bluuebunny/crossref_metadata_2025 huggingface dataset:
Association of Missense Mutations in Epoxyalkane Coenzyme M Transferase with Adaptation of
Mycobacterium
sp. Strain JS623 to Growth on Vinyl Chloride
Authors: Jin Yang Oh , Cheung Samantha , Coleman Nicholas V. , Mattes Timothy E.
Published: April 2010

Vinyl chloride (VC) is a toxic groundwater pollutant associated with plastic manufacture and chlorinated solvent use. Aerobic bacteria that grow on VC as a carbon and energy source can evolve in the laboratory from bacteria that grow on ethene, but the genetic changes involved are unknown. We investigated VC adaptation in two variants (JS623-E and JS623-T) of the ethene-oxidizing
Mycobacterium
strain JS623. Missense mutations in the EtnE gene developed at two positions (W243 and R257) in cultures exposed to VC but not in cultures maintained on ethene. Epoxyalkane-coenzyme M transferase (EaCoMT) activities in cell extracts of JS623-E and JS623-T (150 and 645 nmol/min/mg protein, respectively) were higher than that of wild-type JS623 (74 nmol/min/mg protein), and in both variant cultures epoxyethane no longer accumulated during growth on ethene. The heterologous expression of two variant
etnE
alleles (W243G [
etnE1
] and R257L [
etnE2
]) from strain JS623 in
Mycobacterium smegmatis
showed that they had 42 to 59% higher activities than the wild type. Recombinant JS623 cultures containing mutant EtnE genes cloned in the vector pMV261 adapted to growth on VC more rapidly than the wild-type JS623 strain, with incubation times of 60 days (wild type), 1 day (pMV
etnE1
), and 35 days (pMV
etnE2
). The JS623(pMV
etnE
) culture did not adapt to VC after more than 60 days of incubation. Adaptation to VC in strain JS623 is consistently associated with two particular missense mutations in the
etnE
gene that lead to higher EaCoMT activity. This is the first report to pinpoint a genetic change associated with the transition from cometabolic to growth-linked VC oxidation in bacteria.
Epidemiology of Seafood-Associated Infections in the United States
Authors: Iwamoto Martha , Ayers Tracy , Mahon Barbara E. , Swerdlow David L.
Published: April 2010

Seafood is part of a healthful diet, but seafood consumption is not risk-free. Seafood is responsible for an important proportion of food-borne illnesses and outbreaks in the United States. Seafood-associated infections are caused by a variety of bacteria, viruses, and parasites; this diverse group of pathogens results in a wide variety of clinical syndromes, each with its own epidemiology. Some seafood commodities are inherently more risky than others, owing to many factors, including the nature of the environment from which they come, their mode of feeding, the season during which they are harvested, and how they are prepared and served. Prevention of seafood-associated infections requires an understanding not only of the etiologic agents and seafood commodities associated with illness but also of the mechanisms of contamination that are amenable to control. Defining these problem areas, which relies on surveillance of seafood-associated infections through outbreak and case reporting, can lead to targeted research and help to guide control efforts. Coordinated efforts are necessary to further reduce the risk of seafood-associated illnesses. Continued surveillance will be important to assess the effectiveness of current and future prevention strategies.
Selective Depletion of
Sulfolobus solfataricus
Transcription Factor E under Heat Shock Conditions
Authors: Iqbal Junaid , Qureshi Sohail A.
Published: April 2010

Archaeal transcriptional machinery is similar to that of eukaryotes. We studied the fates of various components of the
Sulfolobus solfataricus
transcriptional apparatus under different stresses and found that in cells incubated at 90°C for 1 h, transcription factor E (TFE) is selectively depleted, but its mRNA levels are increased. We discuss the implications of these findings.
Functional Dissection of the Conjugative Coupling Protein TrwB
Authors: de Paz Héctor D. , Larrea Delfina , Zunzunegui Sandra , Dehio Christoph , de la Cruz Fernando , Llosa Matxalen
Published: April 2010

The conjugative coupling protein TrwB is responsible for connecting the relaxosome to the type IV secretion system during conjugative DNA transfer of plasmid R388. It is directly involved in transport of the relaxase TrwC, and it displays an ATPase activity probably involved in DNA pumping. We designed a conjugation assay in which the frequency of DNA transfer is directly proportional to the amount of TrwB. A collection of point mutants was constructed in the TrwB cytoplasmic domain on the basis of the crystal structure of TrwBΔN70, targeting the nucleotide triphosphate (NTP)-binding region, the cytoplasmic surface, or the internal channel in the hexamer. An additional set of transfer-deficient mutants was obtained by random mutagenesis. Most mutants were impaired in both DNA and protein transport. We found that the integrity of the nucleotide binding domain is absolutely required for TrwB function, which is also involved in monomer-monomer interactions. Polar residues surrounding the entrance and inside the internal channel were important for TrwB function and may be involved in interactions with the relaxosomal components. Finally, the N-terminal transmembrane domain of TrwB was subjected to random mutagenesis followed by a two-hybrid screen for mutants showing enhanced protein-protein interactions with the related TrwE protein of
Bartonella tribocorum
. Several point mutants were obtained with mutations in the transmembranal helices: specifically, one proline from each protein may be the key residue involved in the interaction of the coupling protein with the type IV secretion apparatus.
Shoulder injuries in skeletally immature throwers: review and current thoughts
Authors: Leonard James , Hutchinson Mark R
Published: April 2010

The incidence of shoulder injuries in the paediatric athletic population continues to increase with increased participation particularly in throwing and overhead sports. While soft tissue injuries can occur, the physis remains the weak link and site of injury in many cases. Injury prevention targets proper throwing mechanics and the avoidance of overuse injuries by monitoring the amount of training and number of throws these young athletes are exposed to.
Diagnosis and management of superior labrum anterior posterior lesions in overhead athletes
Authors: Abrams Geoffrey D , Safran Marc R
Published: April 2010

Shoulder pain is a common complaint in overhead athletes, and superior labrum anterior posterior (SLAP) lesions are a common cause of this pain. The pathological cascade which results in the SLAP lesion consists of a combination of posterior inferior capsular tightness and scapular dyskinesis, resulting in a ‘peel back’ phenomenon at the biceps anchor and leading to the SLAP tear. Physical exam tests vary in their sensitivity and specificity in detecting SLAP lesions, so MRI is helpful in demonstrating the anatomical alteration. Treatment can be conservative, with posterior inferior capsular stretching and scapular open and closed chain exercises. Many SLAP lesions in overhead athletes require surgical treatment that involves repair of the labrum back to the glenoid. Treatment of concomitant injuries such as rotator cuff tears and Bankart lesions in conjunction with the SLAP repair may be necessary.
Clinical tests in shoulder examination: how to perform them
Authors: Moen Maarten Hendrik , de Vos Robert-Jan , Ellenbecker Todd S , Weir Adam
Published: April 2010

Background

This article describes the best clinical tests of shoulder function and injury as identified in a recent systematic review published in theBritish Journal of Sports Medicine.

Discussion

A description of the different tests is given, with photographs of the exact test procedure.
Steady-state drainage in a liquid collection system with two different slopes
Authors: Ke Han , Chen Yunmin , Fredlund Delwyn G.
Published: April 2010

Liquid collection layers are commonly used as part of modern landfills. These collection layers are often composed of two sections with different slopes. Design methods are presently available for limited cases where there is no drain at the connection between the two sections. This paper presents a computational solution based on the Dupuit assumption to calculate the maximum liquid depth and provide the liquid profile for the drainage systems comprising two different slopes. A case study showed that, in most cases, the maximum depth of the downstream section is determined by the total horizontal length of the two sections, the slope of the downstream section, and the inflow rate. The application of a geocomposite in the downstream section can significantly reduce the maximum liquid depth in both the upstream and downstream sections of the drainage system. The application of a geocomposite in the upstream section can only influence the maximum depth in the upstream section of the drainage system. Simplified procedures are proposed that can estimate the maximum depth in the upstream and downstream sections if the drainage layer consists of one material.
Mechanical characterization of matrix coarse-grained soils with a large-sized triaxial device
Authors: Seif El Dine Bassel , Dupla Jean Claude , Frank Roger , Canou Jean , Kazan Youssam
Published: April 2010

This paper presents an experimental program that characterizes the mechanical behavior of heterogeneous soils using a large-sized triaxial apparatus (300 mm diameter and 600 mm height). A particular class of heterogeneous soil called matrix coarse-grained soil, composed of a mixture of a sandy matrix (Fontainebleau sand) and inclusions (gravels), was studied. The experimental procedure to rebuild samples is presented first with a description of a typical test setup. A synthesis of the experimental results obtained is then presented. A particular focus is placed on studying the influence of basic soil parameters: the properties of the inclusions (volumetric fraction, particle size, grading parameter) and the initial state of stress in the soil. The two classical methods used to study the mechanical properties of matrix coarse-grained soils in the laboratory (clipping and clipping-substitution) are evaluated.
SINGLE-PARTICLE RESONANCES IN Ca ISOTOPES
Authors: ZHANG ZI-ZHEN , LIN HAI , MI YIN-MEI
Published: April 2010

Single-particle resonant states in Ca isotopes are studied systematically by real stabilization method (RSM) in coordinate space within the framework of the self-consistent relativistic mean field (RMF) theory. Phase shifts are obtained by scattering phase shift method. The resonant parameters (the energies, widths) are extracted by fitting energy and phase shift. Wave functions of resonances are obtained by matching conditions of bound and scattering states. Taking 60 Ca as an example, results are compared with corresponding results obtained from the analytic continuation in the coupling constant approach and the scattering phase shift method. Satisfied agreements are found. The rules of resonant parameters changing in Ca isotopes are also analyzed.
A SUPERSTRUCTURE OVER THE FARHI–SUSSKIND TECHNICOLOR MODEL
Authors: ZUBKOV M. A.
Published: April 2010

We suggest the model with the gauge group ⋯ ⊗ SU(6)⊗ SU(5) ⊗ SU(4)⊗ SU(3)⊗ SU(2)⊗ U(1) . This group is the infinite continuation of the gauge group SU(4)⊗ SU(3)⊗ SU(2) ⊗ U(1) of Farhi–Susskind model. The constructed model contains fermions from the fundamental representations of any SU (N) subgroups of the gauge group. In the construction of the model we use essentially the requirement that it possesses an additional discrete symmetry [Formula: see text] that is the continuation of the Z6 symmetry of the Standard Model. It has been found that there exists such a choice of the hypercharges of the fermions that the chiral anomaly is absent while the symmetry [Formula: see text] is preserved.
NONMONOTONIC TARGET EXCITATION DEPENDENCE OF PION CLANS IN RELATIVISTIC NUCLEUS–NUCLEUS COLLISIONS
Authors: GHOSH DIPAK , DEB ARGHA , DUTTA SRIMONTI
Published: April 2010

Target excitation dependence of fluctuation of produced pions (i.e. classifying data of the fluctuation pattern on pions on the basis of the number of gray tracks) is studied for nucleus–nucleus collisions at different projectile energies. In each set the experimental multiplicity distribution is compared with the negative binomial distribution (NBD), which is found to describe the experimental distribution quite well. Target excitation dependence is studied in respect of the clan model parameters [Formula: see text] and [Formula: see text], which are extracted from the NBD fit parameters [Formula: see text] and k. A detailed comparison between different interactions at the same energy and the same interactions at different energies is also drawn. A nonmonotonic dependence of [Formula: see text] on 〈ng〉 is revealed, which is also a characteristic of multiplicity fluctuations at RHIC data.
SPHERICALLY SYMMETRIC AND ROTATING WORMHOLES PRODUCED BY LIGHTLIKE BRANES
Authors: GUENDELMAN EDUARDO , KAGANOVICH ALEXANDER , NISSIMOV EMIL , PACHEVA SVETLANA
Published: April 2010

Lightlike p-branes (LL-branes) with dynamical (variable) tension allow simple and elegant Polyakov-type and dual to it Nambu–Goto-like worldvolume action formulations. Here we first briefly describe the dynamics of LL-branes as test objects in various physically interesting gravitational backgrounds of black hole type, including rotating ones. Next we show that LL-branes are the appropriate gravitational sources that provide proper matter energy–momentum tensors in the Einstein equations of motion needed to generate traversable wormhole solutions, in particular, self-consistent cylindrical rotating wormholes, with the LL-branes occupying their throats. Here a major role is being played by the dynamical LL-brane tension which turns out to be negative but may be of arbitrary small magnitude. As a particular solution we obtain traversable wormhole with Schwarzschild geometry generated by a LL-brane positioned at the wormhole throat, which represents the correct consistent realization of the original Einstein–Rosen "bridge" manifold.
CANONICAL QUANTIZATION OF THE WZW MODEL WITH DEFECTS AND CHERN–SIMONS THEORY
Authors: SARKISSIAN GOR
Published: April 2010

We perform canonical quantization of the WZW model with defects and permutation branes. We establish symplectomorphism between phase space of WZW model with N defects on cylinder and phase space of Chern–Simons theory on annulus times R with N Wilson lines, and between phase space of WZW model with N defects on strip and Chern–Simons theory on disk times R with N + 2 Wilson lines. We obtained also symplectomorphism between phase space of the N-fold product of the WZW model on strip with boundary conditions specified by permutation branes, and phase space of Chern–Simons theory on sphere times R with N holes and two Wilson lines.
AN AUTOMATED MULTI-OBJECTIVE INVIGILATOR-EXAM ASSIGNMENT SYSTEM
Authors: OZTURK ZEHRA KAMISLI , OZTURK GURKAN , SAGIR MUJGAN
Published: April 2010

This paper is concerned with the invigilator-exam assignment problem. A web-based Automated Invigilator Assignment System (AIAS), consists of a mathematical model; a database storing the information and web-based user interfaces is constructed to solve the problem by providing an environment for a practical usage. The core of the system is the mathematical model developed for obtaining the exact solution. We conclude the paper by presenting a real-life problem solved by the proposed approach.
APPLICATION OF NOVEL CLONAL ALGORITHM IN MULTIOBJECTIVE OPTIMIZATION
Authors: CHEN JIANYONG , LIN QIUZHEN , HU QINGBIN
Published: April 2010

In this paper, a novel clonal algorithm applied in multiobjecitve optimization (NCMO) is presented, which is designed from the improvement of search operators, i.e. dynamic mutation probability, dynamic simulated binary crossover (D-SBX) operator and hybrid mutation operator combining with Gaussian and polynomial mutations (GP-HM) operator. The main notion of these approaches is to perform more coarse-grained search at initial stage in order to speed up the convergence toward the Pareto-optimal front. Once the solutions are getting close to the Pareto-optimal front, more fine-grained search is performed in order to reduce the gaps between the solutions and the Pareto-optimal front. Based on this purpose, a cooling schedule is adopted in these approaches, reducing the parameters gradually to a minimal threshold, the aim of which is to keep a desirable balance between fine-grained search and coarse-grained search. By this means, the exploratory capabilities of NCMO are enhanced. When compared with various state-of-the-art multiobjective optimization algorithms developed recently, simulation results show that NCMO has remarkable performance.
AVE–CPFR WORKING CHAINS ON THE BASIS OF SELECTION MODEL OF COLLABORATIVE CREDIT-GRANTING GUARANTEE APPROACHES
Authors: SHU TONG , CHEN SHOU , XIE CHI , WANG SHOUYANG , LAI KIN KEUNG
Published: April 2010

This paper presents AVE and CPFR concepts and their characteristics, establishes and analyzes the AVE-based CPFR working flow, and illustrates the content of the grid resource management and the mission in relation to the corresponding grid resource management system. It focuses on the working flow of the AVE-based CPFR. On this basis, it proposes the AVE-related CPFR mechanism grounded on grid, and further analyzes its working principles, grid methods matching the AVE-related CPFR working flow, the strengths of this mechanism as well as the n-tier prediction working flow. In addition, it constructs the selection model of credit-granting guarantee approaches and provides evidence for it. Under this mechanism, credit risk in the AVE enterprises can be optimized, and the AVE chain matches the working mechanism of CPFR in their capacities of real-time resource sharing, n-tier resource allocation, mission assignment, control, and supervision. It is hoped that the distance management and risk blockage could be achieved in supply chains within AVE enterprises by establishing a strong self-organized and self-control working chain.
ON LORENZ-LIKE DYNAMIC SYSTEMS WITH STRENGTHENED NONLINEARITY AND NEW PARAMETERS
Authors: LIAO BO , TANG YUAN YAN , AN LU
Published: April 2010

This paper introduces two types of Lorenz-like three-dimensional quadratic autonomous chaotic systems with 7 and 8 new parameters free of choice, respectively. Both systems are investigated at the equilibriums to study their chaotic characteristics. We focus our attention on the second type of the introduced system which consists of three nonlinear quadratic equations. Predictably, coordinates of the equilibriums are prohibitively complex. Therefore, instead of directly analyzing their stability, we prove the asymptotical characterization of equilibriums by utilizing our preliminary results derived for the first type of system. Our result shows that, though the coordinates of equilibriums satisfy a ternary quadratic, the system still contains only three equilibriums in circumstances of chaos. Sufficient conditions for the chaotic appearance of systems are derived. Our results are further verified by numerical simulations and the maximum Lyapunov exponent for several examples. Our research takes a first step in investigating chaos in Lorenz-like dynamic systems with strengthened nonlinearity and general forms of parameters.
ON AN EFFICIENT SPARSE REPRESENTATION OF OBJECTS OF GENERAL SHAPE VIA CONTINUOUS EXTENSION AND WAVELET APPROXIMATION
Authors: SAITO NAOKI , ZHANG ZHIHUA
Published: April 2010

In this paper, we discuss the continuous extension and wavelet approximation of the detected object on a general domain Ω of ℝ2. We first extend continuously the image to a square T such that it vanishes on the boundary ∂T. On T∖Ω, the extension has a simple and clear representation which is determined by the equation of the boundary ∂Ω. We expand the extension into wavelet series on ℝ2. Since the extension tools are polynomials, by the moment theorem, we know that the sequence of wavelet coefficients obtained by us is sparse. Therefore, we can approximate and analyze the internal information of the object very well even if we only store a few wavelet coefficients.
New heuristic and interactive approaches to 2D rectangular strip packing
Authors: Lesh N. , Marks J. , McMahon A. , Mitzenmacher M.
Published: April 2010

In this paper, we consider the two-dimensional rectangular strip packing problem. A standard simple heuristic, Bottom-Left-Decreasing (BLD), has been shown to perform quite well in practice. We introduce and demonstrate the effectiveness of BLD*, a stochastic search variation of BLD. While BLD places the rectangles in decreasing order of height, width, area, and perimeter, BLD* successively tries random orderings, chosen from a distribution determined by their Kendall-tau distance from one of these fixed orderings. Our experiments on benchmark problems show that BLD* produces significantly better packings than BLD after only 1 min of computation. Furthermore, we also show that BLD* outperforms recently reported metaheuristics. Furthermore, we observe that people seem able to reason about packing problems extremely well. We incorporate our new algorithms in an interactive system that combines the advantages of computer speed and human reasoning. Using the interactive system, we are able to quickly produce significantly better solutions than BLD* by itself.
Combining speed-up techniques for shortest-path computations
Authors: Holzer Martin , Schulz Frank , Wagner Dorothea , Willhalm Thomas
Published: April 2010

In practice, computing a shortest path from one node to another in a directed graph is a very common task. This problem is classically solved by Dijkstra's algorithm. Many techniques are known to speed up this algorithm heuristically, while optimality of the solution can still be guaranteed. In most studies, such techniques are considered individually. The focus of our work is
combination
of speed-up techniques for Dijkstra's algorithm. We consider all possible combinations of four known techniques, namely,
goal-directed search
,
bidirectional search
,
multilevel approach
, and
shortest-path containers
, and show how these can be implemented. In an extensive experimental study, we compare the performance of the various combinations and analyze how the techniques harmonize when jointly applied. Several real-world graphs from road maps and public transport and three types of generated random graphs are taken into account.
In search for efficient heuristics for minimum-width graph layering with consideration of dummy nodes
Authors: Nikolov Nikola S. , Tarassov Alexandre , Branke Jürgen
Published: April 2010

We propose two fast heuristics for solving the NP-hard problem of graph layering with the minimum width and consideration of dummy nodes. Our heuristics can be used at the layer-assignment phase of the Sugiyama method for drawing of directed graphs. We evaluate our heuristics by comparing them to the widely used fast-layering algorithms in an extensive computational study with nearly 6000 input graphs. We also demonstrate how the well-known longest-path and Coffman--Graham algorithms can be used for finding narrow layerings with acceptable aesthetic properties.
Approximating interval coloring and max-coloring in chordal graphs
Authors: Pemmaraju Sriram V. , Penumatcha Sriram , Raman Rajiv
Published: April 2010

We consider two coloring problems: interval coloring and max-coloring for chordal graphs. Given a graph
G
= (
V
,
E
) and positive-integral vertex weights
w
:
V
→
N
, the
interval-coloring
problem seeks to find an assignment of a real interval
I
(
u
) to each vertex
u
∈
V
, such that two constraints are satisfied: (i) for every vertex
u
∈
V
, |
I
(
u
)| =
w
(
u
) and (ii) for every pair of adjacent vertices
u
and
v
,
I
(
u
)∩
I
(
v
) = ∅. The goal is to minimize the
span
|∪

v
∈
V

I
(
v
)|. The
max-coloring problem
seeks to find a proper vertex coloring of
G
whose color classes
C
1
C
2
, …,
C

k

, minimize the sum of the weights of the heaviest vertices in the color classes, that is, ∑

k

i
= 1

max

v
ϵ
C

i

w
(
v
). Both problems arise in efficient memory allocation for programs. The interval-coloring problem models the compile-time memory allocation problem and has a rich history dating back at least to the 1970s. The max-coloring problem arises in minimizing the total buffer size needed by a dedicated memory manager for programs. In another application, this problem models scheduling of conflicting jobs in batches to minimize the
makespan
. Both problems are NP-complete even for interval graphs, although there are constant-factor approximation algorithms for both problems on interval graphs. In this paper, we consider these problems for
chordal graphs
, a subclass of perfect graphs. These graphs naturally generalize interval graphs and can be defined as the class of graphs that have no induced cycle of length >3. Recently, a 4-approximation algorithm (which we call GeomFit) has been presented for the max-coloring problem on perfect graphs (Pemmaraju and Raman 2005). This algorithm can be used to obtain an interval coloring as well, but without the constant-factor approximation guarantee. In fact, there is no known constant-factor approximation algorithm for the interval-coloring problem on perfect graphs. We study the performance of GeomFit and several simple
O
(log(
n
))-factor approximation algorithms for both problems. We experimentally evaluate and compare four simple heuristics: first-fit, best-fit, GeomFit, and a heuristic based on partitioning the graph into vertex sets of similar weight. Both for max-coloring and for interval coloring, GeomFit deviates from OPT by about 1.5%, on average. The performance of first-fit comes close second, deviating from OPT by less than 6%, on average, for both problems. Best-fit comes third and graph-partitioning heuristic comes a distant last. Our basic data comes from about 10,000 runs of each of the heuristics for each of the two problems on randomly generated chordal graphs of various sizes, sparsity, and structure.
Partitioning graphs to speedup Dijkstra's algorithm
Authors: Möhring Rolf H. , Schilling Heiko , Schütz Birk , Wagner Dorothea , Willhalm Thomas
Published: April 2010

We study an acceleration method for point-to-point shortest-path computations in large and sparse directed graphs with given nonnegative arc weights. The acceleration method is called the
arc-flag approach
and is based on Dijkstra's algorithm. In the arc-flag approach, we allow a preprocessing of the network data to generate additional information, which is then used to speedup shortest-path queries. In the preprocessing phase, the graph is divided into regions and information is gathered on whether an arc is on a shortest path into a given region. The arc-flag method combined with an appropriate partitioning and a bidirected search achieves an average speedup factor of more than 500 compared to the standard algorithm of Dijkstra on large networks (1 million nodes, 2.5 million arcs). This combination narrows down the search space of Dijkstra's algorithm to almost the size of the corresponding shortest path for long-distance shortest-path queries. We conduct an experimental study that evaluates which partitionings are best suited for the arc-flag method. In particular, we examine partitioning algorithms from computational geometry and a multiway arc separator partitioning. The evaluation was done on German road networks. The impact of different partitions on the speedup of the shortest path algorithm are compared. Furthermore, we present an extension of the speedup technique to multiple levels of partitions. With this multilevel variant, the same speedup factors can be achieved with smaller space requirements. It can, therefore, be seen as a compression of the precomputed data that preserves the correctness of the computed shortest paths.
Succinct backward-DAWG-matching
Authors: Fredriksson Kimmo
Published: April 2010

We consider single and multiple string matching in small space and optimal average time. Our algorithm is based on the combination of compressed self-indexes and Backward-DAWG-Matching (BDM) algorithm. We consider several implementation techniques having different space/time and implementation complexity trade-offs. The experimental results show that our approach has much smaller space requirements than BDM, while being much faster and easier to implement. We show that some of our techniques can boost the search speed of compressed self-indexes as well, using a small amount of additional space.
Efficiently implementing maximum independent set algorithms on circle graphs
Authors: Nash Nicholas , Lelait Sylvain , Gregg David
Published: April 2010

Circle graphs are an important class of graph with applications in a number of areas, including compiler optimization, VLSI design and computational geometry. In this article, we provide an experimental evaluation of the two most efficient algorithms for computing the maximum independent set of a circle graph. We provide details of our implementations of the algorithms of Apostolico et al. and Valiente [2003], together with time, space, and other measurements. We describe optimizations to the algorithm of Apostolico et al. that significantly reduce both its running time and its memory consumption. We also correct an error in this algorithm. In addition, we show how to restructure and simplify Valiente's algorithm, allowing us to remove redundant computations from the algorithm resulting in much improved performance. Moreover, in the case of both algorithms, when the density of the circle graph's associated interval representation is increased beyond a certain point the efficacy of the optimizations we apply increases dramatically and as a function of the density. We provide experimental results over dense and sparse random circle graphs, as well as for circle graphs that arise when performing register allocation of software pipelined loops in a compiler.
Inversion-sensitive sorting algorithms in practice
Authors: Elmasry Amr , Hammad Abdelrahman
Published: April 2010

We study the performance of the most practical inversion-sensitive internal sorting algorithms. Experimental results illustrate that adaptive AVL sort consumes the fewest number of comparisons unless the number of inversions is less than 1%; in such case Splaysort consumes the fewest number of comparisons. On the other hand, the running time of Quicksort is superior unless the number of inversions is less than 1.5%; in such case Splaysort has the shortest running time. Another interesting result is that although the number of cache misses for the cache-optimal Greedysort algorithm was the least, compared to other adaptive sorting algorithms under investigation, it was outperformed by Quicksort.
A domain decomposition algorithm for constraint satisfaction
Authors: Naanaa Wady
Published: April 2010

This article presents a domain decomposition algorithm for solving constraint satisfactions problems (CSPs). The proposed algorithm relies on a weak form of neighborhood substitutability referred to as directional substitutability. The main idea is that although two values may not be neighborhood substitutable if we consider the whole neighborhood of a given variable, they could be substitutable if we only focus on a part of the neighborhood induced by an orientation of the constraint graph. Directional substitutability provides a mean to decompose value domains into chains of directionally substitutable values that can be attempted simultaneously during search.

We report experiments carried out on several binary CSPs which clearly indicate that variations of classical algorithms which exploit directional substitutability often outperform the original algorithms.
Ranking tournaments
Authors: Coleman Tom , Wirth Anthony
Published: April 2010

Ranking is a fundamental activity for organizing and, later, understanding data. Advice of the form “
a
should be ranked before
b
” is given. If this advice is consistent, and complete, then there is a total ordering on the data and the ranking problem is essentially a sorting problem. If the advice is consistent, but incomplete, then the problem becomes topological sorting. If the advice is inconsistent, then we have the feedback arc set (FAS) problem: The aim is then to rank a set of items to satisfy as much of the advice as possible. An instance in which there is advice about every pair of items is known as a tournament. This ranking task is equivalent to ordering the nodes of a given directed graph from left to right, while minimizing the number of arcs pointing left.

In the past, much work focused on finding good, effective heuristics for solving the problem. Recently, a proof of the NP-completeness of the problem (even when restricted to tournaments) has accompanied new algorithms with approximation guarantees, culminating in the development of a PTAS (polynomial time approximation scheme) for solving FAS on tournaments.

In this article, we reexamine many existing algorithms and develop some new techniques for solving FAS. The algorithms are tested on both synthetic and nonsynthetic datasets. We find that, in practice, local-search algorithms are very powerful, even though we prove that they do not have approximation guarantees. Our new algorithm is based on reversing arcs whose nodes have large indegree differences, eventually leading to a total ordering. Combining this with a powerful local-search technique yields an algorithm that is as strong, or stronger than, existing techniques on a variety of data sets.
An experimental investigation of set intersection algorithms for text searching
Authors: Barbay Jérémy , López-Ortiz Alejandro , Lu Tyler , Salinger Alejandro
Published: April 2010

The intersection of large ordered sets is a common problem in the context of the evaluation of boolean queries to a search engine. In this article, we propose several improved algorithms for computing the intersection of sorted arrays, and in particular for searching sorted arrays in the intersection context. We perform an experimental comparison with the algorithms from the previous studies from Demaine, López-Ortiz, and Munro [ALENEX 2001] and from Baeza-Yates and Salinger [SPIRE 2005]; in addition, we implement and test the intersection algorithm from Barbay and Kenyon [SODA 2002] and its randomized variant [SAGA 2003]. We consider both the random data set from Baeza-Yates and Salinger, the Google queries used by Demaine et al., a corpus provided by Google, and a larger corpus from the TREC Terabyte 2006 efficiency query stream, along with its own query log. We measure the performance both in terms of the number of comparisons and searches performed, and in terms of the CPU time on two different architectures. Our results confirm or improve the results from both previous studies in their respective context (comparison model on real data, and CPU measures on random data) and extend them to new contexts. In particular, we show that value-based search algorithms perform well in posting lists in terms of the number of comparisons performed.
Reduction rules deliver efficient FPT-algorithms for covering points with lines
Authors: Estivill-Castro Vladimir , Heednacram Apichat , Suraweera Francis
Published: April 2010

We present efficient algorithms to solve the Line Cover Problem exactly. In this NP-complete problem, the inputs are
n
points in the plane and a positive integer
k
, and we are asked to answer if we can cover these
n
points with at most
k
lines. Our approach is based on fixed-parameter tractability and, in particular, kernelization. We propose several reduction rules to transform instances of Line Cover into equivalent smaller instances. Once instances are no longer susceptible to these reduction rules, we obtain a problem kernel whose size is bounded by a polynomial function of the parameter
k
and does not depend on the size
n
of the input. Our algorithms provide exact solutions and are easy to implement. We also describe the design of algorithms to solve the corresponding optimization problem exactly. We experimentally evaluated ten variants of the algorithms to determine the impact and trade-offs of several reduction rules. We show that our approach provides tractability for a larger range of values of the parameter and larger inputs, improving the execution time by several orders of magnitude with respect to earlier algorithms that use less rules.
Improving the testability of object oriented software through software contracts
Authors: Singh Yogesh , Saha Anju
Published: April 2010

Software testing is one of the most expensive phases of the software development life cycle. Testing object oriented software is more expensive due to various features like abstraction, inheritance etc. The cost of testing can be reduced by improving the software testability. Software testability of a class is generally measured in terms of the testing effort which is equal to the number of test cases required to test a class. Hence testability can be improved if the test cases can be reduced. Software contracts (method preconditions, method postcondtions, and class invariant) can be used in improving the testability of the software. This paper demonstartes how software contracts can be used to reduce the number of test cases and hence improve the testability of an object oriented software. To accomplish this, software contracts are instrumented in a class and test cases are designed for this class using the path testing technique and then it is compared with the class without instrumenting the software contracts. We found that the instrumentation of software contracts reduces the number of test cases and hence improves the testability.
Combining hierarchical and goal-directed speed-up techniques for dijkstra's algorithm
Authors: Bauer Reinhard , Delling Daniel , Sanders Peter , Schieferdecker Dennis , Schultes Dominik , Wagner Dorothea
Published: April 2010

In recent years, highly effective hierarchical and goal-directed speed-up techniques for routing in large road networks have been developed. This article makes a systematic study of combinations of such techniques. These combinations turn out to give the best results in many scenarios, including graphs for unit disk graphs, grid networks, and time-expanded timetables. Besides these quantitative results, we obtain general insights for successful combinations.
Heuristic initialization for bipartite matching problems
Authors: Langguth Johannes , Manne Fredrik , Sanders Peter
Published: April 2010

It is a well-established result that improved pivoting in linear solvers can be achieved by computing a bipartite matching between matrix entries and positions on the main diagonal. With the availability of increasingly faster linear solvers, the speed of bipartite matching computations must keep up to avoid slowing down the main computation. Fast algorithms for bipartite matching, which are usually initialized with simple heuristics, have been known for a long time. However, the performance of these algorithms is largely dependent on the quality of the heuristic. We compare combinations of several known heuristics and exact algorithms to find fast combined methods, using real-world matrices as well as randomly generated instances. In addition, we present a new heuristic aimed at obtaining high-quality matchings and compare its impact on bipartite matching algorithms with that of other heuristics. The experiments suggest that its performance compares favorably to the best-known heuristics, and that it is especially suited for application in linear solvers.
Optimizing MEMS-based storage devices for mobile battery-powered systems
Authors: Khatib Mohammed G. , Hartel Pieter H.
Published: April 2010

An emerging storage technology, called MEMS-based storage, promises nonvolatile storage devices with ultrahigh density, high rigidity, a small form factor, and low cost. For these reasons, MEMS-based storage devices are suitable for battery-powered mobile systems such as PDAs. For deployment in such systems, MEMS-based storage devices must consume little energy. This work mainly targets reducing the energy consumption of this class of devices.

We derive the operation modes of a MEMS-based storage device and systemically devise a policy in each mode for energy saving. Three types of policies are presented: power management, shutdown, and data-layout policy. Combined, these policies reduce the total energy consumed by a MEMS-based storage device. A MEMS-based storage device that enforces these policies comes close to Flash with respect to energy consumption and response time. However, enhancement on the device level is still needed; we present some suggestions to resolve this issue.
Superblock FTL
Authors: Jung Dawoon , Kang Jeong-UK , Jo Heeseung , Kim Jin-Soo , Lee Joonwon
Published: April 2010

In NAND flash-based storage systems, an intermediate software layer called a Flash Translation Layer (FTL) is usually employed to hide the erase-before-write characteristics of NAND flash memory. We propose a novel superblock-based FTL scheme, which combines a set of adjacent logical blocks into a superblock. In the proposed Superblock FTL, superblocks are mapped at coarse granularity, while pages inside the superblock are mapped freely at fine granularity to any location in several physical blocks. To reduce extra storage and flash memory operations, the fine-grain mapping information is stored in the spare area of NAND flash memory. This hybrid address translation scheme has the flexibility provided by fine-grain address translation, while reducing the memory overhead to the level of coarse-grain address translation. Our experimental results show that the proposed FTL scheme significantly outperforms previous block-mapped FTL schemes with roughly the same memory overhead.
Mining problem-solving strategies from HCI data
Authors: Fern Xiaoli , Komireddy Chaitanya , Grigoreanu Valentina , Burnett Margaret
Published: April 2010

Can we learn about users' problem-solving strategies by observing their actions? This article introduces a data mining system that extracts complex behavioral patterns from logged user actions to discover users' high-level strategies. Our application domain is an HCI study aimed at revealing users' strategies in an end-user debugging task and understanding how the strategies relate to gender and to success. We cast this problem as a sequential pattern discovery problem, where user strategies are manifested as sequential behavior patterns. Problematically, we found that the patterns discovered by standard data mining algorithms were difficult to interpret and provided limited information about high-level strategies. To help interpret the patterns as strategies, we examined multiple ways of clustering the patterns into meaningful groups. This collectively led to interesting findings about users' behavior in terms of both gender differences and debugging success. These common behavioral patterns were novel HCI findings about differences in males' and females' behavior with software, and were verified by a parallel study with an independent data set on strategies. As a research endeavor into the interpretability issues faced by data mining techniques, our work also highlights important research directions for making data mining more accessible to non-data-mining experts.
Finding shortest contractible and shortest separating cycles in embedded graphs
Authors: Cabello Sergio
Published: April 2010

We give a polynomial-time algorithm to find a shortest contractible cycle (i.e., a closed walk without repeated vertices) in a graph embedded in a surface. This answers a question posed by Hutchinson. In contrast, we show that finding a shortest contractible cycle through a given vertex is NP-hard. We also show that finding a shortest separating cycle in an embedded graph is NP-hard. This answers a question posed by Mohar and Thomassen.
Approximate shared-memory counting despite a strong adversary
Authors: Aspnes James , Censor Keren
Published: April 2010

A new randomized asynchronous shared-memory data structure is given for implementing an approximate counter that can be incremented once by each of
n
processes in a model that allows up to
n
-1 crash failures. For any fixed ϵ, the counter achieves a relative error of δ with high probability, at the cost of
O
(((1/δ) log
n
)

O
(1/ϵ)

) register operations per increment and
O
(
n
4/5+ϵ
((1/δ) log
n
)

O
(1/ϵ)

) register operations per read. The counter combines randomized sampling for estimating large values with an expander for estimating small values. This is the first counter implementation that is sublinear the number of processes and works despite a strong adversary scheduler that can observe internal states of processes.

An application of the improved counter is an improved protocol for solving randomized shared-memory consensus, which reduces the best previously known individual work complexity from
O
(
n
log
n
) to an optimal
O
(
n
), resolving one of the last remaining open problems concerning consensus in this model.
Comparison-based time-space lower bounds for selection
Authors: Chan Timothy M.
Published: April 2010

We establish the first nontrivial lower bounds on time-space trade-offs for the selection problem. We prove that any comparison-based randomized algorithm for finding the median requires Ω(
n
log log

S

n
) expected time in the RAM model (or more generally in the comparison branching program model), if we have
S
bits of extra space besides the read-only input array. This bound is tight for all
S
> log
n
, and remains true even if the array is given in a random order. Our result thus answers a 16-year-old question of Munro and Raman [1996], and also complements recent lower bounds that are restricted to sequential access, as in the multipass streaming model [Chakrabarti et al. 2008b].

We also prove that any comparison-based, deterministic, multipass streaming algorithm for finding the median requires Ω(
n
log
*
(
n
/
s
)+
n
log

s

n
) worst-case time (in scanning plus comparisons), if we have
s
cells of space. This bound is also tight for all
s
>log
2
n
. We get deterministic lower bounds for I/O-efficient algorithms as well.

The proofs in this article are self-contained and do not rely on communication complexity techniques.
Shortest paths in directed planar graphs with negative lengths
Authors: Klein Philip N. , Mozes Shay , Weimann Oren
Published: April 2010

We give an
O
(
n
log
2
n
)-time, linear-space algorithm that, given a directed planar graph with positive and negative arc-lengths, and given a node
s
, finds the distances from
s
to all nodes.
Optimization problems in multiple-interval graphs
Authors: Butman Ayelet , Hermelin Danny , Lewenstein Moshe , Rawitz Dror
Published: April 2010

Multiple-interval graphs are a natural generalization of interval graphs where each vertex may have more then one interval associated with it. We initiate the study of optimization problems in multiple-interval graphs by considering three classical problems: Minimum Vertex Cover, Minimum Dominating Set, and Maximum Clique. We describe applications for each one of these problems, and then proceed to discuss approximation algorithms for them.

Our results can be summarized as follows: Let
t
be the number of intervals associated with each vertex in a given multiple-interval graph. For Minimum Vertex Cover, we give a (2−1/
t
)-approximation algorithm which also works when a
t
-interval representation of our given graph is absent. Following this, we give a
t
2
-approximation algorithm for Minimum Dominating Set which adapts well to more general variants of the problem. We then proceed to prove that Maximum Clique is
NP
-hard already for 3-interval graphs, and provide a (
t
2
−
t
+1)/2-approximation algorithm for general values of
t
≥ 2, using bounds proven for the so-called transversal number of
t
-interval families.