bluuebunny/crossref_metadata_2025 huggingface dataset:
Establishing a Method of Inoculum Preparation for Susceptibility Testing of
Trichophyton rubrum
and
Trichophyton mentagrophytes
Authors: Santos D. A. , Barros M. E. S. , Hamdan J. S.
Published: January 2006

A total of 92 clinical isolates of dermatophytes (52 of
Trichophyton rubrum
and 40 of
Trichophyton mentagrophytes
) were selected for testing with six antifungal drugs (terbinafine, griseofulvin, clotrimazole, miconazole, isoconazole, and fluconazole) and two pairs of drug combinations (ketoconazole-cyclopiroxolamine and itraconazole-cyclopiroxolamine). Two methods of inoculum preparation for susceptibility testing were evaluated that used (i) inocula consisting only of microconidia of dermatophytes filtered in Whatman filter model 40 and (ii) unfiltered inocula consisting of hyphae and microconidia. We followed the recommendations of approved document M38-A of CLSI (formerly NCCLS) with some adaptations, including an incubation period of 7 days and an incubation temperature of 28°C. Reference strains of
Candida parapsilosis, Candida krusei, Trichophyton rubrum
, and
Trichophyton mentagrophytes
were included as quality-control strains. MICs were consistently higher (usually 1 to 2 dilutions for drugs tested individually) when nonfiltered inocula were tested (
P
< 0.01) except for terbinafine. Larger MICs were seen when testing drugs with nonfiltered inocula. The curves of drug interaction were used to analyze the reproducibility of the test, and it was shown that high levels of reproducibility were achieved using the methodology that included the filtration step. The standardization of methodologies is the first step to yield reliability of susceptibility testing and to proceed with clinical laboratory studies to correlate MICs with clinical outcomes.
Microsatellite megatracts in the maize (Zea maysL.) genome
Authors: Ananiev E V , Chamberlin M A , Klaiber J , Svitashev S
Published: January 2006

Long tracts (megatracts) of (CAG)n, (TAG)n, and (GAA)nmicrosatellite sequences capable of forming composite DNA segments were found in the maize (Zea mays L.) genome. Some of the (CAG)nand (TAG)nmegatracts were organized in clusters of up to 1 Mb on several chromosomes, as detected by fluorescence in situ hybridization (FISH), as well as on extended DNA fibers. Extensive polymorphism was found among different maize inbred lines with respect to the number and size of microsatellite megatract clusters on the A chromosomes. Polymorphism was also common among B chromosomes of different nuclei in the inbred line Zapalote Chico. Different retrotransposable elements were often inserted into the microsatellite tracts. Size variation in some (TAG)nand (GAA)nmegatracts was observed in consecutive generations among siblings of the inbred lines, indicating that these loci are highly unstable and predisposed to dynamic mutations similar to those described in mammalian systems.Key words: maize, microsatellites, SSR, markers, FISH.
A comparative analysis of the rainbow trout genome with 2 other species of fish (Arctic charr and Atlantic salmon) within the tetraploid derivative Salmonidae family (subfamily: Salmoninae)
Authors: Danzmann Roy G , Cairney Margaret , Davidson William S , Ferguson Moira M , Gharbi Karim , Guyomard Rene , Holm Lars-Erik , Leder Erica , Okamoto Nobuaki , Ozaki Akiyuki , Rexroad III Caird E , Sakamoto Takashi , Taggart John B , Woram Rachael A
Published: January 2006

We updated the genetic map of rainbow trout (Oncorhynchus mykiss) for 2 outcrossed mapping panels, and used this map to assess the putative chromosome structure and recombination rate differences among linkage groups. We then used the rainbow trout sex-specific maps to make comparisons with 2 other ancestrally polyploid species of salmonid fishes, Arctic charr (Salvelinus alpinus) and Atlantic salmon (Salmo salar) to identify homeologous chromosome affinities within each species and ascertain homologous chromosome relationships among the species. Salmonid fishes exhibit a wide range of sex-specific differences in recombination rate, with some species having the largest differences for any vertebrate species studied to date. Our current estimate of female:male recombination rates in rainbow trout is 4.31:1. Chromosome structure and (or) size is associated with recombination rate differences between the sexes in rainbow trout. Linkage groups derived from presumptive acrocentric type chromosomes were observed to have much lower sex-specific differences in recombination rate than metacentric type linkage groups. Arctic charr is karyotypically the least derived species (i.e., possessing a high number of acrocentric chromosomes) and Atlantic salmon is the most derived (i.e., possessing a number of whole-arm fusions). Atlantic salmon have the largest female:male recombination ratio difference (i.e., 16.81:1) compared with rainbow trout, and Arctic charr (1.69:1). Comparisons of recombination rates between homologous segments of linkage groups among species indicated that when significant experiment-wise differences were detected (7/24 tests), recombination rates were generally higher in the species with a less-derived chromosome structure (6/7 significant comparisons). Greater similarity in linkage group syntenies were observed between Atlantic salmon and rainbow trout, suggesting their closer phylogenetic affinities, and most interspecific linkage group comparisons support a model that suggests whole chromosome arm translocations have occurred in the evolution of this group. However, some possible exceptions were detected and these findings are discussed in relation to their influence on segregation distortion patterns. We also report unusual meiotic segregation patterns in a female parent involving the duplicated (homeologous) linkage group pair 12/16 and discuss several models that may account for these patterns.Key words: linkage analysis, genetic markers, polyploidy, tetrasomic inheritance, segregation distortion, recombination rate.
Physical organization of the major duplication onBrassica oleraceachromosome O6 revealed through fluorescence in situ hybridization withArabidopsisandBrassicaBAC probes
Authors: Howell E C , Armstrong S J , Barker G C , Jones G H , King G J , Ryder C D , Kearsey M J
Published: January 2006

The close relationship between Brassica oleracea and Arabidopsis thaliana has been used to explore the genetic and physical collinearity of the two species, focusing on an inverted segmental chromosome duplication within linkage group O6 of B. oleracea. Genetic evidence suggests that these segments share a common origin with a region of Arabidopsis chromosome 1. Brassica oleracea and Arabidopsis bacterial artificial chromosome probes have been used for fluorescence in situ hybridization analysis of B. oleracea pachytene chromosomes to further characterize the inverted duplication. This has been highly effective in increasing the local resolution of the cytogenetic map. We have shown that the physical order of corresponding genetic markers is highly conserved between the duplicated regions in B. oleracea and the physical lengths of the regions at pachytene are similar, while the genetic distances are considerably different. The physical marker order is also well conserved between Arabidopsis and B. oleracea, with only one short inversion identified. Furthermore, the relative physical distances between the markers in one segment of B. oleracea and Arabidopsis have stayed approximately the same. The efficacy of using fluorescence in situ hybridization, together with other forms of physical and genetic mapping, for elucidating such issues relating to synteny is discussed.Key words: collinearity, cytogenetic map, pachytene chromosomes, Brassica, Arabidopsis.
Transferability of wheat microsatellites to diploidAegilopsspecies and determination of chromosomal localizations of microsatellites in the S genome
Authors: Adonina I G , Salina E A , Pestsova E G , Röder M S
Published: January 2006

Overall, 253 genomic wheat (Triticum aestivum) microsatellite markers were studied for their transferability to the diploid species Aegilops speltoides, Aegilops longissima, and Aegilops searsii, representing the S genome. In total, 88% of all the analyzed primer pairs of markers derived from the B genome of hexaploid wheat amplified DNA fragments in the genomes of the studied species. The transferability of simple sequence repeat (SSR) markers of the T. aestivum A and D genomes totaled 74%. Triticum aestivum – Ae. speltoides, T. aestivum – Ae. longissima, and T. aestivum – Ae. searsii chromosome addition lines allowed us to determine the chromosomal localizations of 103 microsatellite markers in the Aegilops genomes. The majority of them were localized to homoeologous chromosomes in the genome of Aegilops. Several instances of nonhomoeologous localization of T. aestivum SSR markers in the Aegilops genome were considered to be either amplification of other loci or putative translocations. The results of microsatellite analysis were used to study phylogenetic relationships among the 3 species of the Sitopsis section (Ae. speltoides, Ae. longissima, and Ae. searsii) and T. aestivum. The dendrogram obtained generally reflects the current views on phylogenetic relationships among these species.Key words: Triticum aestivum, Aegilops speltoides, Aegilops longissima, Aegilops searsii, microsatellite, SSR, chromosome addition lines, phylogeny.
Modelling, testing, and construction of the first Ductal® canopy in the world
Authors: Adeeb S M , Scholefield B W.J , Brown T G , Shrive N G , Kroman J , Perry V H , Tadros G
Published: January 2006

Two series of nine architectural shell structures — constructed of a 20 mm thick layer of a new ultra-high performance cement (UPHC) composite with organic fibres (Ductal®) — were proposed to form the roofs of a new station for the light rail transit system in Calgary. Each section of the roofs consists of three panels each 6 m × 4.5 m connected to provide an 18 m continuous system. The City of Calgary required testing of a full-scale prototype panel for both static and dynamic responses. Finite element analysis (FEA) was used to determine the boundary conditions to be imposed on one edge of the prototype panel during the tests to simulate the presence of the other two in the actual structure. The FEA was also used to determine the critical (independent) snow and wind loading cases. The analyses and the testing procedures for the full-scale instrumented panel are described. The panel withstood both full factored loads without damage. The methods for manufacturing and assembling the canopy and roofs are also described.Key words: UHPC, shell structure, finite element analysis, static test, dynamic test.
Fungi in the diets of northern flying squirrels and lodgepole chipmunks in the Sierra Nevada
Authors: Meyer Marc D , North Malcolm P , Kelt Douglas A
Published: January 2006

The diets of a fungal specialist, northern flying squirrel (Glaucomys sabrinus (Shaw, 1801)), and a dietary generalist, lodgepole chipmunk (Neotamias speciosus (Merriam, 1890)), were examined in the old-growth, mixed-conifer forest at the Teakettle Experimental Forest in California's southern Sierra Nevada. Spores of fungi were identified from fecal pellets collected from both species during spring and summer of 1999 through 2002. Frequency of fungi in the diets of both squirrel species was consistently high across all seasons and years of study. Overall, G. sabrinus diets contained about 30% greater richness and evenness of fungal taxa than N. speciosus diets. There were no seasonal differences in richness and evenness of fungal taxa in squirrel diets. Richness of fungal taxa in diets was positively correlated with hypogeous sporocarp biomass and rainfall from June through August for N. speciosus but not for G. sabrinus. Dietary overlap between G. sabrinus and N. speciosus was high with respect to the most frequently consumed fungal taxa, although Gautieria and Gastroboletus were consumed in greater proportions by G. sabrinus than N. speciosus. Our results indicate that in the southern Sierra Nevada both G. sabrinus and N. speciosus were frequent consumers of a similar, diverse assemblage of fungal taxa and that consumption was proportional to seasonal differences in availability. For the more strongly mycophagist G. sabrinus, however, diet had a greater proportion of select fungal taxa and avoidance of less desirable taxa.
Capercaillie broods in pristine boreal forest in northwestern Russia: the importance of insects and cover in habitat selection
Authors: Wegge Per , Olstad Thomas , Gregersen Håkon , Hjeljord Olav , Sivkov Andrey V
Published: January 2006

Capercaillie (Tetrao urogallus L., 1758), the largest and most size-dimorphic species of grouse, is decreasing in number throughout its man-modified range in the boreal forests of the Palaearctic. Poor reproduction owing to direct and indirect effects of commercial forestry is considered a main cause of the decline. We studied brood habitats in a pristine forest in northwestern Russia to identify key elements in habitat selection in the natural environment of this species. We monitored the movement of 10 radio-marked broods during their first 7 weeks of life, and compared the abundance of insects and cover at their locations (N = 120) with nearby random control sites. The broods preferentially used moist spruce forest and the insect-rich herb spruce forest, but were most often located in the more abundant vaccinium spruce forest, which was richest in bilberry (Vaccinium myrtillus L.) and associated lepidopteran larvae. Brood locations were consistently richer in insects than random controls in 3 of the 4 habitat types studied. The most pronounced difference was in the density of lepidopteran larvae, a food source known to form an important part of the diet of young capercaille chicks. Broods continued to select insect-rich sites throughout the 7 week age period; in the preferred moist spruce forest, larval abundance increased at brood locations, while it remained constant at control sites. Compared to the distribution of insects, cover did not appear to be as an important determinant of brood habitat selection, possibly because the structural characteristics were rather similar among the most widely used habitat types. Shrub cover tended to be higher at brood locations than at controls, whereas vertical cover along the ground was not different. This relationship to cover factors may reflect an adaptation to avoid predation by goshawk (Accipiter gentilis (L., 1758)), the most important predator of grouse in this pristine boreal forest.
MULTITHREADED PARALLELISM WITH OPENMP
Authors: RUFAI RAIMI , BOZYIGIT MUSLIM , ALGHAMDI JARALLA , AHMED MOATAZ
Published: January 2006

While multithreaded programming is an effective way to exploit concurrency, multithreaded programs are notoriously hard to program, debug and tune for performance. In this paper, we present OpenMP shared memory programming as a viable alternative and a much simpler way to write multithreaded programs. We show through empirical results obtained by running, on a single processor machine, a simple matrix multiplication program written in OpenMP C that the drop in performance compared with the single threaded version even on a uniprocessor machine may be negligible. However, this is well compensated for by the increased programmer productivity resulting from the ease of programming, debugging, tuning and the relative ease of OpenMP skill acquisition.
USE OF PREDICTIVE PERFORMANCE MODELING DURING LARGE-SCALE SYSTEM INSTALLATION
Authors: KERBYSON DARREN J. , HOISIE ADOLFY , WASSERMAN HARVEY J.
Published: January 2006

In this paper we describe an important use of predictive application performance modeling - the validation of measured performance during a new large-scale system installation. Using a previously-developed and validated performance model for SAGE, a multidimensional, 3D, multi-material hydrodynamics code with adaptive mesh refinement, we were able to help guide the stabilization of the first phase of the Los Alamos ASCI Q supercomputer. We review the salient features of an analytical model for this code that has been applied to predict its performance on a large class of Tera-scale parallel systems. We describe the methodology applied during system installation and upgrades to establish a baseline for the achievable "real" performance of the system. We also show the effect on overall application performance of certain key subsystems such as PCI bus speed and multi-rail networks. We show that utilization of predictive performance models is also a powerful system debugging tool.
ADVANCES IN MODELLING AND SIMULATION OF LARGE PARALLEL/DISTRIBUTED SYSTEMS
Authors: Nethi Murali K. , Aylor James H.
Published: January 2006

Many systems being designed today are extremely large and are being used to solve huge computational problems. The new system architectures being proposed are huge distributed and parallel systems with thousands of processors distributed widely over space and executing large applications. These new systems are used to solve the Grand Challenge problems. Significant emphasis has been placed on the evaluation of the performance of these systems. This paper surveys recent performance evaluation tools that have been developed to evaluate the performance of such parallel and distributed systems. A new methodology of performance evaluation using hardware description languages is proposed and its advantages over the existing approaches are discussed.
PERFORMANCE EVALUATION OF BLAS ON THE TRIDENT PROCESSOR
Authors: SOLIMAN MOSTAFA I. , SEDUKHIN STANISLAV G.
Published: January 2006

Different subtasks of an application usually have different computational, memory, and I/O requirements that result in different needs for computer capabilities. Thus, the more appropriate approach for both high performance and simple programming model is designing a processor having multi-level instruction set architecture (ISA). This leads to high performance and minimum executable code size.

Since the fundamental data structures for a wide variety of existing applications are scalar, vector, and matrix, our research Trident processor has three-level ISA executed on zero-, one-, and two-dimensional arrays of data. These levels are used to express a great amount of fine-grain data parallelism to a processor instead of the dynamical extraction by a complicated logic or statically with compilers. This reduces the design complexity and provides high-level programming interface to hardware.

In this paper, the performance of Trident processor is evaluated on BLAS, which represent the kernel operations of many data parallel applications. We show that Trident processor proportionally reduces the number of clock cycles per floating-point operation by increasing the number of execution datapaths.
PARALLEL ADAPTIVE QUANTUM TRAJECTORY METHOD FOR WAVEPACKET SIMULATIONS
Authors: CARIÑO RICOLINDO L. , BANICESCU IOANA , VADAPALLI RAVI K. , WEATHERFORD CHARLES A. , ZHU JIANPING
Published: January 2006

Time-dependent wavepackets are widely used to model various phenomena in physics. One approach in simulating the wavepacket dynamics is the quantum trajectory method (QTM). Based on the hydrodynamic formulation of quantum mechanics, the QTM represents the wavepacket by an unstructured set of pseudoparticles whose trajectories are coupled by the quantum potential. The governing equations for the pseudoparticle trajectories are solved using a computationally-intensive moving weighted least squares (MWLS) algorithm, and the trajectories can be computed in parallel. This paper contributes a strategy for improving the performance of wavepacket simulations using the QTM. Specifically, adaptivity is incorporated into the MWLS algorithm, and loop scheduling techniques are employed to dynamically load balance the parallel computation of the trajectories. The adaptive MWLS algorithm reduces the amount of computations without sacrificing accuracy, while adaptive loop scheduling addresses the load imbalance introduced by the algorithm and the runtime system. Results of experiments on a Linux cluster are presented to confirm that the adaptive MWLS reduces the trajectory computation time by up to 24%, and adaptive loop scheduling achieves parallel efficiencies of up to 85% when simulating a free particle.
IMPROVING SCHEDULING OF COMMUNICATION INTENSIVE PARALLEL APPLICATIONS ON HETEROGENEOUS COMPUTING ENVIRONMENTS
Authors: ISHII RENATO P. , DE MELLO RODRIGO F. , SENGER LUCIANO J. , SANTANA MARCOS J. , SANTANA REGINA H. C. , YANG LAURENCE TIANRUO
Published: January 2006

This paper presents a new model for the evaluation of the impacts of processing operations resulting from the communication among processes. This model quantifies the traffic volume imposed on the communication network by means of the latency parameters and the overhead. Such parameters represent the load that each process imposes over the network and the delay on CPU, as a consequence of the network operations. This delay is represented on the model by means of metric measurements slowdown. The equations that quantify the costs involved in the processing operation and message exchange are defined. In the same way, equations to determine the maximum network bandwidth are used in the decision-making scheduling. The proposed model uses a constant that delimitates the communication network maximum allowed usage, this constant defines two possible scheduling techniques: group scheduling or through communication network. Such techniques are incorporated to the DPWP policy, generating an extension of this policy. Experimental and simulation results confirm the performance enhancement of parallel applications under supervision of the extended DPWP policy, compared to the executions supervised by the original DPWP.
A Genetic Algorithm for Energy Aware Task Scheduling in Heterogeneous Systems
Authors: Lin Man , Ng Sai Man
Published: January 2006

In distributed systems, an application can be decomposed to tasks which can be executed on different processors in parallel. Modern processors allow variable supply voltages and dynamic voltage scaling (DVS) provides the possibility to reduce the power consumption. In this paper, we present a static scheduling approach to integrate task mapping, scheduling and voltage selection to minimize energy consumption of real-time dependent tasks executing on a number of heterogeneous processors. The approach is based on Genetic Algorithms. The simulation results show that the proposed algorithm is very effective and reduces the energy consumption ranging from 20% to 90% under different system configurations. We also compare the proposed genetic-algorithm-based energy aware algorithm with other three algorithms, namely earliest-deadline-first-based, longest-time-first-based and simulated-annealing-based energy aware algorithms. The comparison results demonstrate that the genetic-algorithm-based energy aware algorithm outperforms other three algorithms.
ADAPTIVE SELECTION OF MATERIALIZED QUERIES IN A MEDIATOR
Authors: JOO KIL HONG , LEE WON SUK
Published: January 2006

In a mediator, query usage should be carefully monitored to determine the optimized set of materialized sub-queries, since the integration schema of a mediator can be incrementally modified and the evaluation frequency of a global query can also be continuously varied. This paper proposes a theoretical basis for adaptive selection of materialized sub-queries such that available storage in a mediator can be highly utilized at any time. In order to differentiate the recent usage of a query from the past, the accumulated usage frequency of a query decays as time goes by. Consequently, it is possible to find the optimum set of materialized sub-queries which minimizes the total evaluation cost of global queries in linear search complexity.
A PARALLELIZATION CASE-STUDY OF MD SIMULATION OF A LOW DENSITY PHYSICAL SYSTEM
Authors: HAYASHI RYOKO , TANAKA KENJI , HORIGUCHI SUSUMU , HIWATARI YASUAKI
Published: January 2006

A case study on the parallelization of a classical molecular dynamics code for simulating the formation of carbon clusters is presented. Parallelization is based on the domain decomposition method, as the Tersoff potentials used are short-range. However, at low particle densities, high-performance parallel execution of MD simulations is quite difficult. Methods for improving the performance achieved by parallelization of low density MD simulations are discussed and initial results for a low density system are presented.
Applying the Feedback Guided Dynamic Loop Scheduling Method for the Shortest Path Problem
Authors: Tabirca Tatiana , Freeman Len , Tabirca Sabin , Yang Laurence Tianruo
Published: January 2006

Feedback Guided Dynamic Loop Scheduling is a recent dynamic method for loop scheduling. The method has been mainly studied for synthetic examples so far and it has always offered the lowest computational times against other dynamic scheduling methods. In this article we show how the method is applied to the shortest path problem and also present some execution times that prove the efficiency.
COMPUTING THE SET OF ALL THE DISTANT HORIZONS OF A TERRAIN
Authors: ARCHAMBAULT DANIEL , EVANS WILLAM , KIRKPATRICK DAVID
Published: January 2006

We study the problem of computing the set of all distant horizons of a terrain, represented as either: (1) the set of all edges that appear on the distant horizon from at least one viewing direction; (2) for every edge e, the set of direction intervals for which e appears on the distant horizon; or (3) a search structure to query for the edges on the distant horizon, or the precise distant horizon, from a fixed viewing direction. We describe an algorithm that solves the first and second forms of the problem in O(n2+∊) time for any constant ∊ > 0 where n is the number of edges of the terrain. This algorithm can be extended to compute a search structure for (3) in O(n2+∊) time. The search structure can return the s edges on the distant horizon in O( log n + s) time. We show solving problem (1) is 3SUM hard. Furthermore, we construct a terrain with a single local maximum in which Θ(n) edges each have Θ(n) direction intervals, showing that our solution to (2) cannot be significantly improved, in the worst case, even for such restricted terrains. This takes advantage of a novel construction in which the convex hull of a set of n linearly moving points, whose trajectories do not intersect, changes Ω(n2) times.
ON MULTI-LEVEL k-RANGES FOR RANGE SEARCH
Authors: FALCONER SEAN M. , NICKERSON BRADFORD G.
Published: January 2006

We investigate an implementation of the multi-level or ℓ-level k-range data structure. The ℓ-level k-range is compared to naive and R*tree search over N randomly generated k-dimensional points. Results indicate that multi-level k-ranges are not competitive due to their (previously unreported) complexity. We show that storage is S(N,k,ℓ) = O(N1+2(k-1)/ℓ) and S(N,k) = Θ(N1+2(k-1)/ log 2N). Our results also indicate that the ℓ-level k-range requires Q(N,k,ℓ) = O((2ℓ)k( log N + A)) time for range search, for A = number of points reported in range.
GENERALIZING MONOTONICITY: ON RECOGNIZING SPECIAL CLASSES OF POLYGONS AND POLYHEDRA
Authors: BOSE PROSENJIT , VAN KREVELD MARC
Published: January 2006

A simple polyhedron is weakly-monotonic in direction [Formula: see text] provided that the intersection of the polyhedron and any plane with normal [Formula: see text] is simply-connected (i.e. empty, a point, a line-segment or a simple polygon). Furthermore, if the intersection is a convex set, then the polyhedron is said to be weakly-monotonic in the convex sense. Toussaint10 introduced these types of polyhedra as generalizations of the 2-dimensional notion of monotonicity. We study the following recognition problems:

Given a simple n-vertex polyhedron in 3-dimensions, we present an O(n log n) time algorithm to determine if there exists a direction [Formula: see text] such that when sweeping over the polyhedron with a plane in direction [Formula: see text], the cross-section (or intersection) is a convex set. If we allow multiple convex polygons in the cross-section as opposed to a single convex polygon, then we provide a linear-time recognition algorithm. For simply-connected cross-sections (i.e. the cross-section is empty, a point, a line-segment or a simple polygon), we derive an O(n2) time recognition algorithm to determine if a direction [Formula: see text] exists.

We then study variations of monotonicity in 2-dimensions, i.e. for simple polygons. Given a simple n-vertex polygon P, we can determine whether or not a line ℓ can be swept over P in a continuous manner but with varying direction, such that any position of ℓ intersects P in at most two edges. We study two variants of the problem: one where the line is allowed to sweep over a portion of the polygon multiple times and one where it can sweep any portion of the polygon only once. Although the latter problem is slightly more complicated than the former since the line movements are restricted, our solutions to both problems run in O(n2) time.
EXACT AND APPROXIMATION ALGORITHMS FOR FINDING AN OPTIMAL BRIDGE CONNECTING TWO SIMPLE POLYGONS
Authors: BHOSLE AMIT M. , GONZALEZ TEOFILO F.
Published: January 2006

Given two simple polygons P and Q we define the weight of a bridge (p,q), with p ∈ ρ(P) and q ∈ ρ(Q), where ρ() denotes the compact region enclosed by the boundary of the polygon, between the two polygons as gd(p,P) + d(p,q) + gd(q,Q), where d(p,q) is the Euclidean distance between the points p and q, and gd(x,X) is the geodesic distance between x and its geodesic furthest neighbor on X. Our problem differs from another version of the problem where the additional restriction of requiring the endpoints of the bridge to be mutually visible was imposed. We show that an optimal bridge always exists such that the endpoints of the bridge lie on the boundaries of the two polygons. Using this critical property, we present an algorithm to find an optimal bridge (of minimum weight) in O(n2 log n) time. We present a polynomial time approximation scheme that for any ∊ > 0 generates a bridge with objective function within a factor of 1 + ∊ of the optimal value in O(kn log kn) time, where [Formula: see text]. An improved polynomial time approximation scheme and algorithms for generalized versions of our problems are also discussed.
ERP Implementation Project at TS Group
Authors: Lee James C. Y. , Lau R. S. M.
Published: January 2006

This case illustrates the challenges and opportunities for TSG, a leading company in household products, to implement an enterprise resource planning (ERP) system. Arguments for and against adopting an ERP solution were discussed throughout the company's decision-making process. Once the implementation project was approved, the company planned to implement the general ledger module in its corporate office in Hong Kong before a full implementation of other modules in China. As experienced by other companies in implementing their ERP systems, technicality was often not so much the major issues as the people, users, and coordination issues. Although the initial rollout in Hong Kong was delayed by three months, twice the time originally planned, the lessons learnt proved to be valuable in guiding the later implementation of such projects for other TSG subsidiaries. This case explores the issues and challenges associated with the implementation of ERP solutions.
Autobiography of a Manager
Authors: Vijayalakshmi C. , Kalra Satish K. , Gupta Rajen K.
Published: January 2006

This is a case written in autobiographical style of an Indian manager. He was 31 years old with nine years' working experiences and currently working for a Software MNC. He was the only son of his parents. After graduating from the Indian Institute of Management, Ahmedabad, he joined an Indian consultancy firm based in Chennai and moved to the company where he is currently working five years later. His brief marriage had ended in a divorce. In his current job he was being shuttled from one crisis to another, fire fighting all the time. He had to decide about an offer to go back to his previous employer. He also had to decide if he wanted to marry again. This case explores the need and challenges in personal goal-setting and decision making.
SPEL: The Quality Journey
Authors: Khan Jamshed Hasan
Published: January 2006

Synthetic Products Enterprises (Private) Limited (SPEL) was one of the few (indigenous) Pakistani companies that had introduced and implemented many quality and productivity improvement initiatives. These included Benchmarking, Statistical Quality Control, Quality Control Circles, and 5S'. A distinguishing feature of these initiatives was the involvement and motivation of its employees. However, with emerging competition coupled with reduced trade barriers, it became imperative for the company to constantly review and improve its current systems, which were predominantly quality driven. SPEL was able to develop a quality culture within its organization whereas several other companies, which had implemented similar kinds of quality tools, failed to develop it. This case explores the process through which a customer focused Total Quality Culture was developed and the conditions needed to facilitate this development.
COMPACTION AND SUPERCOILING OF SINGLE, LONG DNA MOLECULES BY HU PROTEIN
Authors: SCHNURR BERNHARD , VORGIAS CONSTANTINOS , STAVANS JOEL
Published: January 2006

The bacterial cell contains the highly conserved protein HU in abundance. To characterize its architectural role, we studied the elastic behavior of single, supercoilable DNA molecules (tens of kilobases long) in solution with HU from B. stearothermophilus (BstHU) by a micromanipulation assay. We point out quantitative yet notable differences to the behavior of HU from E. coli (EcoHU) observed by others. Our main contribution here, however, is to characterize the interaction of BstHU with single molecules of DNA in arbitrary states of supercoiling. BstHU clearly distinguishes under- and overwound substrates, breaking the characteristic symmetry in the elastic response of bare DNA. We demonstrate that BstHU shifts the preferred linking number of the complex, consistent with a model in which bound proteins untwist the double helix. The model qualitatively explains various features, such as overall compaction and weaker dependence on supercoiling, by a softening of the DNA to twist and bending. Previously reported reversal of binding effects at protein concentrations above a threshold also extends to supercoiling. All observed effects are highly sensitive to salt concentrations. Their range and magnitude lend HU great versatility in dynamically altering the physical properties and organization of the nucleoid.
NEW DEVELOPMENTS FOR THE SITE-SPECIFIC ATTACHMENT OF PROTEIN TO SURFACES
Authors: CAMARERO JULIO A.
Published: January 2006

Protein immobilization on surfaces is of great importance in numerous applications in biology and biophysics. The key for the success of all these applications relies on the immobilization technique employed to attach the protein to the corresponding surface. Protein immobilization can be based on covalent or noncovalent interaction of the molecule with the surface. Noncovalent interactions include hydrophobic interactions, hydrogen bonding, van der Waals forces, electrostatic forces, or physical adsorption. However, since these interactions are weak, the molecules can get denatured or dislodged, thus causing loss of signal. They also result in random attachment of the protein to the surface. Site–specific covalent attachment of proteins onto surfaces, on the other hand, leads to molecules being arranged in a definite, orderly fashion and uses spacers and linkers to help minimize steric hindrances between the protein and the surface. This work reviews in detail some of the methods most commonly used as well as the latest developments for the site-specific covalent attachment of protein to solid surfaces.
Nitric oxide augments fetal pulmonary artery endothelial cell angiogenesis in vitro
Authors: Balasubramaniam Vivek , Maxey Anne M. , Fouty Brian W. , Abman Steven H.
Published: January 2006

Growth and development of the lung normally occur in the low oxygen environment of the fetus. The role of this low oxygen environment on fetal lung endothelial cell growth and function is unknown. We hypothesized that low oxygen tension during fetal life enhances pulmonary artery endothelial cell (PAEC) growth and function and that nitric oxide (NO) production modulates fetal PAEC responses to low oxygen tension. To test this hypothesis, we compared the effects of fetal (3%) and room air (RA) oxygen tension on fetal PAEC growth, proliferation, tube formation, and migration in the presence and absence of the NO synthase (NOS) inhibitor Nω-nitro-l-arginine (LNA), and an NO donor, S-nitroso- N-acetylpenicillamine (SNAP). Compared with fetal PAEC grown in RA, 3% O2 increased tube formation by over twofold ( P < 0.01). LNA treatment reduced tube formation in 3% O2 but had no affect on tube formation in RA. Treatment with SNAP increased tube formation during RA exposure to levels observed in 3% O2. Exposure to 3% O2 for 48 h attenuated cell number (by 56%), and treatment with LNA reduced PAEC growth by 44% in both RA and 3% O2. We conclude that low oxygen tension enhances fetal PAEC tube formation and that NO is essential for normal PAEC growth, migration, and tube formation. Furthermore, we conclude that in fetal cells exposed to the relative hyperoxia of RA, 21% O2, NO overcomes the inhibitory effects of the increased oxygen, allowing normal PAEC angiogenesis and branching. We speculate that NO production maintains intrauterine lung vascular growth and development during exposure to low O2 in the normal fetus. We further speculate that NO is essential for pulmonary angiogenesis in fetal animal exposed to increased oxygen tension of RA and that impaired endothelial NO production may contribute to the abnormalities of angiogenesis see in infants with bronchopulmonary dysplasia.
Prostaglandin E2promotes cell survival of glomerular epithelial cells via the EP4 receptor
Authors: Aoudjit Lamine , Potapov Anna , Takano Tomoko
Published: January 2006

Visceral glomerular epithelial cells (GEC) are crucial for glomerular permselectivity and structural integrity in the kidney. The current study addressed the role of cyclooxygenase (COX)-2 and its product prostaglandin (PG) E2in GEC survival. We generated a subclone of cultured rat GEC, which overexpress COX-2 in an inducible manner. When COX-2 was induced, GEC survived better in serum-deprived conditions. Induction of COX-2 was correlated with increased PGE2generation, increased activation of extracellular signal-regulated kinase, decreased apoptosis, and increased cell proliferation. Rat GEC abundantly expressed the EP4 isoform of PGE2receptor. Induction of COX-2 and addition of exogenous PGE2both lead to decreased serum deprivation-induced apoptosis, which was accompanied by activation of the survival kinase Akt. Anti-apoptotic effect of COX-2 induction was reversed by the specific inhibitor of the EP4 receptor, L-161982. PGE2also inhibited puromycin aminonucleoside-induced GEC apoptosis in vitro. Acute puromycin aminonucleoside nephrosis (PAN) is a rat model of GEC injury and proteinuria. In rats with PAN, glomerular apoptosis, quantified as caspase-3 activity, as well as urinary protein excretion were significantly increased, compared with control rats. Administration of L-161982 in rats with PAN further exacerbated caspase-3 activation and proteinuria. Thus COX-2 and its product PGE2may have anti-apoptotic/protective effect on GEC via the EP4 receptor of PGE2.
Effect of altering starting length and activation timing of muscle on fiber strain and muscle damage
Authors: Butterfield Timothy A. , Herzog Walter
Published: January 2006

Muscle strain injuries are some of the most frequent injuries in sports and command a great deal of attention in an effort to understand their etiology. These injuries may be the culmination of a series of subcellular events accumulated through repetitive lengthening (eccentric) contractions during exercise, and they may be influenced by a variety of variables including fiber strain magnitude, peak joint torque, and starting muscle length. To assess the influence of these variables on muscle injury magnitude in vivo, we measured fiber dynamics and joint torque production during repeated stretch-shortening cycles in the rabbit tibialis anterior muscle, at short and long muscle lengths, while varying the timing of activation before muscle stretch. We found that a muscle subjected to repeated stretch-shortening cycles of constant muscle-tendon unit excursion exhibits significantly different joint torque and fiber strains when the timing of activation or starting muscle length is changed. In particular, measures of fiber strain and muscle injury were significantly increased by altering activation timing and increasing the starting length of the muscle. However, we observed differential effects on peak joint torque during the cyclic stretch-shortening exercise, as increasing the starting length of the muscle did not increase torque production. We conclude that altering activation timing and muscle length before stretch may influence muscle injury by significantly increasing fiber strain magnitude and that fiber dynamics is a more important variable than muscle-tendon unit dynamics and torque production in influencing the magnitude of muscle injury.
Systemic Augmentation of Nitric Oxide: Is There an Immediate Effect on the Urinary Flow Rate in Healthy Men?
Authors: Müntener Michael , Reitz André , Wefer Björn , Schurch Brigitte
Published: January 2006

Introduction: Nitric oxide (NO) is an important neurotransmitter in the lower urinary tract. Data from experimental studies in animals and humans suggest that NO donors like isosorbide dinitrate could be used to lower the infravesical resistance. Despite the potentially significant clinical benefit of such an effect, it has hardly been studied in vivo in men. We investigated the immediate effect of isosorbide dinitrate on the urinary flow rate and the functional bladder capacity in healthy young men. Patients and Methods: A free urinary flow was measured in 20 healthy male volunteers on two consecutive micturitions. 15–25 min prior to the second micturition, 10 mg of the NO donor isosorbide dinitrate was administered sublingually. Results: We found no significant difference between baseline measurement and the micturition after NO administration with regard to the totally voided volume, the maximal or the average flow rate as well as the flow rate corrected for the voided volume. Conclusion: Systemic augmentation of NO does not produce a relevant immediate effect on the urinary flow rate or the functional bladder capacity in healthy men.
Double Dissociation of Hangul and Hanja Reading in Korean Patients with Stroke
Authors: Kwon Miseon , Kim Jong S. , Lee Jae-Hong , Sim Hyeonsub , Nam Kichun , Park Heasuk
Published: January 2006

The orthographic system of the Korean language consists of both phonogram (Hangul) and ideogram (Hanja). We report 2 patients who revealed selective impairment in reading either of orthographies after the brain damages. YJ, a 67-year-old man, showed Broca’s aphasia and severe apraxia of speech after a stroke in the left inferior parietal lobe. He demonstrated predominant difficulties in reading phonogram. KS, a 51-year-old woman, had an intracerebral hemorrhage in the left parietal lobe. She showed anomic aphasia and a selective impairment on reading ideogram. These findings support the notion that recognition of visual words is processed in different ways depending on the characteristics of orthographic systems.
Impact of Mouse Strain Differences in Innate Hindlimb Collateral Vasculature
Authors: Helisch Armin , Wagner Shawn , Khan Nadeem , Drinane Mary , Wolfram Swen , Heil Matthias , Ziegelhoeffer Tibor , Brandt Ulrike , Pearlman Justin D. , Swartz Harold M. , Schaper Wolfgang
Published: January 2006

Objective—

To assess the importance of genetic background for collateral artery development.

Methods and Results—

C57BL/6, BALB/c and 129S2/Sv mice were studied after femoral artery ligation by laser Doppler imaging, visible light oximetry, time-of-flight–magnetic resonance imaging, and treadmill testing; C57BL/6 and BALB/c also underwent electron paramagnetic resonance (EPR) oximetry, x-ray angiography, and histology. C57BL/6 had the least initial distal ischemia and most complete recovery. BALB/c had the most severe initial ischemia and poorest recovery. BALB/c had some vasodilatory reserve in their ligated limbs not seen in the other strains at 3 weeks. By in vivo TOF-magnetic resonance angiography, C57BL/6 had larger preexistent and developed collaterals. By x-ray angiography, C57BL/6 had a higher collateral-dependent filling score and number of visible collaterals immediately after femoral ligation and a higher number of visible collaterals at 1 week but not at 4 weeks. EPR oximetry and histology revealed hypoxia and tissue damage in regions of collateral growth of BALB/c but not C57BL/6 mice. In C57BL/6 BrdUrd uptake in the thigh was limited to larger vessels and isolated perivascular cells. Proliferative activity in collateral arterioles was similar in both strains.

Conclusions—

Genetic differences in preexistent collateral vasculature can profoundly affect outcome and milieu for compensatory collateral artery growth after femoral artery occlusion.
Reduction of Caspase-8 and -9 Cleavage Is Associated With Increased c-FLIP and Increased Binding of Apaf-1 and Hsp70 After Neonatal Hypoxic/Ischemic Injury in Mice Overexpressing Hsp70
Authors: Matsumori Yasuhiko , Northington Frances J. , Hong Shwuhuey M. , Kayama Takamasa , Sheldon R. Ann , Vexler Zinaida S. , Ferriero Donna M. , Weinstein Philip R. , Liu Jialing
Published: January 2006

Background and Purpose—

Caspase-8 and caspase-9 are essential proteases of the extrinsic and intrinsic apoptotic pathways, respectively. We investigated whether neuroprotection associated with overexpression of heat-shock protein 70 (Hsp70), a natural cellular antiapoptotic protein, is mediated by caspase-8 and caspase-9 signaling in the neonatal mouse brain after hypoxia/ischemia (H/I) injury.

Methods—

Postnatal day 7 transgenic mice overexpressing rat Hsp70 (Hsp70 Tg) and their wild-type (Wt) littermates underwent unilateral common carotid artery ligation followed by 30 minutes of exposure to 8% O
2
. The expression of apoptotic proteins was quantified by Western blot analysis, and the specific interaction between Hsp70 and apoptotic protease activating factor 1 (Apaf-1) was determined by coimmunoprecipitation.

Results—

Hsp70 overexpression reduced cytosolic translocation of cytochrome c without affecting the levels of Apaf-1 and pro–caspase-9 24 hours after H/I. The expression of these apoptotic proteins in the naïve neonatal brains was also not affected by Hsp70 overexpression. Reduced caspase-9 cleavage occurred in Hsp70 Tg mice compared with Wt littermates 24 hours after H/I and correlated with increased binding of Hsp70 and Apaf-1. Increased cellular Fas-associated death domain–like interleukin-1β–converting enzyme inhibitory protein (FLIP) expression and decreased caspase-8 cleavage were also observed in Hsp70 Tg compared with Wt mice 24 hours after H/I.

Conclusions—

Our results suggest that the extrinsic and intrinsic apoptotic pathways mediate the neuroprotective effects of Hsp70 overexpression in neonatal H/I, specifically by upregulating FLIP and sequestering Apaf-1, leading to reduced cleavage of caspase-8 and caspase-9.