bluuebunny/crossref_metadata_2025 huggingface dataset:
A NOVEL APPROACH TO DNA COPY NUMBER DATA SEGMENTATION
Authors: WANG SILING , WANG YUHANG , XIE YANG , XIAO GUANGHUA
Published: December 2010

DNA copy number (DCN) is the number of copies of DNA at a region of a genome. The alterations of DCN are highly associated with the development of different tumors. Recently, microarray technologies are being employed to detect DCN changes at many loci at the same time in tumor samples. The resulting DCN data are often very noisy, and the tumor sample is often contaminated by normal cells. The goal of computational analysis of array-based DCN data is to infer the underlying DCNs from raw DCN data. Previous methods for this task do not model the tumor/normal cell mixture ratio explicitly and they cannot output segments with DCN annotations.

We developed a novel model-based method using the minimum description length (MDL) principle for DCN data segmentation. Our new method can output underlying DCN for each chromosomal segment, and at the same time, infer the underlying tumor proportion in the test samples. Empirical results show that our method achieves better accuracies on average as compared to three previous methods, namely Circular Binary Segmentation, Hidden Markov Model and Ultrasome.
IMPROVED SEQUENCE-BASED PREDICTION OF STRAND RESIDUES
Authors: KEDARISETTI KANAKA DURGA , MIZIANTY MARCIN J. , DICK SCOTT , KURGAN LUKASZ
Published: December 2010

Accurate identification of strand residues aids prediction and analysis of numerous structural and functional aspects of proteins. We propose a sequence-based predictor, BETArPRED, which improves prediction of strand residues and β-strand segments. BETArPRED uses a novel design that accepts strand residues predicted by SSpro and predicts the remaining positions utilizing a logistic regression classifier with nine custom-designed features. These are derived from the primary sequence, the secondary structure (SS) predicted by SSpro, PSIPRED and SPINE, and residue depth as predicted by RDpred. Our features utilize certain local (window-based) patterns in the predicted SS and combine information about the predicted SS and residue depth. BETArPRED is evaluated on 432 sequences that share low identity with the training chains, and on the CASP8 dataset. We compare BETArPRED with seven modern SS predictors, and the top-performing automated structure predictor in CASP8, the ZHANG-server. BETArPRED provides statistically significant improvements over each of the SS predictors; it improves prediction of strand residues and β-strands, and it finds β-strands that were missed by the other methods. When compared with the ZHANG-server, we improve predictions of strand segments and predict more actual strand residues, while the other predictor achieves higher rate of correct strand residue predictions when under-predicting them.
THE VELDKAMP SPACE OF GQ(2, 4)
Authors: SANIGA M. , GREEN R. M. , LÉVAY P. , VRANA P. , PRACNA P.
Published: December 2010

It is shown that the Veldkamp space of the unique generalized quadrangle GQ(2, 4) is isomorphic to PG(5, 2). Since the GQ(2, 4) features only two kinds of geometric hyperplanes, namely point's perp-sets and GQ(2, 2)s, the 63 points of PG(5, 2) split into two families; 27 being represented by perp-sets and 36 by GQ(2, 2)s. The 651 lines of PG(5, 2) are found to fall into four distinct classes: in particular, 45 of them feature only perp-sets, 216 comprise two perp-sets and one GQ(2, 2), 270 consist of one perp-set and two GQ(2, 2)s and the remaining 120 are composed solely of GQ(2, 2)s, according to the intersection of two distinct hyperplanes determining the (Veldkamp) line is, respectively, a line, an ovoid, a perp-set and a grid (i.e. GQ(2, 1)) of a copy of GQ(2, 2). A direct "by-hand" derivation of the above-listed properties is followed by their heuristic justification based on the properties of an elliptic quadric of PG(5, 2) and complemented by a proof employing combinatorial properties of a 2-(28, 12, 11)-design and associated Steiner complexes. Surmised relevance of these findings for quantum (information) theory and the so-called black hole analogy is also outlined.
BLASCHKE'S PROBLEM FOR TIMELIKE SURFACES IN PSEUDO-RIEMANNIAN SPACE FORMS
Authors: WANG PENG
Published: December 2010

We show that isothermic surfaces and S-Willmore surfaces are also the solutions to the corresponding Blaschke's problem for both spacelike and timelike surfaces in pseudo-Riemannian space forms. For timelike surfaces both Willmore and isothermic, we obtain a description by minimal surfaces similar to the classical results of Thomsen.
THE CANONICAL EIGHT-FORM ON MANIFOLDS WITH HOLONOMY GROUP SPIN(9)
Authors: CASTRILLÓN LÓPEZ M. , GADEA P. M. , MYKYTYUK I. V.
Published: December 2010

An explicit expression of the canonical 8-form on a Riemannian manifold with a Spin(9)-structure, in terms of the nine local symmetric involutions involved, is given. The list of explicit expressions of all the canonical forms related to Berger's list of holonomy groups is thus completed. Moreover, some results on Spin(9)-structures as G-structures defined by a tensor and on the curvature tensor of the Cayley planes, are obtained.
A NEW EXAMPLE FOR MINIMALITY OF MONOIDS
Authors: Ateş Firat , Karpuz Eylem G. , Güngör A. Dilek , Çevik A. Sinan
Published: December 2010

By considering the split extension of a free abelian monoid having finite rank by a finite monogenic monoid, the main purposes of this paper are to present examples of efficient monoids and, also, minimal but inefficient monoids.

Although results presented in this paper seem as in the branch of pure mathematics, they are actually related to applications of Combinatorial and Geometric Group-Semigroup Theory, especially computer science, network systems, cryptography and physics etc., which will not be handled here.
ON n-NORMED LINEAR SPACE VALUED STRONGLY (C,1)-SUMMABLE DIFFERENCE SEQUENCES
Authors: Dutta Hemen
Published: December 2010

In this article we extend the notion of famous strongly ( C ,1)-summable or strongly Cesàro summable real sequences to n-normed linear space valued difference sequences. Consequently we introduce the notions of n-normed linear space (n-nls) valued strongly Cesàro [Formula: see text]-summable, strongly Cesàro [Formula: see text]-null and strongly Cesàro [Formula: see text]-bounded sequences. Further we extend and investigate the notion of n-norm and derived (n - l) - norms, for all l = 1, 2, …, n - 1 on the spaces of these three types of sequences. We also prove the Fixed point theorem for these spaces, which are n-Banach spaces under certain conditions and compute the n-isometrically isomorphic spaces. This article also introduces an idea for constructing n-norm on spaces of n-nls valued summable difference sequences.
CERTAIN RESULTS ON THREE-DIMENSIONAL CONTACT METRIC MANIFOLDS
Authors: Ghosh Amalendu
Published: December 2010

In this paper we study 3-dimensional contact metric manifolds satisfying certain conditions on the tensor fields *-Ricci tensorS*, h(= ½Lξφ), τ(= Lξg = 2hφ) and the Ricci operator Q. First, we prove that a 3-dimensional non-Sasakian contact metric manifold satisfies. [Formula: see text] (where ⊕X,Y,Z denotes the cyclic sum over X,Y,Z) if and only if M is a generalized (κ, μ)-space. Next, we prove that a 3-dimensional contact metric manifold with vanishing *-Ricci tensor is a generalized (κ, μ)-space. Finally, some results on 3-dimensional contact metric manifold with cyclic η-parallel h or cyclic η-parallel τ or η-parallel Ricci tensor are presented.
THE RELATION BETWEEN THE UNIFORM EXPONENTIAL DICHOTOMY AND THE UNIFORM ADMISSIBILITY OF THE PAIR (lp, lq) on ⊝
Authors: Hai Pham Viet
Published: December 2010

The goal of this paper is to present a characterization of the uniform exponential dichotomy property for linear skew-product semiflows using a discrete-time approach.
EXISTENCE AND CONTROLLABILITY RESULTS FOR INFINITE DELAY PARTIAL FUNCTIONAL DIFFERENTIAL SYSTEMS WITH MULTI-VALUED IMPULSES IN BANACH SPACES
Authors: Ning Hanwen , Liu Bing
Published: December 2010

This paper is concerned with the existence and controllability of solutions for infinite delay functional differential systems with multi-valued impulses in Banach space. Sufficient conditions for the existence are obtained by using a fixed point theorem for multi-valued maps due to Dhage. An example is also given to illustrate our results.
SOME INCLUSION RELATIONSHIPS ASSOCIATED WITH A CERTAIN CLASS OF INTEGRAL OPERATORS
Authors: Srivastava H. M. , Aouf M. K. , El-Ashwah R. M.
Published: December 2010

In this paper, we introduce and study some new subclasses of p-valently starlike, p-valently convex, p-valently close-to-convex and p-valently quasi-convex functions which are defined by means of a certain class of integral operators. Several inclusion relationships for these p-valently analytic function classes are established and an integral operator associated with the functions in these subclasses is discussed.
A GENERAL ITERATIVE ALGORITHM FOR EQUILIBRIUM PROBLEMS AND VARIATIONAL INEQUALITY PROBLEMS IN A HILBERT SPACE
Authors: Thianwan Tanakit
Published: December 2010

In this paper, we introduce a general iterative algorithm for finding a common element of the set of solutions of an equilibrium problem, the set of common fixed points of a finite family of nonexpansive mappings and the set of solutions of the variational inequality for a relaxed cocoercive mapping in a Hilbert space. Then, we prove that the iterative sequence converges strongly to a common element of the three sets. The results obtained in this paper extend and improve the several recent results in this area.
THE UNIQUE EQUIVALENCE CLASS OF CHROMATIC RECTANGLE FREE 3-COLORINGS OF A 10 × 10 CHESSBOARD
Authors: Waters L. K.
Published: December 2010

Consider an M × N chess board with each space colored one of K colors. A chromatic rectangle is a rectangular collection of spaces with all four corner spaces colored the same. An M × N : K NCR board is an M × N board for which there exists a K coloring with no chromatic rectangles. If every K coloring includes a chromatic rectangle, then that board is called an M × N : K CR board. The classification as NCR versus CR has been settled for K ∈ {1, 2, 3} and all positive integers N and M.

Note that transposition, or interchanging rows, columns, or colors, will preserve the existence of chromatic rectangles within a coloring. With this in mind, two colorings of a board are called equivalent if one can be produced from the other by such manipulations. This paper establishes that all 10 × 10 : 3 NCR colorings are equivalent.

The results stem from characterizations of NCR colorings. These characterizations permit devising and implementing a backtracking algorithm for finding NCR colorings within a significantly restricted search space. In the 10 × 10 : 3 case, the restricted search space is small enough to complete an exhaustive search in about an hour.

Several NCR colorings for larger boards, with K > 3, are also included.
AN HBV MODEL WITH DIFFUSION AND AGE OF INFECTION
Authors: Yang Junyuan , Zheng Fu , Wang Xiaoyan , Li Xuezhi
Published: December 2010

In this paper, a hepatitis B virus (HBV) model with spatial diffusion and age of infection is investigated. By analyzing the corresponding characteristic equations, the local stabilities of an infected steady state and an uninfected steady state are discussed. Furthermore, it is proved that if the basic reproductive number is less than unity, the uninfected steady state is globally asymptotically stable. Numerical simulations are carried out to illustrate the main results.
SIMPLE YET EFFICIENT ALGORITHM FOR SOLVING NONLINEAR EQUATIONS
Authors: KHATTRI SANJAY KUMAR , NOOR MUHAMMAD ASLAM
Published: December 2010

In this work, we develop a simple yet robust and highly practical algorithm for constructing iterative methods of higher convergence orders. The algorithm can be easily implemented in software packages for achieving desired convergence orders. Convergence analysis shows that the algorithm can develop methods of various convergence orders which is also supported through the numerical work. The algorithm is shown to converge even if the derivative of the function vanishes during the iterative process. Computational results ascertain that the developed algorithm is efficient and demonstrate equal or better performance as compared with other well known methods and the classical Newton method.
The Dawangou auxiliary GSSP (Xinjiang autonomous region, China) of the base of the Upper Ordovician Series: putting global chitinozoan biostratigraphy to the test
Authors: Hennissen Jan , Vandenbroucke Thijs R. A. , Chen Xu , Tang Peng , Verniers Jacques
Published: December 2010

Abstract. The Dawangou section, an auxiliary Global Stratoype Section and Point (GSSP) for the base of the Upper Ordovician Series, was sampled for chitinozoans. The 32 samples taken from the black shales of the Saergan Formation, spanning the Pterograptus elegans, Didymograptus murchisoni and Nemagraptus gracilis graptolite biozones, yielded 6536 chitinozoan vesicles. In addition to a diverse endemic assemblage, species important for international correlation were recovered, which enables the subdivision of the Saergan Formation into two chitinozoan biozones, one subzone and one provisionally recognized biozone: the Baltoscandian Laufeldochitina striata Biozone and the Laurentian Lagenochitina sp. A (sensu Achab, 1984) (/Belonechitina hirsuta) Biozone, and the Belonechitina tuberculata Subzone are recognized based on the presence of the index species, while the Baltoscandian Laufeldochitina stentor Biozone is provisionally recognized on the presence of Laufeldochitina sp. A aff. striata sensu Grahn et al., 1996 which has a range confined to the latter biozone. One new chitinozoan species is described: Cyathochitina giraffa sp. nov. and two species were assigned to a different genus: Belonechitina tuberculata comb. nov. and Hercochitina seriespinosa comb. nov.
Kataspinifera baumannii: a new genus and species of deep photic coccolithophores resembling the non-calcifying haptophyte Chrysochromulina
Authors: Andruleit Harald , Young Jeremy R.
Published: December 2010

Abstract. An unusual new coccolithophore species is described from the deep photic zone. The species is dimorphic with small body coccoliths bearing short spines and larger spine-coccoliths with exceptionally long, hollow, quadrate spines. The species is rare but has been observed in the Pacific, Indian and Atlantic Oceans reinforcing other evidence that the deep photic zone nannoflora is more diverse and heterogeneous than previously assumed.The species also shows remarkable morphological similarity to some species of the non-calcifying haptophyte Chysochromulina of a type which has frequently been cited as evidence for possible multiple origins of calcification in haptophytes. However, the coccolith structure strongly indicates that the species is a member of the Papposphaeraceae. Available phylogenetic data from molecular genetics and biomineralization modes make it extremely unlikely that the Papposphaeraceae are closely related to the spine-bearing Chrysochromulina species and so the striking morphological similarity is almost certainly a case of homoeomorphy, and possibly functional convergence.
Compositional Machine Transliteration
Authors: Kumaran A. , Khapra Mitesh M. , Bhattacharyya Pushpak
Published: December 2010

Machine transliteration is an important problem in an increasingly multilingual world, as it plays a critical role in many downstream applications, such as machine translation or crosslingual information retrieval systems. In this article, we propose compositional machine transliteration systems, where multiple transliteration components may be composed either to improve existing transliteration quality, or to enable transliteration functionality between languages even when no direct parallel names corpora exist between them. Specifically, we propose two distinct forms of composition: serial and parallel. Serial compositional system chains individual transliteration components, say, X → Y and Y → Z systems, to provide transliteration functionality, X → Z. In parallel composition evidence from multiple transliteration paths between X → Z are aggregated for improving the quality of a direct system. We demonstrate the functionality and performance benefits of the compositional methodology using a state-of-the-art machine transliteration framework in English and a set of Indian languages, namely, Hindi, Marathi, and Kannada. Finally, we underscore the utility and practicality of our compositional approach by showing that a CLIR system integrated with compositional transliteration systems performs consistently on par with, and sometimes better than, that integrated with a direct transliteration system.
An Information-Extraction System for Urdu---A Resource-Poor Language
Authors: Mukund Smruthi , Srihari Rohini , Peterson Erik
Published: December 2010

There has been an increase in the amount of multilingual text on the Internet due to the proliferation of news sources and blogs. The Urdu language, in particular, has experienced explosive growth on the Web. Text mining for information discovery, which includes tasks such as identifying topics, relationships and events, and sentiment analysis, requires sophisticated natural language processing (NLP). NLP systems begin with modules such as word segmentation, part-of-speech tagging, and morphological analysis and progress to modules such as shallow parsing and named entity tagging. While there have been considerable advances in developing such comprehensive NLP systems for English, the work for Urdu is still in its infancy. The tasks of interest in Urdu NLP includes analyzing data sources such as blogs and comments to news articles to provide insight into social and human behavior. All of this requires a robust NLP system. The objective of this work is to develop an NLP infrastructure for Urdu that is customizable and capable of providing basic analysis on which more advanced information extraction tools can be built. This system assimilates resources from various online sources to facilitate improved named entity tagging and Urdu-to-English transliteration. The annotated data required to train the learning models used here is acquired by standardizing the currently limited resources available for Urdu. Techniques such as bootstrap learning and resource sharing from a syntactically similar language, Hindi, are explored to augment the available annotated Urdu data. Each of the new Urdu text processing modules has been integrated into a general text-mining platform. The evaluations performed demonstrate that the accuracies have either met or exceeded the state of the art.
An Optimized Hardware Architecture of a Multivariate Gaussian Random Number Generator
Authors: Saiprasert Chalermpol , Bouganis Christos-S. , Constantinides George A.
Published: December 2010

Monte Carlo simulation is one of the most widely used techniques for computationally intensive simulations in mathematical analysis and modeling. A multivariate Gaussian random number generator is one of the main building blocks of such a system. Field Programmable Gate Arrays (FPGAs) are gaining increased popularity as an alternative means to the traditional general purpose processors targeting the acceleration of the computationally expensive random number generator block. This article presents a novel approach for mapping a multivariate Gaussian random number generator onto an FPGA by optimizing the computational path in terms of hardware resource usage subject to an acceptable error in the approximation of the distribution of interest. The proposed approach is based on the eigenvalue decomposition algorithm which leads to a design with different precision requirements in the computational paths. An analysis on the impact of the error due to truncation/rounding operation along the computational path is performed and an analytical expression of the error inserted into the system is presented. Based on the error analysis, three algorithms that optimize the resource utilization and at the same time minimize the error in the output of the system are presented and compared. Experimental results reveal that the hardware resource usage on an FPGA as well as the error in the approximation of the distribution of interest are significantly reduced by the use of the optimization techniques introduced in the proposed approach.
Efficient Heterogeneous Architecture Floorplan Optimization using Analytical Methods
Authors: Kahoul Asma , Smith Alastair M. , Constantinides George A. , Cheung Peter Y. K.
Published: December 2010

This paper argues the case for the use of analytical models in FPGA architecture exploration. We show that the problem, when simplified, is amenable to formal optimization techniques such as integer linear programming. However, the simplification process may lead to inaccurate models. To test the overall methodology, we feed the resulting architectures to VPR 5.0 and quantify their performance in comparison with traditional design methodologies. Our results show that the resulting architectures are better than those found using parameter sweep techniques. In addition, we show that these architectures can be further improved by combining the accuracy of VPR 5.0 with the efficiency of analytical techniques. This is achieved using a closed loop framework which iteratively refines the analytical model using the place and route outputs from VPR.
A Variable-Grain Logic Cell and Routing Architecture for a Reconfigurable IP Core
Authors: Inoue Kazuki , Zhao Qian , Okamoto Yasuhiro , Yosho Hiroki , Amagasaki Motoki , Iida Masahiro , Sueyoshi Toshinori
Published: December 2010

In the present study, we investigate the use of reconfigurable logic devices (RLDs) as intellectual properties (IPs) for system on a chip (SoC). Using RLDs, SoCs can achieve both high performance and high flexibility. However, conventional RLDs have problems related to performance, area, and power consumption. In order to resolve these problems, we investigated the features of RLD architecture. RLDs are classified into fine-grained and coarse-grained devices based on their architecture. Generally, the granularity of an RLD is limited to either type, which means that a device can only achieve high performance in applications that are suited to its architecture. Therefore, we propose a variable-grain logic cell (VGLC) architecture that can overcome the trade-off between fine-grained and coarse-grained architectures, which are required for the implementation of random and arithmetic logics, respectively. The VGLC is based on a 4-bit adder including configuration bits, which can perform arithmetic and random logic operations unlike the LUT. In the present paper, a local interconnection architecture for the VGLC is proposed. Several types of local interconnections composed of different crossbars are compared, and the trade-off between hardware resources and flexibility is discussed. Using local interconnection, the routing area is reduced by a maximum of 49%.
Optimized System-on-Chip Integration of a Programmable ECC Coprocessor
Authors: Guo Xu , Schaumont Patrick
Published: December 2010

Most hardware/software (HW/SW) codesigns of Elliptic Curve Cryptography have focused on the computational aspect of the ECC hardware, and not on the system integration into a System-on-Chip (SoC) architecture. We study the impact of the communication link between CPU and coprocessor hardware for a typical ECC design, and demonstrate that the SoC may become performance-limited due to coprocessor data- and instruction-transfers. A dual strategy is proposed to remove the bottleneck: introduction of control hierarchy as well as local storage. The performance of the ECC coprocessor can be almost independent of the selection of bus protocols. Besides performance, the proposed ECC coprocessor is also optimized for scalability. Using design space exploration of a large number of system configurations of different architectures, our proposed ECC coprocessor architecture enables trade-offs between area, speed, and security.
A New Timing Driven Placement Algorithm for Dependable Circuits on SRAM-based FPGAs
Authors: Sterpone Luca
Published: December 2010

Electronic systems for safety critical applications such as space and avionics need the maximum level of dependability for guarantee the success of their missions. Simultaneously the computation capabilities required in these fields are constantly increasing for afford the implementation of different kind of applications ranging from signal processing to networking. SRAM-based FPGAs are the candidate devices to achieve this goal thanks to their high versatility of implementing complex circuits with a very short development time. However, in critical environments, the presence of Single Event Upsets (SEUs) affecting the FPGA’s functionalities, requires the adoption of specific fault tolerant techniques, like Triple Modular Redundancy (TMR), able to increase the protection capability against radiation effects, but on the other side, introducing a dramatic penalty in terms of performances. In this paper, it is proposed a new timing-driven placement algorithm for implementing soft-errors resilient circuits on SRAM-based FPGAs with a negligible degradation of performance. The algorithm is based on a placement heuristic able to remove the crossing error domains while decreasing the routing congestions and delay inserted by the TMR routing and voting scheme. Experimental analysis performed by timing analysis and SEU static analysis point out a performance improvement of 29% on the average with respect to standard TMR approach and an increased robustness against SEU affecting the FPGA’s configuration memory. Accurate analyses of SEUs sensitivity and performance optimization have been performed on a real microprocessor core demonstrating an improvement of performances of more than 62%.
Exploiting Self-Reconfiguration Capability to Improve SRAM-based FPGA Robustness in Space and Avionics Applications
Authors: Lanuzza M. , Zicari P. , Frustaci F. , Perri S. , Corsonello P.
Published: December 2010

This article presents a novel configuration scrubbing core, used for internal detection and correction of radiation-induced configuration single and multiple bit errors, without requiring external scrubbing. The proposed technique combines the benefits of fast radiation-induced fault detection with fast restoration of the device functionality and small area and power overheads. Experimental results demonstrate that the novel approach significantly improves the availability in hostile radiation environments of FPGA-based designs. When implemented using a Xilinx XC2V1000 Virtex-II device, the presented technique detects and corrects single bit upsets and double, triple and quadruple multi bit upsets, occupying just 1488 slices and dissipating less than 30 mW at a 50MHz running frequency.
Evaluation of Random Delay Insertion against DPA on FPGAs
Authors: Lu Yingxi , O’Neill Maire , McCanny John
Published: December 2010

Side-channel attacks (SCA) threaten electronic cryptographic devices and can be carried out by monitoring the physical characteristics of security circuits. Differential Power Analysis (DPA) is one the most widely studied side-channel attacks. Numerous countermeasure techniques, such as Random Delay Insertion (RDI), have been proposed to reduce the risk of DPA attacks against cryptographic devices. The RDI technique was first proposed for microprocessors but it was shown to be unsuccessful when implemented on smartcards as it was vulnerable to a variant of the DPA attack known as the Sliding-Window DPA attack.

Previous research by the authors investigated the use of the RDI countermeasure for Field Programmable Gate Array (FPGA) based cryptographic devices. A split-RDI technique was proposed to improve the security of the RDI countermeasure. A set of critical parameters was also proposed that could be utilized in the design stage to optimize a security algorithm design with RDI in terms of area, speed and power. The authors also showed that RDI is an efficient countermeasure technique on FPGA in comparison to other countermeasures.

In this article, a new RDI logic design is proposed that can be used to cost-efficiently implement RDI on FPGA devices. Sliding-Window DPA and realignment attacks, which were shown to be effective against RDI implemented on smartcard devices, are performed on the improved RDI FPGA implementation. We demonstrate that these attacks are unsuccessful and we also propose a realignment technique that can be used to demonstrate the weakness of RDI implementations.
Towards a theory of search queries
Authors: Fletcher George H. L. , Van Den Bussche Jan , Van Gucht Dirk , Vansummeren Stijn
Published: December 2010

The need to manage diverse information sources has triggered the rise of very loosely structured data models, known as dataspace models. Such information management systems must allow querying in simple ways, mostly by a form of searching. Motivated by these developments, we propose a theory of search queries in a general model of dataspaces. In this model, a dataspace is a collection of data objects, where each data object is a collection of data items. Basic search queries are expressed using filters on data items, following the basic model of Boolean search in information retrieval. We characterize semantically the class of queries that can be expressed by searching. We apply our theory to classical relational databases, where we connect search queries to the known class of fully generic queries, and to dataspaces where data items are formed by attribute-value pairs. We also extend our theory to a more powerful, associative form of searching, where one can ask for objects that are similar to objects satisfying given search conditions. Such associative search queries are shown to correspond to a very limited kind of joins. We show that the basic search language extended with associative search can exactly define the queries definable in a restricted fragment of the semijoin algebra working on an explicit relational representation of the dataspace.
Incremental XPath evaluation
Authors: Björklund Henrik , Gelade Wouter , Martens Wim
Published: December 2010

Incremental view maintenance for XPath queries asks to maintain a materialized XPath view over an XML database. It assumes an underlying XML database
D
and a query
Q
. One is given a sequence of updates
U
to
D
, and the problem is to compute the result of
Q
(
U
(
D
)): the result of evaluating query
Q
on database
D
after having applied updates
U
. This article initiates a systematic study of the Boolean version of this problem. In the Boolean version, one only wants to know whether
Q
(
U
(
D
)) is empty or not.

In order to quickly answer this question, we are allowed to maintain an auxiliary data structure. The complexity of the maintenance algorithms is measured in, (1) the size of the auxiliary data structure, (2) the worst-case time per update needed to compute
Q
(
U
(
D
)), and (3) the worst-case time per update needed to bring the auxiliary data structure up to date. We allow three kinds of updates: node insertion, node deletion, and node relabeling. Our main results are that downward XPath queries can be incrementally maintained in time O(depth(
D
)·poly(|
Q
|)) per update and conjunctive forward XPath queries in time O(depth(
D
) · log(width(
D
))·poly(|
Q
|)) per update, where |
Q
| is the size of the query, and depth(
D
) and width(
D
) are the nesting depth and maximum number of siblings in database
D
, respectively. The auxiliary data structures for maintenance are linear in |
D
| and polynomial in |
Q
| in all these cases.
Scalable virtual machine storage using local disks
Authors: Hansen Jacob Gorm , Jul Eric
Published: December 2010

In virtualized data centers, storage systems have traditionally been treated as black boxes administered separately from the compute nodes. Direct-attached storage is often left unused, to not have VM availabilty depend on individual hosts. Our work aims to integrate storage and compute, addressing the fundamental limitations of contemporary centralized storage solutions. We are building Lithium, a distributed storage system designed specifically for virtualization workloads running in large-scale data centers and clouds. Lithium aims to be scalable, highly available, and compatible with commodity hardware and existing application software. The design of Lithium borrows techniques from Byzantine Fault Tolerance, stream processing, and distributed version control software, and demonstrates their practical applicability to the performance-sensitive task of virtual machine storage
Report on the second ACM workshop on hot topics in software upgrades (HotSWUp'09)
Authors: Dumitraş Tudor , Neamtiu Iulian , Tilevich Eli
Published: December 2010

The Second ACM SIGPLAN Workshop on Hot Topics in Software Upgrades (HotSWUp'09) was held on 25 October 2009 in Orlando, FL. The workshop was co-located with OOPSLA 2009 and was sponsored by ACM SIGPLAN. Twenty researchers and practitioners, from the programming languages, systems, software engineering and database communities, attended HotSWUp'09.

The goal of HotSWUp is to identify, through interdisciplinary collaboration, cutting-edge research ideas for implementing software upgrades.

The workshop combined presentations of peer-reviewed research papers with invited presentations from well-known experts and a keynote speech on the practical issues related to performing large-scale upgrades. The audience included researchers and practitioners from academia, the industry (Facebook, ABB, Oracle) and the open-source community (AppUpdater). In addition to the technical presentations, the program allowed ample time for discussions, which were driven by debate questions provided in advance by the presenters

HotSWUp provides a premier forum for discussing problems that are often considered niche topics in the established research communities. For example, the technical discussions at HotSWUp'09 covered dynamic software updates, package management tools, database schema upgrades, upgrades of systems with real-time constraints, etc., and highlighted many synergies among these topics. Perhaps more interestingly, the industry presentations provided real-world examples of systems that a have strong requirement for online upgrades. These examples emphasized the magnitude of the software upgrade problems that the industry is facing today
Systems research and development at VMware
Authors: Herrod Stephen Alan
Published: December 2010

Over the last twelve years, VMware has grown from a small startup with an interesting idea to an 8000+ person company that is changing the landscape of the datacenter and how IT happens in the enterprise. The VMware story has been one of intense technological innovation delivered consistently as a series of products and releases. We will briefly look at the history of innovation at VMware and how we have balanced research, advanced development and product delivery to set the context for the papers in this issue
Algorithmic information theory may explain the pathogenic number of DNA repeats in myotonic dystrophy type 1 (and in similar diseases)
Authors: Koshelev Misha , Longpré Luc
Published: December 2010

Myotonic Dystrophy Type 1 (DM1), the most common form of adult-onset muscular dystrophy, is caused by an abnormal number of repeats of the trinucleotide sequence CTG outside of the protein-coding part of DNA -- more than fifty repeats can cause disease. Several other diseases are caused by similar repeats in non-coding regions; in most of these diseases, up to approximately fifty repeats is normal, while pathogenic cases usually have > 50 repetitions. The fact that this level of approximately fifty repeats can be seen in many diseases, with different repeating sequences, indicates that there may be a fundamental explanation for this threshold.

In this paper, we conjecture that such an explanation may come from Algorithmic Information Theory. Crudely speaking, this threshold can be viewed as a measure of the redundancy in healthy DNA; this indirect estimate of the measure of redundancy is in good accordance with a more direct estimate { based on the fact that approximately 1=50 of DNA is directly functionally useful (e.g., protein-coding).
SIGACT news algorithms column
Authors: Kuller Samir , Mahoney Michael W.
Published: December 2010

The 2010 Workshop on Algorithms for Modern Massive Data Sets (MMDS 2010) was held at Stanford University, June 15-18. The goals of MMDS 2010 were (1) to explore novel techniques for modeling and analyzing massive, high-dimensional, and nonlinearly-structured scientific and Internet data sets; and (2) to bring together computer scientists, statisticians, applied mathematicians, and data analysis practitioners to promote cross-fertilization of ideas. MMDS 2010 followed on the heels of two previous MMDS workshops. The first, MMDS 2006, addressed the complementary perspectives brought by the numerical linear algebra and theoretical computer science communities to matrix algorithms in modern informatics applications [1]; and the second, MMDS 2008, explored more generally fundamental algorithmic and statistical challenges in modern large-scale data analysis [2].

The MMDS 2010 program drew well over 200 participants, with 40 talks and 13 poster presentations from a wide spectrum of researchers in modern large-scale data analysis. This included both academic researchers as well as a wide spectrum of industrial practitioners. As with the previous meetings, MMDS 2010 generated intense interdisciplinary interest and was extremely successful, clearly indicating the desire among many research communities to begin to distill out and establish the algorithmic and statistical basis for the analysis of complex large-scale data sets, as well as the desire to move increasingly-sophisticated theoretical ideas to the solution of practical problems.
Prosthetic Valve Endocarditis: A Complication of Spinal Epidural Abscess
Authors: Bedoya Armando , Gentilesco Bethany
Published: December 2010

Epidural injections for chronic low back pain are controversial, and their effectiveness is debated. Although epidural injections are considered a minor procedure with low morbidity, catastrophic complications may occur. We describe a case of prosthetic valve endocarditis secondary to an epidural abscess after epidural injection to alert clinicians to this unusual association.
Recent Developments in Maximum Power Point Tracking Technologies for Photovoltaic Systems
Authors: Onat Nevzat
Published: December 2010

In photovoltaic (PV) system applications, it is very important to design a system for operating of the solar cells (SCs) under best conditions and highest efficiency. Maximum power point (MPP) varies depending on the angle of sunlight on the surface of the panel and cell temperature. Hence, the operating point of the load is not always MPP of PV system. Therefore, in order to supply reliable energy to the load, PV systems are designed to include more than the required number of modules. The solution to this problem is that switching power converters are used, that is called maximum power point tracker (MPPT). In this study, the various aspects of these algorithms have been analyzed in detail. Classifications, definitions, and basic equations of the most widely used MPPT technologies are given. Moreover, a comparison was made in the conclusion.
Refusal of Cancer-Directed Surgery Strongly Impairs Survival of Patients with Localized Hepatocellular Carcinoma
Authors: Wang Jue , Wang Fen Wei
Published: December 2010

Background: This study investigated the frequency of patients with HCC who refused cancer-directed surgery and the characteristics and outcomes of these patients.Patients and Methods: A retrospective study was performed using data from the Surveillance, Epidemiology, and End Results (SEER) Program. Characteristics of patients who refused CDS were compared with those who accepted surgery using logistic regression. The effect of refusing CDS on mortality was evaluated by Cox proportional hazards analysis.Results: Among 4373 surgical candidates, 142 patients (3.2%) refused the recommended CDS. The patients who refused CDS were frequently older, African American, widowed or divorced, and had advanced-stage tumors. In a logistic regression analysis, older age, African American, and being divorced or widowed were independently associated with refusal of CDS. After adjusting for other patient and tumor characteristics, the patients who refused CDS had a 2.5-fold (95% confidence interval, 2.339–3.189) higher risk of dying from HCC in comparison with patients who had CDS. Conclusions: The high rate of refusal may contribute in part to the disparity in utilization of CDS. Of greatest concern is that the patients who declined CDS had an impaired survival. This information might be helpful for patients to make a better-informed decision.
A Signal Processing Method to Explore Similarity in Protein Flexibility
Authors: Vasilache Simina , Mirshahi Nazanin , Ji Soo-Yeon , Mottonen James , Jacobs Donald J. , Najarian Kayvan
Published: December 2010

Understanding mechanisms of protein flexibility is of great importance to structural biology. The ability to detect similarities between proteins and their patterns is vital in discovering new information about unknown protein functions. A Distance Constraint Model (DCM) provides a means to generate a variety of flexibility measures based on a given protein structure. Although information about mechanical properties of flexibility is critical for understanding protein function for a given protein, the question of whether certain characteristics are shared across homologous proteins is difficult to assess. For a proper assessment, a quantified measure of similarity is necessary. This paper begins to explore image processing techniques to quantify similarities in signals and images that characterize protein flexibility. The dataset considered here consists of three different families of proteins, with three proteins in each family. The similarities and differences found within flexibility measures across homologous proteins do not align with sequence-based evolutionary methods.
Fixed Point and Best Proximity Theorems under Two Classes of Integral-Type Contractive Conditions in Uniform Metric Spaces
Authors: De la Sen M
Published: December 2010

This paper investigates the existence of fixed points and best proximity points of p-cyclic self-maps on a set of subsets of a certain uniform space under integral-type contractive conditions. The parallel properties of the associated restricted composed maps from any of the subsets to itself are also investigated. The subsets of the uniform space are not assumed to intersect.
Cooperative Control of Active Power Filters in Power Systems without Mutual Communication
Authors: Tlustý Josef , Škramlík Jiří , Švec Jan , Valouch Viktor
Published: December 2010

The procedure for calculating controller parameters of the APFs implemented into a multibus industrial power system for harmonic voltage mitigation is presented. The node‐voltage‐detection control strategy is applied and the basic controller parameters are found under the condition that the demanded THD factors at the buses where the APFs are placed will be obtained. A cooperative control of several APFs without mutual communication is proposed, simulated, and experimentally verified. By tuning the controller gains without considering the power circuit parameters, all APFs used tend to share harmonic load currents approximately equally regardless of the operation modes of the nonlinear loads in different parts of the power system.
Mechanical Properties of Fiber Reinforced Lightweight Concrete Containing Surfactant
Authors: Kim Yoo-Jae , Hu Jiong , Lee Soon-Jae , You Byung-Hee
Published: December 2010

Fiber reinforced aerated lightweight concrete (FALC) was developed to reduce concrete's density and to improve its fire resistance, thermal conductivity, and energy absorption. Compression tests were performed to determine basic properties of FALC. The primary independent variables were the types and volume fraction of fibers, and the amount of air in the concrete. Polypropylene and carbon fibers were investigated at 0, 1, 2, 3, and 4% volume ratios. The lightweight aggregate used was made of expanded clay. A self-compaction agent was used to reduce the water-cement ratio and keep good workability. A surfactant was also added to introduce air into the concrete. This study provides basic information regarding the mechanical properties of FALC and compares FALC with fiber reinforced lightweight concrete. The properties investigated include the unit weight, uniaxial compressive strength, modulus of elasticity, and toughness index. Based on the properties, a stress-strain prediction model was proposed. It was demonstrated that the proposed model accurately predicts the stress-strain behavior of FALC.
Gene Carriers and Transfection Systems Used in the Recombination of Dendritic Cells for Effective Cancer Immunotherapy
Authors: Chen Yu-Zhe , Yao Xing-Lei , Tabata Yasuhiko , Nakagawa Shinsaku , Gao Jian-Qing
Published: December 2010

Dendritic cells (DCs) are the most potent antigen‐presenting cells. They play a vital role in the initiation of immune response by presenting antigens to T cells and followed by induction of T‐cell response. Reported research in animal studies indicated that vaccine immunity could be a promising alternative therapy for cancer patients. However, broad clinical utility has not been achieved yet, owing to the low transfection efficiency of DCs. Therefore, it is essential to improve the transfection efficiency of DC‐based vaccination in immunotherapy. In several studies, DCs were genetically engineered by tumor‐associated antigens or by immune molecules such as costimulatory molecules, cytokines, and chemokines. Encouraging results have been achieved in cancer treatment using various animal models. This paper describes the recent progress in gene delivery systems including viral vectors and nonviral carriers for DC‐based genetically engineered vaccines. The reverse and three‐dimensional transfection systems developed in DCs are also discussed.
Pleomorphic Giant Cell Carcinoma of the Pancreas with Hepatic Metastases—Initially Presenting as a Benign Serous Cystadenoma: A Case Report and Review of the Literature
Authors: Athanasios Petrou , Alexandros Papalambros , Nicholas Brennan , Dimitrios Karles , Kostantinos Bramis , Antonio Manzelli , Efstathios Papalambros
Published: December 2010

Introduction. Pleomorphic giant cell pancreatic cancer is a very rare and aggressive pancreatic neoplasm. A case of pleomorphic giant cell pancreatic cancer presenting as a cystic lesion and in association with a serous cystadenoma presents a unique case which has not been described before. Case Presentation. A 44-year-old alcoholic man presented with abdominal pain, vomiting, and weight loss. Initially, imaging suspected a pancreatic pseudocyst measuring 4.2 cm. Endoscopic ultrasound- (EUS-) guided fine-needle aspiration revealed a serous cystadenoma. With conservative intervention only (fluid resuscitation, analgesia, and antiemetics) the patient improved and was discharged under close observation. Follow-up scan at four months revealed minimal change. Three months later, he was admitted acutely. Repeat scans demonstrated mild cyst enlargement with new liver lesions. Laparoscopic biopsy revealed pleomorphic giant cell carcinoma with the organ of origin the pancreas. Conclusion. This unusual case highlights the challenges in managing pancreatic cystic lesions and emphasizes the importance of considering less common forms of pancreatic cystic masses when the findings are atypical for the presentation. Surgical excision in these cases over conservative steps may be the most appropriate management.