minutes," Curtis F. Bourland, president, pointed out at an open house attended by potential users. The company plans similar facilities in Denver, Houston, San Francisco, and Orange County (California). The ACM Portal is published by the Association for Computing Machinery. Copyright © 2010 ACM, Inc. Terms of Usage Privacy Policy Code of Ethics Contact Us Useful downloads: Adobe Acrobat QuickTime Windows Media Player Real Player
C Simplified
Authors: Jeffrey D. Jones
Venue:  (2008)

A complete yet easy to follow programming book for the C beginner as well as a great reference book for the more experienced programmer. Unlike many other programming language books, C Simplified was developed specifically for use in the classroom and has been critiqued by thousands of students over a dozen years before finally being made available to the general public. It encompasses all the major features of C including the History of C; the Standard Library; Identifiers; Arithmetic, Compound, Relational, Logical, and Bitwise Operators; Data Types; Pointers; Flow Control statements; Arrays and Strings; Input and Output; Functions; the C Preprocessor; Structures, Unions and Enumeration types; and Linked List data structures In addition to its straightforward style of explanation, this book contains many examples along with numerous exercises, with answers, to help assure a thorough understanding of how C functions. C Simplified is one book that truly lives up to its name.
Local curvature constrained level set segmentation using minimal weights covered tree on curvature density graph
Authors: Fahima Djabelkhir
Venue: Proceedings of the 7th WSEAS International Conference on Signal Processing, Robotics and Automation (2008)

Owing to the inhomogeneity and ill defined edges present in images, the incorporation of prior knowledge into level set models, in image segmentation, is a field of active researches. In this paper, a new way of incorporating prior information to constrain the evolution of the level set model during the segmentation is presented. This technique allows resolving the problem of applying the same curvature coefficient in all image regions. We construct, based on Kruskal algorithm, the minimal weights covered tree of the initial density graph due to boundary curvature. The simulation results using different kind of images show that we get better results with respect to propagation, precision and homogeneity between the final propagating contour and local regions, compared to the classical level set method.
Games, Time, and Probability: Graph Models for System Design and Analysis
Authors: Thomas A. Henzinger
Venue: Proceedings of the 33rd conference on Current Trends in Theory and Practice of Computer Science (2007)

Digital technology is increasingly deployed in safety-critical situations. This calls for systematic design and verification methodologies that can cope with three major sources of system complexity: concurrency, real time, and uncertainty. We advocate a two-step process: formal modeling followed by algorithmic analysis (or, "model building" followed by "model checking"). We model the concurrent components of a reactive system as potential collaborators or adversaries in a multi-player game with temporal objectives, such as system safety. The real-time aspect of embedded systems requires models that combine discrete state transitions and continuous state evolutions. Uncertainty in the environment is naturally modeled by probabilistic state changes. As a result, we obtain three orthogonal extensions of the basic state-transition graph model for reactive systems --game graphs, timed graphs, and stochastic graphs-- as well as combinations thereof. In this short text, we provide a uniform exposition of the underlying definitions. For verification algorithms, we refer the reader to the literature.
Robust Designs for Directed Edge Overstriking CNNs with Applications
Authors: Yongmei Su, Lequan Min, Xinjian Zhuo
Venue: Proceedings of the 5th international symposium on Neural Networks: Advances in Neural Networks, Part II (2008)

A kind of templates of coupled Cellular Neural Network (CNN) are introduced, which are able to generate gray edges to a binary image and overstrike them "directionally". The robustness analysis gives the template parameter inequalities which guarantee the corresponding CNNs to work well for performing prescribed tasks. As applications, the CNNs may be used to generate art letters.
Symbolic Computation of Petri Nets
Authors: Andres Iglesias, Sinan Kapcak
Venue: Proceedings of the 7th international conference on Computational Science, Part II (2007)

Petri nets are receiving increasing attention from the scientific community during the last few years. They provide the users with a powerful formalism for describing and analyzing a variety of information processing systems such as finite-state machines, concurrent systems, multiprocessors and parallel computation, formal languages, communication protocols, etc. Although the mathematical theory of Petri nets has been intensively analyzed from several points of view, the symbolic computation of these nets is still a challenge, particularly for general-purpose computer algebra systems (CAS). In this paper, a new Mathematica package for dealing with some Petri nets is introduced.
Integration of an online digital logic design lab for it education
Authors: Abdullah Y. Al-Zoubi, Sabina Jeschke, Nicole Martina Natho, Jarir Nsour, Olivier Frederic Pfeiffer
Venue: Proceedings of the 9th ACM SIGITE conference on Information technology education (2008)

Digital electronics is a fundamental course in electrical engineering and many information technology programs, as well as most other science programs. In this paper, we present web-based system aimed at teaching logic design concepts and practices for computer science and engineering students implemented using LabVIEW. Experiments, which include digital logic gates, combinational logic circuits, seven segment display, sequential logic and counters are easily constructed and performed, both in traditional and online setups. This course is as an example of how to integrate a combination of theory and lab experiments simultaneously in a blended learning environment, where lectures can present the material for students to access, and at the same time per-form the experiments online into the curriculum.
An analytical study of E-learning on new thinking direction and its application in education
Authors: Rong-Jyue Fang, Yao-Ming Chu, Hung-Jen Yang, Hua-Lin Tsai, Chi-Jen Lee, Pofen Wang
Venue: Proceedings of the 8th WSEAS International Conference on Multimedia systems and signal processing (2008)

Along with the fast development of internet, it gets up the computer conjunction of the whole world. It also causes the change of social and living types; and it has the significant influence to the traditional education. Sharing the wisdom mutually and providing the cooperation opportunity academically are on the rise with the teaching activity. E-learning uses the World Wide Web as a medium, and achieves the Web-based Learning (WBL). Help through the learning environment of the teachers or the teaching organizations; let the learners have projects to complete learning. The Ministry of Education promotes to apply information science and technology actively on the education in the last few years. (The Ministry of Education, 2001) Along with the popularization of the internet, the distance learning and on-line teaching also develop rapidly. In recent years, PDA has been taken as a tool for wireless surfing gadget; it clamps under the huge study resources; the convenient potential mobile study and the electronic book bags. It enables several studies become the tidal waves and the new tendency which keeps laws far behind. Study follows the definition, development, and related learning theories of E-learning, as well as influence, deliver contents, such as way of merits and shortcoming...etc. into analytical.
Design for All --- from Idea to Practise
Authors: Christian Bühler
Venue: Proceedings of the 11th international conference on Computers Helping People with Special Needs (2008)

Design for all (DfA) is on the agenda of research for more than 10 years. It is to be seen as a complement to concepts like assistive technology and barrier free accessibility in a continuum of solutions. After several national policy actions around the globe, recently on international policy level, in the "UN Convention on the Rights of Persons with Disabilities", reference has been given to Universal Design, a concept closely related to DfA. However, the level of take up of DfA in the design processes of industries and services stays behind the expectations. The idea has obviously been welcomed as a good one, but the implementation shows slow progress. The current development consists of threats and challenges towards a successful implementation of DfA and the market opportunities connected. "What are the key elements, what are the actions needed, which could be the next steps" are the kind of questions to be answered in order to conclude with a DfA roadmap and reflected in this paper.
Performance Analysis and Comparison of the MIPv6 and mSCTP Based Vertical Handoff
Authors: Shi Yan, Chen Shanzhi, Ai Ming, Hu Bo
Venue: Proceedings of the 7th international conference on Computational Science, Part IV: ICCS 2007 (2007)

Vertical handoff is the key technology supporting session mobility in the future heterogeneous network environments. Based on the asymmetry feature of vertical handoff, this paper analyzes the handoff procedure of MIPv6 and mSCTP in forced and unforced handoff scenarios. Qualitative and quantitative analysis and comparison of the handoff performance including handoff delay, handoff packet loss and signaling overhead are given accordingly. Besides, the main factors influencing vertical handoff performance are pointed out and possible performance improvement schemes are discussed.
A Multiobjective Evolutionary Tracking Indoor Positioning Algorithm for Smart Space
Authors: Hang Qin, Youfu Du
Venue: Proceedings of the 2008 Second International Conference on Genetic and Evolutionary Computing (2008)

This paper is mainly devoted to identify an evolutionary approach based on search strategy, namely multiobjective evolutionary algorithm for indoor positioning (MEIP). Each subproblem is optimized by information from its several neighboring subproblems, which makes MEIP lower computational complexity at each generation and be capable of determining the user position with high accuracy. Experimental results have demonstrated that MEIP is able to achieve accuracy significantly better than the current WLAN location determination systems. It has been shown that MEIP using objective normalization can deal with disparately scaled objectives, and MEIP with an advanced decomposition method can generate a set of very evenly distributed solutions for n-objective test instances. The ability of MEIP to track a large number of users and to be used with large areas, the scalability and sensitivity of MEIP have also been experimentally investigated in this paper.
Hairpin Completion Versus Hairpin Reduction
Authors: Florin Manea, Victor Mitrana
Venue: Proceedings of the 3rd conference on Computability in Europe: Computation and Logic in the Real World (2007)

We define the hairpin reduction as the inverse operation of a formal operation on words and languages suggested by DNA biochemistry, namely the hairpin completion, introduced in [3]. We settle the closure properties of some classes in the Chomsky hierarchy as well as some complexity classes under the non-iterated version of the hairpin reduction, in comparison with the hairpin completion. Then an algorithm that decides whether or not a regular language coincides with its primitive hairpin root is presented. Finally, we discuss a cubic time algorithm for computing the common ancestors of two given words. This algorithm may be used also for computing the closest or farthest primitive hairpin root of a given word.
Some Applications of Gröbner Bases
Authors: Eugenio Roanes-Lozano, Eugenio Roanes-Macias, Luis M. Laita
Venue: Computing in Science and Engineering (2004)

In the March/April issue of CiSE, we discussed the geometry of linear and algebraic systems. We also defined ideals and bases so that we could introduce the concept of Gröbner bases for algebraic system solving. In this article, we give more details about Gröbner bases and describe their main application (algebraic system solving) along with some surprising derived ones: inclusion of varieties, automatic theorem-proving in geometry, expert systems, and railway interlocking systems.
Bug Attacks
Authors: Eli Biham, Yaniv Carmeli, Adi Shamir
Venue: Proceedings of the 28th Annual conference on Cryptology: Advances in Cryptology (2008)

In this paper we present a new kind of cryptanalytic attack which utilizes bugs in the hardware implementation of computer instructions. The best known example of such a bug is the Intel division bug, which resulted in slightly inaccurate results for extremely rare inputs. Whereas in most applications such bugs can be viewed as a minor nuisance, we show that in the case of RSA (even when protected by OAEP), Pohlig-Hellman, elliptic curve cryptography, and several other schemes, such bugs can be a security disaster: Decrypting ciphertexts on any computer which multiplies even one pair of numbers incorrectly can lead to full leakage of the secret key, sometimes with a single well-chosen ciphertext.
Reflect: An Interactive Table for Regulating Face-to-Face Collaborative Learning
Authors: Khaled Bachour, Frédéric Kaplan, Pierre Dillenbourg
Venue: Proceedings of the 3rd European conference on Technology Enhanced Learning: Times of Convergence: Technologies Across Learning Contexts (2008)

In face-to-face collaborative learning, unbalanced participation often leads to the undersirable result of some participants experiencing lower learning outcomes than others. Providing feedback to the participants on the level of their participation could have a positive effect on their ability to self-regulate, leading to a more balanced collaboration. We propose a new approach for providing this feedback that takes the shape of a meeting table with a reactive visualization displayed on its surface. The meeting table monitors the collaborative interaction taking place around it using embedded microphones and displays a real-time feedback to the participants on an array of LEDs, inviting them to balance their collaboration. We report on an ongoing study that currently shows a positive effect our table has on group regulation.
Topology and Knowledge of Multiple Agents
Authors: Bernhard Heinemann
Venue: Proceedings of the 11th Ibero-American conference on AI: Advances in Artificial Intelligence (2008)

A multi-agent version of Moss and Parikh's logic of knowledge and effort is developed in this paper. This is done with the aid of particular modalities identifying the agents involved in the system in question. Throughout the paper, special emphasis is placed on foundational issues.
A Two-Phase Model Based on SVM and Conjoint Analysis for Credit Scoring
Authors: Kin Keung Lai, Ligang Zhou, Lean Yu
Venue: Proceedings of the 7th international conference on Computational Science, Part II (2007)

In this study, we use least square support vector machines (LSSVM) to construct a credit scoring model and introduce conjoint analysis technique to analyze the relative importance of each input feature for making the decision in the model. A test based on a real-world credit dataset shows that the proposed model has good classification accuracy and can help explain the decision. Hence, it is an alternative model for credit scoring tasks.
Compressed Prefix Sums
Authors: O'Neil Delpratt, Naila Rahman, Rajeev Raman
Venue: Proceedings of the 33rd conference on Current Trends in Theory and Practice of Computer Science (2007)

We consider the prefix sums problem: given a (static) sequence of positive integers $\vec{x} = (x_1, \ldots, x_n)$, such that $\sum_{i=1}^n x_i = m$, we wish to support the operation ${\sf sum}(\vec{x},j)$, which returns $\sum_{i=1}^{j} x_i$. Our interest is in minimising the space required for storing $\vec{x}$, where `minimal space' is defined according to some compressibility criteria, while supporting sum as rapidly as possible.There are two main compressibility criteria: (a) the succinct space bound, $B(m, n) = \lceil \log_2 {{m-1}\choose{n-1}} \rceil$ bits, applies to any sequence $\vec{x}$ whose elements add up to m; (b) data-aware measures, which depend on the values in $\vec{x}$, and can be lower than the succinct bound for some sequences. Appropriate data-aware measures have been studied extensively in the information retrieval (IR) community [17].We demonstrate a close connection between the data-aware measure that is the best in practice for an important IR application and the succinct bound. We give theoretical solutions that use space close to other data-aware compressibility measures (often within o(n) bits), and support sum in doubly-logarithmic (or better) time, and experimental evaluations of practical variants thereof.A bit-vector is a data structure that supports `rank/select' on a bit-string, and is fundamental to succinct and compressed data structures. We describe a new bit-vector that is robust and efficient.
Encoding and Retrieval in a CA1 Microcircuit Model of the Hippocampus
Authors: Vassilis Cutsuridis, Stuart Cobb, Bruce P. Graham
Venue: Proceedings of the 18th international conference on Artificial Neural Networks, Part II (2008)

Recent years have witnessed a dramatic accumulation of knowledge about the morphological, physiological and molecular characteristics, as well as connectivity and synaptic properties of neurons in the mammalian hippocampus. Despite these advances, very little insight has been gained into the computational function of the different neuronal classes; in particular, the role of the various inhibitory interneurons in encoding and retrieval of information remains elusive. Mathematical and computational models of microcircuits play an instrumental role in exploring microcircuit functions and facilitate the dissection of operations performed by diverse inhibitory interneurons. A model of the CA1 microcircuitry is presented using biophysical representations of its major cell types: pyramidal, basket, axo-axonic, bistratified and oriens lacunosum-moleculare cells. Computer simulations explore the biophysical mechanisms by which encoding and retrieval of spatio-temporal input patterns are achieved by the CA1 microcircuitry. The model proposes functional roles for the different classes of inhibitory interneurons in the encoding and retrieval cycles.
Blind hero: enabling guitar hero for the visually impaired
Authors: Bei Yuan, Eelke Folmer
Venue: Proceedings of the 10th international ACM SIGACCESS conference on Computers and accessibility (2008)

Very few video games have been designed or adapted to allow people with vision impairment to play. Music/rhythm games however are particularly suitable for such people as they are perfectly capable of perceiving audio signals. Guitar Hero is a popular rhythm game yet it is not accessible to the visually impaired as it relies on visual stimuli. This paper explores replacing visual stimuli with haptic stimuli as a viable strategy to make games accessible. We developed a glove that transforms visual information into haptic feedback using small pager motors attached to the tip of each finger. This allows a blind player to play Guitar Hero. Several tests have been conducted and despite minor changes to the gameplay, visually impaired players are able to play the game successfully and enjoy the challenge the game provides. The results of the study also give valuable insights on how to make mainstream games blind-accessible.