ppxscal/embedding_network huggingface dataset:
A fragment of 21 ORFs around the direct repeat (DR) region of Mycobacterium tuberculosis is absent from the other sequenced mycobacterial genomes: implications for the evolution of the DR region: Short Communications
Authors: Karina Caimi, Angel Cataldi
Venue: Comparative and Functional Genomics (2004)

The direct repeat (DR) region is a singular locus of the Mycobacterium tuberculosis complex genome. This region consists of 36 bp repetitive sequences separated by non-repetitive unique spacer sequences. Around this region there are several genes coding for proteins of unknown function. To determine whether the M. smegmatis, M. avium, M. marinum and M. leprae genomes contain sequences and ORFs similar to those of the DR locus of the M. tuberculosis complex, we analysed the corresponding regions in these species. As a first step, some conserved genes that flank the DR genes [Rv2785c (rpsO), Rv2786c (ribF), Rv2790c (ltp1), Rv2793c (truB), Rv2800, Rv2825, Rv2828, Rv2831 (echA16), Rv2838 (rbfA) and Rv2845 (proS)] were used as markers to locate the corresponding orthologues in M. smegmatis, M. avium, M. marinum and M. leprae in silico. Most of these M. tuberculosis marker genes have highly similar orthologues located in the same order and orientation in the other mycobacteria. In contrast, no orthologues were found for ORFs Rv2801&ndash;Rv2824, suggesting that these genes are unique to M. tuberculosis within the genus Mycobacterium. We observed that in M. smegmatis and M. avium, Rv2800 and Rv2825 are adjacent. This observation was experimentally confirmed by PCR. In conclusion, as the DR locus and the ORFs around it are absent in M. smegmatis and M. avium and, as it is possible that these species are older than M. tuberculosis, we postulated that the DR locus was acquired by the M. tuberculosis complex species or by an ancestor bacterium. Copyright &copy; 2004 John Wiley & Sons, Ltd.
Fabrication of barrier ribs of PDP via powder injection molding
Authors: H.-N. Choi, Y.-S. Kim
Venue: Microsystem Technologies (2005)

In this paper, an attempt was made to explore a possibility of powder micro injection molding process in manufacturing ceramic microstructures such as barrier ribs of plasma display panel. The barrier ribs are glass matrix composites with ceramic powder (alumina and/or titania) filler. In this molding process, a thermosetting paste was molded into polydimethlsilosane soft molds prepared by replication of thick film resist (SU-8) molds. The SU-8 mold was patterned with UV-lithography. The effects of powder content in the paste on paste viscosity and sintering characteristics of molded samples were examined. In addition, effect of molding speed on pore trapping in the microstructure was studied. These results indicated that the powder micro injection molding process at ambient temperature has merits of low-pressure injection molding process with superior mold release characteristics.
Fluid ontologies for digital museums
Authors: Ramesh Srinivasan, Jeffrey Huang
Venue: International Journal on Digital Libraries (2005)

With the advent and accessibility of the Internet, artistic and indigenous communities are beginning to realize how digital technologies can be used as a means for documenting and preserving their histories and cultures. However, it is not yet clear what knowledge architectures are most appropriate for creating a digital museum in order to facilitate an effective collection, organization, conservation, and experience of cultural and artistic heritage. In this paper, we discuss the concept of &#x201c;fluid ontologies,&#x201d; a novel, dynamic structure for organizing and browsing knowledge in a digital museum. Fluid ontologies are flexible knowledge structures that evolve and adapt to communities&#x2019; interest based on contextual information articulated by human contributors, curators, and viewers, as well as artificial bots that are able to track interaction histories and infer relationships among knowledge pieces and preferences of viewers. Fluid ontologies allow for a tighter coupling between communities&#x2019; interests and the browsing structure of a digital museum. We present the key ideas behind the use of fluid ontologies within the context of digital museum design and seminal work in metadata/dynamic ontologies, particularly as it pertains to objects of cultural heritage, and discuss these characteristics in three concrete examples: (1) Village Voice, an online agora that ties together the narratives created by a group of Somali refugees using an iteration of community-designed ontologies, (2) Eventspace, a node-based collaborative archive for design activities, and (3) Tribal Peace, an online digital museum still under construction and evaluation that uses proactive agents to tie distributed Kumeyaay, Luiseno, and Cupeno reservations together in their quest to achieve greater political sovereignty .
Web search strategies and human individual differences: Cognitive and demographic factors, Internet attitudes, and approaches: Research Articles
Authors: Nigel Ford, David Miller, Nicola Moss
Venue: Journal of the American Society for Information Science and Technology (2005)

The research reported here was an exploratory study that sought to discover the effects of human individual differences on Web search strategy. These differences consisted of (a) study approaches, (b) cognitive and demographic features, and (c) perceptions of and preferred approaches to Web-based information seeking. Sixty-eight master's students used AltaVista to search for information on three assigned search topics graded in terms of complexity. Five hundred seven search queries were factor analyzed to identify relationships between the individual difference variables and Boolean and best-match search strategies. A number of consistent patterns of relationship were found. As task complexity increased, a number of strategic shifts were also observed on the part of searchers possessing particular combinations of characteristics. A second article (published in this issue of JASIST; Ford, Miller, & Moss, 2005) presents a combined analyses of the data including a series of regression analyses. &copy; 2005 Wiley Periodicals, Inc.
Image Clustering System on WWW using Web Texts
Authors: Wataru Sunayama, Akiko Nagata, Masahiko Yachida
Venue: Proceedings of the Fourth International Conference on Hybrid Intelligent Systems (2004)

As the internet becomes the basic resource of information, not only texts but image retrieval systems have appeared. However, many supply only a list of images, so we must seek desired images one by one. Image labeling is one solution to such a problem, in which various words are labeled to an image when extracted from a single Web page. Therefore, this paper proposes an image clustering system that labels images by words related to a search keyword. Relationships are measured by Web pages in WWW. In experiments, users found the intended images faster than ordinary image search system.
Performance evaluation of TCP under dynamic allocation scheme for down-link transmission rate in W-CDMA systems: Research Articles
Authors: Yutaka Fukuda, Hiroyuki Koga, Takeshi Ikenaga, Yuji Oie
Venue: Wireless Communications Mobile Computing (2004)

IMT-2000 has attracted much attention as the Next Generation Mobile Communication System. IMT-2000 can provide high-bit-rate data communication service, so that a great number of packets conveyed by TCP (transmission control protocol) can be transmitted over a wireless link. W-CDMA, standardized in 3GPP (which standardizes IMT-2000), allows dynamically allocating transmission rates to flow over a wireless link in response to a changing FER for each flow, which is thought to be essential for a next generation mobile communication system. Therefore, in this paper, we study the characteristics of the dynamic allocation scheme when TCP flows share a wireless link, and, in particular, we focus on the throughput performance of these TCP flows. First, we use simulations to examine the effectiveness of the dynamically allocating down-link transmission rate for TCP flows in response to changing the frame error rate (FER). Through the simulation results, we will show how it can improve the total throughput performance of TCP flows. Furthermore, we can obtain an effective way to allocate transmission rates to flows with different FERs in order to achieve high total throughput. Finally, we will deal with a case of multiple flows from a fixed host to a mobile host. In actual networks, this often happens. In this case, we will show that the total throughput of TCP flows degrades less than in the single-flow case, even when the FER is high. Copyright &copy; 2004 John Wiley & Sons, Ltd.
Bayesian Super-Resolution of Text in Video with a Text-Specific Bimodal Prior
Authors: Katherine Donaldson, Gregory K. Myers
Venue: Proceedings of the 2005 IEEE Computer Society Conference on Computer Vision and Pattern Recognition (CVPR'05) - Volume 1 - Volume 01 (2005)

To increase the range of sizes of video scene text recognizable by optical character recognition (OCR), we developed a Bayesian super-resolution algorithm that uses a text-specific bimodal prior. We evaluated the effectiveness of the bimodal prior, compared with and in conjunction with a piecewise smoothness prior, visually and by measuring the accuracy of the OCR results on the variously super-resolved images. The bimodal prior improved the readability of 4- to 7-pixel-high scene text significantly better than bicubic interpolation, and increased the accuracy of OCR results better than the piecewise smoothness prior.
Using Optimal Foraging Models to Evaluate Learned Robotic Foraging Behavior
Authors: Patrick Ulam, Tucker Balch
Venue: Adaptive Behavior - Animals, Animats, Software Agents, Robots, Adaptive Systems (2004)

A key challenge in designing robot teams is determining how to allocate team members to specific roles according to their abilities and the demands of the environment. In this paper we explore this issue in the context of multi-robot foraging, and we show that optimal foraging theory can be used to evaluate our work in learned multi-robot foraging tasks. We present a means by which members of a multi-robot team may use reinforcement learning to allocate themselves to specific foraging roles appropriate to their environment and their abilities. We test this approach in environments with different distributions of various types of attractors and by varying the relative effectiveness of different foraging strategies. We then examine the effectiveness of the algorithm by comparing the distributions learned by the individual robots to those predicted by several optimal foraging models. We show the resulting learned distributions are substantially similar to those predicted by the optimal foraging theory models.
User-process model approach to improve user interface usability: Book Reviews
Authors: Boryung Ju, Myke Gluck
Venue: Journal of the American Society for Information Science and Technology (2005)

Our purpose in this study is to inductively reorganize software interface menu items based on a user's process model. The proposed menu interface in this study used direct users' input, such as goals and strategies for solving their information needs, to reorganize and re-label menus. To assess its effectiveness, efficiency, and user satisfaction with actual users, we implemented and compared this new menu version to the original interface that was based upon a traditional categorical menu organization. The significance of this study is that it incorporates user process modeling into the design of the user interface, providing insights into the impact of such modeling on the usability of an information system. Results from the usability testing do indicate that the proposed menu and the traditional menu are similarly effective for users in terms of task completion time and accuracy. User preferences and debriefing comments from usability testing also indicate users preferred the user-process based arrangement of menu items as displayed. However, the types of tasks (different problem type) suggest significant differences for results in task completion time and in accuracy, sometimes favoring the new version. In other words, usable and effective menu organization depends more on the types of tasks and the domain of knowledge than mere menu organization, although menu organization is a factor in the process. &copy; 2005 Wiley Periodicals, Inc.
Selected AI-Related Dissertations Bibliography
Authors: Bob Krovetz, Susanne M. Humphrey
Venue: ACM SIGART Bulletin (1991)

The following are citations selected by title and abstract as being related to AI, resulting from a computer search, using BRS Information Technologies, of the Dissertation Abstracts Online database produced by University Microfilms International (UMI).The online file includes abstracts, which are not published in this listing, but the citations below do include reference to the published Dissertation Abstracts International (DAI), which contains the abstracts. Other elements of the citation are author; university, degree, and, if available, number of pages; title; UMI order number and year-month of DAI; and one or more DAI subject descriptors chosen by the author of the dissertation. The listing may include masters abstracts, denoted by MAI (Masters Abstracts International) instead of DAI. References are sorted by subject descriptor; in the event that there is more than one descriptor, the first is used. Within each descriptor, entries are sorted by author.Unless otherwise specified, paper or microform copies of dissertations may be ordered from University Microfilms International, Dissertation Copies, Post Office Box 1764, Ann Arbor, MI 48106; telephone for U.S. (except Michigan, Hawaii, Alaska): 1-800-521-3042, for Canada: 1-800-268-6090. Price lists and other ordering and shipping information are in the introduction to the published DAI. Agriculture, Forestry and Wildlife
Using regular expressions in Java
Authors: David R. Naugler
Venue: Journal of Computing Sciences in Colleges (2005)

Regular expressions provide a useful and terse way to specify lexical elements. They have long been used in Linux/Unix utilities such as the various greps, ed, vi, sed and awk. They were not widely available in programming languages used outside of the Unix/Linux environment until the programming language Perl, and indeed are one of Perl highlights. Quite recently regular expressions have become much more broadly available in mainstream programming languages, such as Java, C#, and Visual Basic .NET. In their chapter All Input is Evil! Howard and LeBlanc [1] strongly recommend the use of regular expressions as a major part of data validation. Unfortunately, many programmers have little knowledge of regular expressions.
Automatic segmentation of liver region based on extracted blood vessels
Authors: Takeshi Saitoh, Yuta Tamura, Toyohisa Kaneko
Venue: Systems and Computers in Japan (2004)

With the rapid progress of CT (Computed Tomography) scanners, four-phase CT images with resolutions as high as 1 mm have started to be used for diagnosing liver diseases. The first-, second-, third-, and fourth-phase CT images correspond to before dye injection, the early stage, the full stage, and the wash-out stage of the injected dye. Such CT data offer useful information for diagnosing hepatic cancer. This paper describes an automatic method for segmenting the liver region using the blood vessel stream in the first- and third-phase CTs by tracing the portal vein and then the hepatic vein. First, the tracing of the veins is carried out by performing a 3D labeling operation in the region extracted with a threshold that separates blood vessels from liver soft tissue. The adjoining stomach and spleen regions are separated by applying erosion and dilation, which are 3D morphological operations. Then, an operation for determining the accurate liver region is carried out to derive an approximate liver region, by enlarging the liver blood vessel region by morphological dilation and then extracting the liver region with an optimal threshold. This method was applied to eight CT data. The resulting regions agree well with the manually detected regions. &copy; 2004 Wiley Periodicals, Inc. Syst Comp Jpn, 35(5): 1&ndash;10, 2004; Published online in Wiley InterScience (). DOI 10.1002&sol;scj.10592
Example-based motion cloning: Research Articles
Authors: Min Je Park, Sung Yong Shin
Venue: Computer Animation and Virtual Worlds (2004)

In this paper, we pose a motion cloning problem of retargeting the motion of a source character to a target character with a different structure. Based on scattered data interpolation, an example-based approach to motion cloning is proposed. Provided with a set of example motions, our method automatically extracts a small number of representative postures called source key-postures. The animator then creates the corresponding key-postures of the target character, breathing his&#x002F;her imagination and creativity into the output animation. Exploiting this correspondence, each input posture is cloned frame by frame to the target character to produce an initial animation, which is further adjusted in space and time for retargeting and timewarping and then finalized with some interactive fine tuning. With rich animation data available, our motion cloning method aims at rapid prototyping of an animation to verify an animator's concept at an early stage. Copyright &copy; 2004 John Wiley & Sons, Ltd.
Adaptive Resource Management in Peer-to-Peer Middleware
Authors: Thomas Repantis, Yannis Drougas, Vana Kalogeraki
Venue: Proceedings of the 19th IEEE International Parallel and Distributed Processing Symposium (IPDPS'05) - Workshop 2 - Volume 03 (2005)

Supporting distributed real-time applications in largescale and heterogeneous distributed environments has attracted much attention recently. However, the decentralized and dynamic characteristics of the systems present a number of challenges in managing the processor and networking resources and scheduling the application execution across multiple peers. In this paper, we address these problems with a novel resource management architecture for scheduling soft real-time applications in overlay networks. Key to our approach is that nodes maintain a partial view of resource availability of their peers in local profiles, keep track of the urgency of the requests and balance application execution across multiple nodes. Our techniques are entirely decentralized and use only local knowledge considering unpredictable latencies and changing resource availability.
A recommendation for IT-driven knowledge sharing
Authors: Atsushi Inuzuka, Yoshiteru Nakamori
Venue: Systems and Computers in Japan (2004)

In this paper, the authors propose a scheme for using simulation techniques to evaluate organizational knowledge sharing. Currently, trials for sharing knowledge within the organization have been undertaken at various corporations, but their effects are not sufficiently understood. Although the objectives for knowledge sharing vary from company to company, if attention is focused only on the reuse of knowledge, its effectiveness can be evaluated from an efficiency standpoint. In this paper, the authors limit the purpose of knowledge sharing to the reuse of knowledge and represent knowledge sharing within an organization hypothetically by modeling the acquisition, storage, and reuse of knowledge. Using this model, they introduce conditions for the superiority of the codification strategy or personalization strategy, which are forms of knowledge sharing. In addition, they propose an application model in which organization-specific conditions are represented and add a detailed analysis to it. Finally, they extend the discussion by taking into consideration the properties of knowledge, and from the results that are obtained, they refer to points that should be considered when looking at IT-driven knowledge sharing, which has been popularized in recent years. &copy; 2004 Wiley Periodicals, Inc. Syst Comp Jpn, 35(3): 1&ndash;11, 2004; Published online in Wiley InterScience (). DOI 10.1002&sol;scj.10560
A Nondegenerate Maximum Principle for the Impulse Control Problem with State Constraints
Authors: A. Arutyunov, D. Karamzin, F. Pereira
Venue: SIAM Journal on Control and Optimization (2005)

In this article, a free-time impulsive control problem with state constraints and equality and inequality constraints on the trajectory endpoints is considered. A weakened maximum principle is obtained for problems with data measurable in the time variable, being the time transversality conditions deduced with the help of some extra convexity assumption on the state constraints. In the case of smooth problems a nondegenerate maximum principle is derived by using a penalty function method.
Subgame-Perfection in Quitting Games with Perfect Information and Differential Equations
Authors: Eilon Solan
Venue: Mathematics of Operations Research (2005)

We introduce a new approach to studying subgame-perfect equilibrium payoffs in stochastic games: the differential equations approach. We apply our approach to quitting games with perfect information. Those are sequential games in which at every stage one ofn players is chosen; each player is chosen with probability 1/ n. The chosen playeri decides whether to quit, in which case the game terminates and the terminal payoff is some vectora i?Rn , or whether to continue, in which case the game continues to the next stage. If no player ever quits, the payoff is some vectora* ?Rn . We define a certain differential inclusion, prove that it has at least one solution, and prove that every vector on a solution of this differential inclusion is a subgame-perfect equilibrium payoff.
DryDock: A Document Firewall
Authors: Deepak Giridharagopal
Venue: Proceedings of the 17th USENIX conference on System administration (2003)

Auditing a web site's content is an arduous task. For any given page on a web server, system administrators are often ill-equipped to determine who created the document, why it's being served, how long it's been publicly viewable, and how it's changed over time.To police our web site, we created a secure web publishing application, DryDock, that governs the replication of content from an internal, developmental web server to a stripped-down, external, production web server. DryDock codifies a formal approval process that forces management to approve all web site changes before they are pushed out to the external machine. Users never interact directly with the production machine; DryDock updates the production server on their behalf. This allows administrators to operate their production web server in a more secure and regimented network environment than normally feasible.DryDock audits documents, tracks revisions, and notifies users of changes via email. Managers can approve files for publication at their leisure without the risk of inappropriate content ever being publicly visible. Web authors can develop pages without intimate knowledge of security policies. And administrators can instantly know the complete history of any file that has ever been published.
Editor's Introduction: Software Design in a Postmodern Era
Authors: Philippe Kruchten
Venue: IEEE Software (2005)

Over the last 30 years, software design has made tremendous progress. But this progress hasn't been continuous: it proceeded by jumps and leaps, with some plateaus in between. Reaching a plateau isn't at all negative; it's a necessary step for a discipline to integrate good practices, to reflect, and to produce a critique that will launch further progress. Perhaps we've reached another, more fundamental plateau, wittily called the era of "postmodern programming" by James Noble and Robert Biddle. The author poses three questions regarding software design and then begins to answer them: Where are we? Where do we want to go from here? And what exactly is software design?