ppxscal/embedding_network huggingface dataset:
Design and Evaluation of a 16S rRNA Gene-based Oligonucleotide Micrroarray for Identification of Plant Associated Beneficial Bacteria (PABB)
Authors: Zhengqiu Cai, Lei Sun, Jigang Han, Menghong Yan, Wei Song, Zhaobiao Guo, Yu Wang, Ruifu Yang
Venue: Proceedings of the 2008 International Conference on BioMedical Engineering and Informatics - Volume 01 (2008)

A variety of plant associated beneficial bacteria (PABB) occur in rhizosphere of many plants. This study developed an oligonucleotide microarray for detection and identification of these PABBs and evaluated the oligonucleotide microarray with 43 pure cultures of PABB which were well-identified by sequencing the initial 600-800bp of the 16S rRNA gene. Ninety six species- or genus-specific oligonucleotide probes targeting 16S rRNA gene of PABB and three control probes were spotted onto silylated glass slides. 16S rDNA sequences of the reference strains were PCR amplified by a pair of bacterial universal primers, and the amplicons were labeled with Cy5-dUTP and hybridized with the oligonucleotide microarray. After hybridization, the microarray was scanned to detect the green Cy5-dUTP signals and generated a series of typical species- or genus-specific hybridization profiles. The microarray was able to differentiate closely related strains, indicating that the oligonucleotide microarray method developed in this study is a useful tool for the detection of pure cultures of PABB strains.
The very small world of the well-connected
Authors: Xiaolin Shi, Matthew Bonner, Lada A. Adamic, Anna C. Gilbert
Venue: Proceedings of the nineteenth ACM conference on Hypertext and hypermedia (2008)

Online networks occupy an increasingly larger position in how we acquire information, how we communicate with one another, and how we disseminate information. Frequently, small sets of vertices dominate various graph and statistical properties of these networks and, because of this, they are relevant for structural analysis and efficient algorithms and engineering. For the web overall, and specifically for social linking in blogs and instant messaging, we provide a principled, rigorous study of the properties, the construction, and the utilization of subsets of special vertices in large online networks. We show that graph synopses defined by the importance of vertices provide small, relatively accurate portraits, independent of the importance measure, of the larger underlying graphs and of the important vertices. Furthermore, they can be computed relatively efficiently.
Improving the performance of question answering with semantically equivalent answer patterns
Authors: Leila Kosseim, Jamileh Yousefi
Venue: Data Knowledge Engineering (2008)

In this paper, we discuss a novel technique based on semantic constraints to improve the performance and portability of a reformulation-based question answering system. First, we present a method for acquiring semantic-based reformulations automatically. The goal is to generate patterns from sentences retrieved from the Web based on lexical, syntactic and semantic constraints. Once these constraints have been defined, we present a method to evaluate and re-rank candidate answers that satisfy these constraints using redundancy. The two approaches have been evaluated independently and in combination. The evaluation on 493 questions from TREC-11 shows that the automatically acquired semantic patterns increase the MRR by 26%, the re-ranking using semantic redundancy increases the MRR by 67%, and the two approaches combined increase the MRR by 73%. This new technique allows us to avoid the manual work of formulating semantically equivalent reformulations; while still increasing performance.
Understanding the SAP Logistics Information System (LIS), 1 edition
Authors: Martin Murray
Venue:  (2007)

Collect, consolidate, and utilize data from SAP using the Logistics Information System (LIS). Gain a holistic understanding of LIS and benefit from an in-depth analysis of supply chain processes, inventory, and purchasing, showing you step-by-step how to fully leverage this often under-utilized tool in SAP. Readers quickly learn how best to manage the collected data in order to produce accurate and relevant reports - and much more.
Improve simulation efficiency using statistical benchmark subsetting: an ImplantBench case study
Authors: Zhanpeng Jin, Allen C. Cheng
Venue: Proceedings of the 45th annual Design Automation Conference (2008)

Motivated by excessively high benchmarking efforts caused by rapidly expanding design space and prevailing practices based on ad-hoc and subjective schemes, this paper seeks to improve simulation efficiency by proposing a novel methodology that combines two statistical analyses and one quantitative heuristic capable of subsetting a given benchmark suite based on the targeted processor configuration and desired variance coverage. We demonstrate the usage and effectiveness of the proposed technique by conducting a thorough case study on ImplantBench suite evaluating high/mid/low-end machine configurations modeled after three commercial embedded processors.
LIBRARIES, SOCIAL SOFTWARE AND DISTANCE LEARNERS: BLOG IT, TAG IT, SHARE IT!
Authors: Jane Secker, Gwyneth Price
Venue: The New Review of Information Networking (2007)

This paper describes a recent project funded by the University of London to explore how social software or Web 2.0 technologies can enhance the use of libraries by distance learners. LASSIE (Libraries And Social Software In Education) involves a team of librarians, learning technologists and archivists. The project first conducted an extensive literature review, which is available online. The literature review provides an overview of key social software and explores the current implementation of these tools by libraries. It also considers the key issues in supporting distance learners' use of libraries and whether social software might provide solutions. The literature review was followed by several case studies to explore specific types of social software in practice. These included the use of social bookmarking for sharing resources, social software and online reading lists, blogging in the library community, the use of social networking sites and podcasting for information literacy support. LASSIE will be completed in December 2007 and a final report with results from the case studies and an updated literature review will be made available from the project website. One of the successes of the project has been to establish a project blog, which provides the project team with an opportunity to reflect on progress, but also to gather opinions from others in the field.
Binary permutation sequences as subsets of Levenshtein codes, spectral null codes, run-length limited codes and constant weight codes
Authors: Khmaies Ouahada, Theo G. Swart, Hendrik C. Ferreira, Ling Cheng
Venue: Designs, Codes and Cryptography (2008)

We investigate binary sequences which can be obtained by concatenating the columns of (0,1)-matrices derived from permutation sequences. We then prove that these binary sequences are subsets of a surprisingly diverse ensemble of codes, namely the Levenshtein codes, capable of correcting insertion/deletion errors; spectral null codes, with spectral nulls at certain frequencies; as well as being subsets of run-length limited codes, Nyquist null codes and constant weight codes.
A predecoding technique for ILP exploitation in Java processors
Authors: Isidoros Sideris, Kiamal Pekmestzi, George Economakos
Venue: Journal of Systems Architecture: the EUROMICRO Journal (2008)

Java processors have been introduced to offer hardware acceleration for Java applications. They execute Java bytecodes directly in hardware. However, the stack nature of the Java virtual machine instruction set imposes a limitation on the achievable execution performance. In order to exploit instruction level parallelism and allow out of order execution, we must remove the stack completely. This can be achieved by recursive stack folding algorithms, such as OPEX, which dynamically transform groups of Java bytecodes to RISC like instructions. However, the decoding throughputs that are obtained are limited. In this paper, we explore microarchitectural techniques to improve the decoding throughput of Java processors. Our techniques are based on the use of a predecoded cache to store the folding results, so that it could be reused. The ultimate goal is to exploit every possible instruction level parallelism in Java programs by having a superscalar out of order core in the backend being fed at a sustainable rate. With the use of a predecoded cache of 2x2048 entries and a 4-way superscalar core we have from 4.8 to 18.3 times better performance than an architecture employing pattern based folding.
Shark
Authors: Christian Igel, Verena Heidrich-Meisner, Tobias Glasmachers
Venue: The Journal of Machine Learning Research (2008)

SHARK is an object-oriented library for the design of adaptive systems. It comprises methods for single- and multi-objective optimization (e.g., evolutionary and gradient-based algorithms) as well as kernel-based methods, neural networks, and other machine learning techniques.
An optimal sdp algorithm for max-cut, and equally optimal long code tests
Authors: Ryan O'Donnell, Yi Wu
Venue: Proceedings of the 40th annual ACM symposium on Theory of computing (2008)

Let G be an undirected graph for which the standard Max-Cut SDP relaxation achieves at least a c fraction of the total edge weight, 1/2 2' algorithm. Thus we have given an efficient, optimal SDP-rounding algorithm for Max-Cut. The fact that it is RPR2 confirms a conjecture of Feige and Langberg [17]. We also describe and analyze the tight connection between SDP gaps and Long Code tests (and the constructions of [25, 3, 4]). Using this connection, we give optimal Long Code tests for Max-Cut. Combining these with results implicit in [27, 29] and ideas from [19], we derive the following conclusions: - The Max-Cut SDP gap curve subject to triangle inequalities is also given by S(c). - No RPR2 algorithm can be guaranteed to find cuts of value larger than S(c) in graphs where the optimal cut is c. (Contrast this with the fact that in the graphs exhibiting the c vs. S(c) SDP gap, our RPR2 algorithm actually finds the optimal cut.) - Further, no polynomial-time algorithm of any kind can have such a guarantee, assuming P ≠ NP and the Unique Games Conjecture.
Design of a self-balancing tower crane
Authors: J. J. Rubio Avila, R. Alcántara-Ramírez, J. Jaimes-ponce, I. I. Siller-Alcalá
Venue: Proceedings of the 2nd WSEAS International Conference on Circuits, Systems, Signal and Telecommunications (2008)

This paper presents the design of a new concept of tower crane, which was greatly reduced the burden and eliminates the anchor, as will be "self-balancing" which involves removing the anchor replaced by a sliding counterweight trolley. The paper involves the design of the mechanics and simulations based on its model and a PID control in order to check optimal performance.
Near-optimal time-space tradeoff for element distinctness
Authors: A. C. -C. Yao
Venue: Proceedings of the 29th Annual Symposium on Foundations of Computer Science (1988)

It was conjectured by A. Borodin et al. that to solve the element distinctness problem requires TS= Omega (n/sup 2/) on a comparison-based branching program using space S and time T, which, if true, would be close to optimal since TS=O(n/sup 2/ log n) is achievable. They showed recently (1987) that TS= Omega (n/sup 3/2/(log n)/sup 1/2/). The author shows a near-optimal tradeoff TS= Omega (n/sup 2- epsilon (n)/), where epsilon (n)=O(1/(log n)/sup 1/2/).
Improved Interleaving Technique for PAPR Reduction in OFDM-MIMO System
Authors: P. Malathi, P. T. Vanathi
Venue: Proceedings of the 2008 Second Asia International Conference on Modelling & Simulation (AMS) (2008)

Orthogonal Frequency Division Multiplexing (OFDM) is of great interest for researchers and research laboratories all over the world. OFDM is widely used in contemporary communication systems for its good robustness in multipath environment, and its high spectral efficiency. The capacity of wireless system can be increased dramatically by employing Multiple Input Multiple Output, (MIMO) antennas. The combination of MIMO and OFDM system is found to be very beneficial. A major drawback of OFDM-MIMO System is its high Peak to Average Power Ratio (PAPR) Reduction. The peak power of a signal is a critical design factor for band limited communication systems, and it is necessary to reduce it as much as possible. Here a modified Interleaving PAPR reduction technique is proposed. The proposed technique for PAPR reduction gives an improvement over the existing technique at a cost of negligible decrease in the data rate.
Bases for parametrized iterativity
Authors: Jiří Adámek, Stefan Milius, Jiří Velebil
Venue: Information and Computation (2008)

Parametrized iterativity of an algebra means the existence of unique solutions of all finitary recursive systems of equations where recursion is allowed to use only some variables (chosen as a parameter). We show how such algebras can be introduced in an arbitrary category A by employing a base, i.e., an operation interpreting objects of A as monads on A. For every base we prove that free base algebras and free iterative base algebras exist. The main result is a coalgebraic construction of the latter: all equation morphisms form a diagram whose colimit is proved to be a free iterative base algebra.
Segmentation of small objects in color images
Authors: V. L. Arlazarov, M. D. Kazanov
Venue: Programming and Computing Software (2008)

A method for effective segmentation of small objects in color images is presented. It can be used jointly with region growing algorithms. Segmentation of small objects in color images is a difficult problem because their boundaries are close to each other. The proposed algorithm accurately determines the location of the boundary points of closely located small objects and finds the skeletons (seed regions) of those objects. The method makes use of conditions obtained by analyzing the change of color characteristics of the edge pixels along the direction that is orthogonal to the boundaries of adjacent objects. These conditions are generalized for the case of the well-known class of color images having misregistration artifacts. If high-quality seed regions are available, the final segmentation can be performed using one of the region growing methods. The segmentation algorithm based on the proposed method was tested using a large number of color images, and it proved to be very efficient.
A new approach to peer-to-peer wireless LANs based on ultra wide band technology
Authors: Anthony Acampora, Marc Krull
Venue: Wireless Networks (2008)

The advent of Ultra Wide Band (UWB) technology offers a unique opportunity to consider a new type of peer-to-peer wireless Local Area Network (LAN) that requires neither access at a peak data rate commensurate with the full bandwidth of the medium nor a conventional medium access protocol. Rather, due to the extraordinarily high bandwidth afforded by UWB, which is typically much greater than the peak bandwidth required by any ad-hoc radio node, one might imagine a network for which pairs of nodes are interconnected by one or more dedicated (non-shared) radio channels created by time, frequency, or code division multiplexing. In this paper, we consider a network containing N ad-hoc nodes and 2N independent radio channels. Starting with (1) an N × N power matrix, where element pi,j represents the power needed for a successful transmission from node i to node j including the effects of path loss and shadow fading, and (2) a second N × N traffic matrix where element ti,j represents the exogenous traffic originating from node i and destined for node j, we seek to assign radio channels and multi-hop route the traffic between source-destination pairs such that the resulting connectivity pattern and traffic flow minimize the average transmit energy needed to deliver a packet between an arbitrarily chosen pair of nodes. With no medium access protocol needed, collisions cannot occur and retransmissions become unnecessary. Moreover, the available capacity grows with the number of channels created (or, alternatively, as some common set of channels are re-used on a non-interfering basis via sufficient spatial separation). In this fashion, such a UWB ad-hoc network takes on the characteristics of a multi-hop Wavelength-Division Multiplexed (WDM) network well known from the multihop lightwave network art, although the constraints and dynamics are certainly different. Since the optimum connectivity and flow problem is shown to be NP hard, several heuristics are considered and compared. These heuristics seek, first, to establish a "good" connectivity graph, and then to flow the traffic in an optimum fashion. Our results suggest that application of these techniques may provide a distinct wireless LAN advantage achievable only via UWB radio technology, and several opportunities for future work based on this novel approach to ad-hoc local area radio networks are identified and discussed.
The effect of pore size on permeability and cell attachment in collagen scaffolds for tissue engineering
Authors: Fergal J. O'Brien, Brendan A. Harley, Mary A. Waller, Ioannis V. Yannas, Lorna J. Gibson, Patrick J. Prendergast
Venue: Technology and Health Care (2007)

The permeability of scaffolds and other three-dimensional constructs used for tissue engineering applications is important as it controls the diffusion of nutrients in and waste out of the scaffold as well as influencing the pressure fields within the construct. The objective of this study was to characterize the permeability/fluid mobility of collagen-GAG scaffolds as a function of pore size and compressive strain using both experimental and mathematical modeling techniques. Scaffolds containing four distinct mean pore sizes (151, 121, 110, 96 microns) were fabricated using a freeze-drying process. An experimental device was constructed to measure the permeability of the scaffold variants at different levels of compressive strain (0, 14, 29 and 40% while a low-density open-cell foam cellular solids model utilizing a tetrakaidecahedral unit cell was used to accurately model the permeability of each scaffold variant at all level of applied strain. The results of both the experimental and the mathematical analysis revealed that scaffold permeability increases with increasing pore size and decreases with increasing compressive strain. The excellent comparison between experimentally measured and predicted scaffold permeability suggests that cellular solids modelling techniques can be utilized to predict scaffold permeability under a variety of physiological loading conditions as well as to predict the permeability of future scaffolds with a wide variety of pore microstructures.
Affine colored partitions (abstract only)
Authors: Sara C. Billey, Stephen A. Mitchell
Venue: ACM Communications in Computer Algebra (2008)

We give a bijection between certain colored partitions and the elements in the quotient of an affine Weyl group modulo its Weyl group. By Bott's formula these colored partitions give rise to some partition identities. In certain types, these identities have previously appeared in the work of Bousquet-Melou-Eriksson, Eriksson-Eriksson and Reiner. In other types the identities appear to be new. Our main application is to determine the rationally smooth Schubert varieties in the affine Grassmannians. Several of the proofs are computer assisted. This is joint work with Steve Mitchell.
An efficient algorithm for solving the phase field crystal model
Authors: Mowei Cheng, James A. Warren
Venue: Journal of Computational Physics (2008)

We present and discuss the development of an unconditionally stable algorithm used to solve the evolution equations of the phase field crystal (PFC) model. This algorithm allows for an arbitrarily large algorithmic time step. As the basis for our analysis of the accuracy of this algorithm, we determine an effective time step in Fourier space. We then compare our calculations with a set of representative numerical results, and demonstrate that this algorithm is an effective approach for the study of the PFC models, yielding a time step effectively 180 times larger than the Euler algorithm for a representative set of material parameters. As the PFC model is just a simple example of a wide class of density functional theories, we expect this method will have wide applicability to modeling systems of considerable interest to the materials modeling communities.
Metaarchive/lockss distributed preservation networks
Authors: Martin Halbert, Katherine Skinner, Tyler Walters
Venue: Proceedings of the 8th ACM/IEEE-CS joint conference on Digital libraries (2008)

The Workshop will provide information and training for institutions seeking to build or join LOCKSS-based distributed digital preservation networks. Such Private LOCKSS Networks (PLNs) enable groups of institutions to establish collaborative partnerships to securely preserve collections. Instructors will address the technical implementation as well as important organizational and legal elements of distributed digital preservation. Attendees will gain an understanding of how to produce and manage a private LOCKSS network.
SmartWorld: More than Meets the Eye in Enterprise Application Integration
Authors: Ismael Rivera, Myriam Mencke, Juan Miguel Gomez, Rubén Posada-Gómez, Angel Garcia-Crespo
Venue: Proceedings of the Third International Conference on Systems (2008)

Current business climate demands a high rate of change with which Enterprise Information Systems Integration is required to cope. Previously isolated, these systems must be converted to service-enabled architectures and integrated efficiently to gear towards the real world of fully automated, complex electronic transactions. Service-Oriented Computing (SOC) holds the visionary promise of a world of cooperating services where application services are encapsulated within old and new applications. This paper presents SmartWorld, a service-oriented architecture (SOA) which attempts to enable integration among Enterprise Information Systems using services as the basic constructs to support the development of rapid, lowcost and easy modeling of Business Process interoperation.
Strategic alignment of software process improvement programs using QFD
Authors: André Luiz Becker, Rafael Prikladnicki, Jorge Luis Nicolas Audy
Venue: Proceedings of the 1st international workshop on Business impact of process improvements (2008)

Software process improvement programs increase the competitiveness of software development organizations. But a critical success factor in this context is the proper alignment between the strategy of such programs and the organization's business strategy. In this paper, we discuss how Quality Function Deployment can be used as a technique to align strategic goals and software process within an organization, presenting results of its application in a small company in Brazil.
Numerical time-series pattern extraction based on irregular piecewise aggregate approximation and gradient specification
Authors: Miho Ohsaki, Hidenao Abe, Takahira Yamaguchi
Venue: New Generation Computing (2007)

This paper proposes and evaluates a method for extracting interesting patterns from numerical time-series data which takes account of user subjectivity. The proposed method conducts irregular sampling on the data preserving the subjectively noteworthy features using a user specified gradient. It also conducts irregular quantization, preserving the intrinsically objective characteristics of the data using statistical distributions. It then extracts representative patterns from the discretized data using group average clustering. Experimental results using benchmark datasets indicate that the proposed method does not destroy the intrinsically objective features, since it has the same performance as the basic subsequence clustering using K-Means algorithm. Results using a dataset from a clinical hepatitis study indicate that it extracts interesting patterns for a medical expert.