bluuebunny/crossref_metadata_2025 huggingface dataset:
In Vitro
Activity of MK-7655, a Novel β-Lactamase Inhibitor, in Combination with Imipenem against Carbapenem-Resistant Gram-Negative Bacteria
Authors: Hirsch Elizabeth B. , Ledesma Kimberly R. , Chang Kai-Tai , Schwartz Michael S. , Motyl Mary R. , Tam Vincent H.
Published: April 2012

Carbapenem-resistant bacteria represent a significant treatment challenge due to the lack of active antimicrobials available. MK-7655 is a novel β-lactamase inhibitor under clinical development. We investigated the combined killing activity of imipenem and MK-7655 against four imipenem-resistant bacterial strains, using a mathematical model previously evaluated in our laboratory. Time-kill studies (TKS) were conducted with imipenem and MK-7655 against a KPC-2-producing
Klebsiella pneumoniae
isolate (KP6339) as well as 3
Pseudomonas aeruginosa
isolates (PA24226, PA24227, and PA24228) with OprD porin deletions and overexpression of AmpC. TKS were performed using 25 clinically achievable concentration combinations in a 5-by-5 array. Bacterial burden at 24 h was determined in triplicate by quantitative culture and mathematically modeled using a three-dimensional response surface. Mathematical model assessments were evaluated experimentally using clinically relevant dosing regimens of imipenem, with or without MK-7655, in a hollow-fiber infection model (HFIM). The combination of imipenem and MK-7655 was synergistic for all strains. Interaction indices were as follows: for KP6339, 0.50 (95% confidence interval [CI], 0.42 to 0.58); for PA24226, 0.60 (95% CI, 0.58 to 0.62); for PA24227, 0.70 (95% CI, 0.66 to 0.74); and for PA24228, 0.55 (95% CI, 0.49 to 0.61). In the HFIM, imipenem plus MK-7655 considerably reduced the bacterial burden at 24 h, while failure with imipenem alone was seen against all isolates. Sustained suppression of bacterial growth at 72 h was achieved with simulated doses of 500 mg imipenem plus 500 mg MK-7655 in 2 (KP6339 and PA24227) strains, and it was achieved in an additional strain (PA24228) when the imipenem dose was increased to 1,000 mg. Additional studies are being conducted to determine the optimal dose and combinations to be used in clinical investigations.
Contribution of Phe-7 to Tat-Dependent Export of β-Lactamase in Xanthomonas campestris
Authors: Lee Chen-Wei , Tseng Yi-Hsuan , Deng Fu-Seng , Lin Juey-Wen , Tseng Yi-Hsiung , Weng Shu-Fen
Published: April 2012

Strains of
Xanthomonas campestris
pv. campestris isolated in Taiwan are commonly resistant to ampicillin owing to the constitutive expression of a chromosomally encoded β-lactamase that is secreted into the periplasm. In this study, we found that levels of β-lactamase vary among
X. campestris
pv. campestris strains, a difference that can be attributed to amino acid substitutions at least at positions 7 and 206, with the former having the major impact. Bioinformatic and PCR analyses indicated that
X. campestris
pv. campestris possesses
tatABC
genes and that the signal peptide of
X. campestris
pv. campestris pre-Bla contains the typical twin-arginine motif (N-R-R-Q-F-L at amino acid residues 3 to 8 in strain
X. campestris
pv. campestris strain 11), suggesting that Bla is secreted via the Tat pathway. To assess the importance of Phe
7
in the efficient export of
X. campestris
pv. campestris Bla, we prepared mutant constructs containing amino acid substitutions and monitored their expression by measuring enzyme activity and detecting Bla protein by Western blotting. The results indicate that replacement of Phe
7
with Leu severely inhibited Bla export whereas replacement with Pro almost abolished it. Although a change to Arg caused moderate inhibition of export, replacement with Tyr had no effect. These results suggest that for efficient export of Bla by
X. campestris
pv. campestris, the aromatic-aromatic interactions and stability of protein structure around the twin-arginine motif are important, since only proteins that can attain a folded state in the cytoplasm are competent for export via the Tat pathway.
The Genome Sequence of Bluetongue Virus Type 10 from India: Evidence for Circulation of a Western Topotype Vaccine Strain
Authors: Maan Sushila , Maan Narender S. , Pullinger Gillian , Nomikou Kyriaki , Morecroft Elizabeth , Guimera Marc , Belaganahalli Manjunatha N. , Mertens Peter P. C.
Published: April 2012

Bluetongue virus
is the type species of the genus
Orbivirus
in the family
Reoviridae
. We report the first complete genome sequence of an isolate (IND2004/01) of bluetongue virus serotype 10 (BTV-10) from Andhra Pradesh, India. This isolate, which is stored in the Orbivirus Reference Collection (ORC) at IAH Pirbright, shows >99% nucleotide identity in all 10 genome segments with a vaccine strain of BTV-10 from the United States.
Flower and seed production as affected by axis category and shoot size in two Patagonian Nothofagus species
Authors: Torres Cristian D. , Puntieri Javier G. , Stecconi Marina
Published: April 2012

Flower distribution within the tree crown may affect both pollination dynamics and the costs of flowering on tree growth. For Nothofagus obliqua (Mirb.) Oerst. and Nothofagus nervosa (Phil.) Krasser, the production of flowers and viable seeds were compared among axes of contrasting size and category in the tree crown. For annual shoots arising from three axis categories (main branches, secondary branches, and twigs), the numbers of nodes, staminate flowers, pistillate flowers and axillary buds, and seed viability were evaluated. Most flowering shoots produced both staminate and pistillate flowers. The number of flowers of each type was related positively with the number of nodes of the shoot. Longer shoots had proportionally more pistillate flowers than short shoots. The three axis categories produced both flower types in direct proportion to the size of their shoots, but main branches presented more axillary vegetative buds than secondary branches and twigs. For N. obliqua, the percentage of viable seeds was lower in secondary branches than in main branches and twigs, perhaps owing to a lower probability of cross-pollination in secondary branches. The coexistence of vegetative and reproductive functions may cause interference between them. Massive allocation of meristems to flowering reduces meristem availability for growth and, especially, flowering in the following growing season.
Cortinarius parkeri, a new species from the Pacific Northwest of North America
Authors: Ammirati Joseph F. , Barlow Tess E. , Seidl Michelle T. , Ceska Oldriska , Berbee Mary , Harrower Emma , Liimatainen Kare
Published: April 2012

Cortinarius parkeri , a new vernal species in subgenus Cortinarius , section Veneti , is described from the Pacific Northwest of North America. Within its subgenus, C. parkeri is unique in that its membranous universal veil is attached to the pileus edge of young mushrooms and extends as a covering over the pileus surface. At maturity, the universal veil forms a sheathing membranous volva-like structure that flares out above the stipe base. Sequences of the nuclear ribosomal DNA internal transcribed spacer region (ITS1-5.8s-ITS2) determined for 13 collections of C. parkeri were all identical, except for a polymorphic two base pair indel. In a phylogeny including other related species from North America and Europe, C. parkeri is monophyletic. In contrast to intraspecific distances, the interspecific genetic distance between C. parkeri and other Veneti species sequences was large. Being dikaryotic, mushrooms of C. parkeri contain genomes from two parents. As expected in a dikaryon in an interbreeding population, the polymorphic indel was homozygous in some collections but heterozygous in three collections, with conflicting sequences resulting from mixed parental types. Taken together, morphological and molecular results strongly support C. parkeri as a new and distinctive species.
FERMI ACCELERATION IN A PERIODICALLY DRIVEN FERMI–ULAM MODEL
Authors: DE ALCANTARA BONFIM O. F.
Published: April 2012

The dynamics of a particle bouncing between two harmonically vibrating walls is analyzed in the context of the static wall approximation. Fermi acceleration is observed for a wide range of the ratio between the frequencies of the oscillating walls and their relative phases. However, no acceleration is observed if the frequency ratio is an integer. In the phase versus frequency-ratio diagram, the region in which Fermi acceleration is observed is separated by an upper and lower boundary. At the lower boundary, after a large number of collisions, the particle average velocity increases with the square-root of the number of collisions (n) with the walls. Between the lower and upper boundaries, the particle average velocity behaves as V(n) ~ nβ, with β in the interval [0.5, 1.0]. Below and near the lower boundary, the average particle velocity initially grows with the number of collisions until it eventually reaches a plateau. In this region, for a fixed frequency ratio, the velocity of the particle exhibits scaling properties over a range of the relative phases of the vibrating walls. Inelastic collisions with the walls cause suppression of the Fermi acceleration inside the previously accelerating region and lead to the particle velocity exhibiting scaling properties with respect to changes in the coefficient of restitution.
DYNAMICS IN EXCITABLE MEDIA SUBJECTED TO A SPECIFIC SPATIOTEMPORAL WAVE UNDER TWO SCHEMES
Authors: YUAN GUOYONG , FENG ZHICHENG , XU AIGUO , WANG GUANGRUI , CHEN SHAOYING
Published: April 2012

The dynamics in excitable media driven by a specific spatiotemporal wave are studied by investigating wave states, the motion of tips and synchronized behaviors. We demonstrate that multiple-armed spiral waves can be generated in excitable media with rest initial conditions by directly injecting a rigidly rotating spiral wave, also that the meandering driver can induce the spiral wave, with the wider excited parts and the same frequency as the driving wave, in the driven system. It is more interesting to find that the higher similarity between the driving and driven waves occurs when the driving strength is smaller. We also study the dynamics of spiral waves in the driven system when the external driving wave is introduced by the form of difference, and find that the stronger synchronized behaviors appear when the driving strength is larger. The dynamical behaviors can be understood by considering various characteristics of the excitable system, for example the existence of "refractory period" and "vulnerable period" and so on.
COMPUTING THE TOPOLOGICAL ENTROPY OF UNIMODAL MAPS
Authors: DILÃO RUI , AMIGÓ JOSÉ
Published: April 2012

We derive an algorithm to determine recursively the lap number (minimal number of monotone pieces) of the iterates of unimodal maps of an interval with free end-points. For this family of maps, the kneading sequence does not determine the lap numbers. The algorithm is obtained by the sign analysis of the itineraries of the critical point and of the boundary points of the interval map. We apply this algorithm to the estimation of the growth number and the topological entropy of maps with direct and reverse bifurcations.
REAL HYPERSURFACES IN COMPLEX TWO-PLANE GRASSMANNIANS WITH GENERALIZED TANAKA–WEBSTER 𝔇⊥-PARALLEL SHAPE OPERATOR
Authors: JEONG IMSOON , LEE HYUNJIN , SUH YOUNG JIN
Published: April 2012

In a paper due to [I. Jeong, H. Lee and Y. J. Suh, Real hypersurfaces in complex two-plane Grassmannians with generalized Tanaka–Webster parallel shape operator, Kodai Math. J.34 (2011) 352–366] we have shown that there does not exist a hypersurface in G2(ℂm+2) with parallel shape operator in the generalized Tanaka–Webster connection (see [N. Tanaka, On non-degenerate real hypersurfaces, graded Lie algebras and Cartan connections, Japan J. Math.20 (1976) 131–190; S. Tanno, Variational problems on contact Riemannian manifolds, Trans. Amer. Math. Soc.314(1) (1989) 349–379]). In this paper, we introduce a new notion of generalized Tanaka–Webster 𝔇⊥-parallel for a hypersurface M in G2(ℂm+2), and give a characterization for a tube around a totally geodesic ℍ Pnin G2(ℂm+2) where m = 2n.
Tectonic subsidence history and source-rock maturation in the Campos Basin, Brazil
Authors: Beglinger Suzanne E. , van Wees Jan-Diederik , Cloetingh Sierd , Doust Harry
Published: April 2012

The Campos Basin is a petroleum-productive, marginal sag basin along the Brazilian margin. It contains a stratigraphic sequence recording lithospheric extension and rift tectonics developing to a fully evolved post-break-up setting. We present a combined approach using subsidence analysis and basin history inversion models to make predictions on source-rock maturation. The classical uniform stretching model does not account for the
observed tectonic subsidence
, and so we consider the thermal and subsidence implications of incorporating different events of magmatic underplating. The post-rift is characterized by one major phase of post-rift thermal subsidence: changes in sediment supply and load, as well as halokinetic movements, cause deviations from normal thermal subsidence and relaxation. The dimensions of these events have been examined and quantified.

Our best-fit forward model is tested against measured borehole temperature (BHT) data. Results show a systematic overestimation of present-day temperatures in the shallow-water wells. Including the effects of hydrothermal convection by raising the conductivity of the top part of the stratigraphic sequence results in an almost perfect fit between predicted and measured BHTs in the shallow-water wells.

Based on these forward models, we predict that the lacustrine shales of the syn-rift Lagoa Feia Fm. could be mature to generate oil and/or gas over a larger area than previously expected. Furthermore, our results suggest that the early post-rift Macaé Fm. is locally mature to generate oil, and that the middle/late post-rift Carapebus/Ubatuba Fm. shales are likely to generate oil as well, if organic-rich facies are indeed present. In light of the most recent pre- and post-salt discoveries made near established oil fields in the Campos Basin, our results support the idea that many more such accumulations may be found.
Dotted interval graphs
Authors: Aumann Yonatan , Lewenstein Moshe , Melamud Oren , Pinter Ron , Yakhini Zohar
Published: April 2012

We introduce a generalization of interval graphs, which we call Dotted Interval Graphs (DIG). A dotted interval graph is an intersection graph of arithmetic progressions (dotted intervals). Coloring of dotted interval graphs naturally arises in the context of high throughput genotyping. We study the properties of dotted interval graphs, with a focus on coloring. We show that any graph is a DIG, but that

DIG
d

graphs, that is, DIGs in which the arithmetic progressions have a jump of at most
d
, form a strict hierarchy. We show that coloring

DIG
d

graphs is NP-complete even for
d
= 2. For any fixed
d
, we provide a 5/6
d
+
o
(
d
) approximation for the coloring of

DIG
d

graphs. Finally, we show that finding the maximal clique in

DIG
d

graphs is fixed parameter tractable in
d
.
Succinct geometric indexes supporting point location queries
Authors: Bose Prosenjit , Chen Eric Y. , He Meng , Maheshwari Anil , Morin Pat
Published: April 2012

We propose designing data structures called succinct geometric indexes of negligible space (more precisely,
o
(
n
) bits) that support geometric queries in optimal time, by taking advantage of the
n
points in the dataset permuted and stored elsewhere as a sequence. Our first and main result is a succinct geometric index that can answer point location queries, a fundamental problem in computational geometry, on planar triangulations in
O
(lg
n
) time. We also design three variants of this index. The first supports point location using lg
n
+ 2√lg
n
+
O
(lg
1/4
n
) point-line comparisons. The second supports point location in
o
(lg
n
) time when the coordinates are integers bounded by
U
. The last variant can answer point location queries in
O
(
H
+ 1) expected time, where
H
is the entropy of the query distribution. These results match the query efficiency of previous point location structures that occupy
O
(
n
) words or
O(n
lg
n
) bits, while saving drastic amounts of space. We generalize our succinct geometric index to planar subdivisions, and design indexes for other types of queries. Finally, we apply our techniques to design the first implicit data structures that support point location in
O
(lg
2
n
) time.
Likert-type scales, statistical methods, and effect sizes
Authors: Robertson Judy
Published: April 2012

The
Communications
Web site, http://cacm.acm.org, features more than a dozen bloggers in the BLOG@CACM community. In each issue of
Communications
, we'll publish selected posts or excerpts.

twitter

Follow us on Twitter at http://twitter.com/blogCACM

http://cacm.acm.org/blogs/blog-cacm

Judy Robertson writes about researchers' use of the wrong statistical techniques to analyze attitude questionnaires.
A workshop revival
Authors: Hyman Paul
Published: April 2012

The success of Germany's Dagstuhl Seminars has inspired a proliferation of Dagstuhl-like venues, especially in India.
Idempotence is not a medical condition
Authors: Helland Pat
Published: April 2012

Messages may be retried. Idempotence means that's OK.
Your mouse is a database
Authors: Meijer Erik
Published: April 2012

Web and mobile applications are increasingly composed of asynchronous and real-time streaming services and push notifications.
An empirical comparison of Java remote communication primitives for intra-node data transmission
Authors: Burdette Philip F. , Jones William F. , Blose Brian C. , Kapfhammer Gregory M.
Published: April 2012

This paper presents a benchmarking suite that measures the performance of using sockets and eXtensible Markup Language remote procedure calls (XML-RPC) to exchange intra-node messages between Java virtual machines (JVMs). The paper also reports on an empirical study comparing sockets and XML-RPC with response time measurements from timers that use both operating system tools and Java language instrumentation. By leveraging packet filters inside the GNU/Linux kernel, the benchmark suite also calculates network resource consumption. Moreover, the framework interprets the response time results in light of memory subsystem metrics characterizing the behavior of the JVM. The empirical findings indicate that sockets perform better when transmitting small to very large objects, while XML-RPC exhibits lower response time than sockets with extremely large bulk data transfers. The experiments reveal trade-offs in performance and thus represent the first step towards determining if Java remote communication primitives can support the efficient exchange of intra-node messages.
Product-form distributions and network algorithms (abstract only)
Authors: Shah Devavrat
Published: April 2012

The "product-form" characterization of the stationary distribution make a queueing network analytically a lot more tractable. This has been the primary source of inspiration in the search for "productform" characterization. In this talk, I will discuss implications of "product-form" distributions for algorithm design by means of two examples: (i) intra-queue scheduling and (ii) inter-queue scheduling in a constrained queueing network. Near the end of the talk, by means of a novel comparison result between stationary distributions of Markov chains, I will briefly discuss notion of "approximate" product-form distributions.
Factorization properties for a MAP-modulated fluid flow model under server vacation policies (abstract only)
Authors: Baek Jung Woo , Lee Ho Woo , Lee Se Won , Ahn Soohan
Published: April 2012

In this paper, we study a MAP-modulated fluid flow model under generalized server vacation policies and propose factorization properties that can be efficiently used to derive the fluid level distributions at an arbitrary time point. Our model is an extension of the conventional Markov modulated fluid flow (MMFF) model to control the servers idle state. We consider two types of fluid increases: vertical increase (Type-V) and linear increase (Type-L). We first describe the MAP-modulated fluid flow model under server vacation policies and prove the factorization principle for each type. Based on the factorization formulae, we derive recursive formulae for performance measures. Lastly, some application examples of the factorization property are presented.
A self-promoting priority model for transplant queues (abstract only)
Authors: Drekic Steve , Stanford David , Woolford Douglas
Published: April 2012

In many jurisdictions, organ allocation is done on the basis of the health status of the patient, either explicitly or implicitly. This presentation presents a Matrix-analytic priority model in which customers self-promote to the higher priority level, to take into account changes in health status over time. In the first variant, all patients arrive as "regular" customers to the queue, but as the health of a patient degrades, their status is promoted to "priority" to reflect the increased urgency of the transplant. Performance measures such as the mean and distribution of the time until transplant are obtained.
An EM algorithm for the model fitting of Markovian binary trees (abstract only)
Authors: Hautphenne Sophie
Published: April 2012

Markovian binary trees are a special class of branching processes in which the lifetime of an individual is controlled by a transient Markovian arrival process. A Markovian binary tree is characterized by the 4-tuple (
?
,D0,B,
d
), where
?
is the vector of initial phase distribution of the first individual, D0 is the matrix of phase transition rates between birth and death events, B is the matrix of birth rates and
d
is the vector of death rates.

In order to use the Markovian binary tree to model the evolution of a real population, we need to determine the parameters (
?
,D0,B,
d
) from observations of that population. In the absence of migration, the only observable changes in a population are those associated with a birth or a death event; no phase transition in the underlying process can actually been seen. We are thus dealing with a problem of parameter estimation from incomplete data, and one way to solve this statistical problem is to make use of the EM algorithm. Our purpose here is thus to specify this algorithm to the Markovian binary tree setting. In the first part of this paper, we introduce a discrete time terminating marked Markov arrival process (MMAP), based on which a class of discrete multivariate phase-type (MPH) distributions is defined. The discrete MPH-distributions hold many of the properties possessed by continuous MPH-distributions (Assaf, et al. (1983), Kulkarni (1988), and O'Cinneide (1990)). It is known that the joint distribution functions of continuous MPH are fairly complicated and difficult to calculate. In contrast, for the discrete MPH introduced here, we provide recursive formulas the joint probabilities and explicit expressions for means, variances, and co-variances.
On a discrete multi-variate phase-type distribution and its applications (abstract only)
Authors: He Qi-Ming , Ren Jiandong
Published: April 2012

In the second part of this paper, we use the discrete MPH-distributions to model multi-variate insurance claim processes in risk analysis, where claims may arrive in batches, the arrivals of different types of batches may be correlated, and the amounts of different types of claims in a batch may be dependent. This provides one natural approach to model the dependencies among claim frequencies as well claim sizes of different types of risks, which is a very important topic in insurance risk theory. Under certain conditions, it is shown that the total amounts of claims accumulated in some random time horizon are discrete MPH random vectors. Matrixrepresentations of the discrete MPH-distributions are constructed explicitly. Efficient computational methods are developed for computing performance measures of the total claims of different types of claim batches and individual types of claims.
Majorization and Extremal
PH
-Distributions (abstract only)
Authors: He Qi-Ming , Zhang Hanqin , Vera Juan
Published: April 2012

This paper presents majorization results for
PH
-generators. Based on the majorization results, Coxian distributions are identified to be extremal
PH
-distributions with respect to the first moment for certain subsets of
PH
-distributions. Bounds on the mean of phase-type distributions are found. In addition, numerical results indicate that Coxian distributions are extremal
PH
-distributions with respect to the moment of any order for certain subsets of
PH
-distributions.
Acceptance-rejection methods for generating random variates from matrix exponential distributions and rational arrival processes (abstract only)
Authors: Horváth Gábor , Telek Miklós
Published: April 2012

Stochastic models based on matrix exponential structures, like matrix exponential distributions and rational arrival processes, have gained popularity in analytical models recently. However the application of these models in simulation based evaluations is not as widespread yet. One of the possible reasons is the lack of efficient random variates generation methods. In this paper we propose methods for efficient random variates generation for matrix exponential stochastic models based on appropriate representations of the models.
Tail asymptotics of the stationary distribution for M/M-JSQ with k parallel queues (abstract only)
Authors: Kobayashi Masahiro , Sakuma Yutaka , Miyazawa Masakiyo
Published: April 2012

We consider a parallel queueing model which has k identical servers. Assume that customers arrive from outside according to a Poisson process and join the shortest queue. Their service times have an
i.i.d
. exponential distribution, which is referred to as an M/MJSQ with k parallel queues. We are interested in the asymptotic behavior of the stationary distribution for the shortest queue length of this model, provided the stability is assumed. For this stationary distribution, it can be guessed conjectured that the tail decay rate is given by the k-th power of the traffic intensity of the corresponding M/M/k queue with a single waiting line. We prove this fact by obtaining the exactly geometric asymptotics. For this, we use two formulations. One is a quasi-birth-and-death (QBD for short) process which is typically used, and the other is a reflecting random walk on the boundary of the k + 1-dimensional orthant which is a key for our proof.
The impact of dampening demand variability in a production/inventory system with multiple retailers (abstract only)
Authors: Van Houdt B. , Pérez J. F.
Published: April 2012

We study a supply chain consisting of a single manufacturer and two retailers. The manufacturer produces goods on a make-to-order basis, while both retailers maintain an inventory and use a periodic replenishment rule. As opposed to the traditional (r, S) policy, where a retailer at the end of each period orders the demand seen during the previous period, we assume that the retailers dampen their demand variability by smoothing the order size. More specifically, the order placed at the end of a period is equal to ß times the demand seen during the last period plus (1?ß) times the previous order size, with ß ? (0, 1] the smoothing parameter.

We develop a GI/M/1-type Markov chain with only two nonzero blocks A
0
and A
d
to analyze this supply chain. The dimension of these blocks prohibits us from computing its rate matrix R in order to obtain the steady state probabilities. Instead we rely on fast numerical methods that exploit the structure of the matrices A
0
and A
d
, i.e., the power method, the Gauss-Seidel iteration and GMRES, to approximate the steady state probabilities.

Finally, we provide various numerical examples that indicate that the smoothing parameters can be set in such a manner that all the involved parties benefit from smoothing. We consider both homogeneous and heterogeneous settings for the smoothing parameters.
Numerical study of Markovian arrival processes (MAP) with time-varying periodic arrival rates
Authors: Margolius Barbara
Published: April 2012

We consider the arrival rate of a Markovian Arrival Process with time-varying periodic transition rates. The arrival rate can vary widely for a MAP with fixed average transition rates by selecting appropriate transition rate functions over the period.
SMCSolver and Q-MAM
Authors: Bini D. , Meini B. , Steffé S. , Pérez J. F. , Van Houdt B.
Published: April 2012

Matrix-analytic methods have advanced considerably since the pioneering work of Marcel Neuts [6, 5] on Quasi-Birth-Death (QBD), GI/M/1- and M/G/1- type Markov chains (MCs). Especially the algorithms involved to (iteratively) solve these structured Markov chains have matured a lot, which has resulted in more efficient, but also more complex algorithms [4, 1]. While the first algorithms were straightforward to implement---as they were based on simple functional iterations---more advanced algorithms/features like cyclic-reduction, the Newton iteration or the shift technique (to accelerate convergence), require more effort; in particular for GI/M/1- and M/G/1-type Markov chains. This has motivated us to develop the Structured Markov Chain Solver (SMCSolver) tool [2], which implements a large number of basic and more advanced algorithms for solving QBD, GI/M/1- and M/G/1-type MCs1 (as well as the more general Non-Skip-Free M/G/1-type MCs). The MATLAB version of the tool consists of a collection of MATLAB functions, while the Fortran version is accompanied by a graphical user-interface (GUI).

Apart from making these more advanced algorithms accessible to non-specialists, the tool is also useful as a platform for the development and study of new algorithms and acceleration techniques. Since its initial release in 2006, various extensions have been made. In [3] different transformation techniques and shift strategies are incorporated in order to speed up and optimize the algorithms, while even more recently an efficient Newton iteration for GI/M/1- and M/G/1-type Markov chains was included [8].

Matrix-analytic methods have also been very effective in the analysis of many queueing systems in both discrete- and continuous-time. The Q-MAM tool [7] is a collection of MATLAB functions that allows one to compute the queue length, waiting time and delay distribution of various queueing systems of infinite size. It includes amongst others implementations of the PH/PH/1, MAP/MAP/1, MAP/M/c, MAP/D/c, RAP/RAP/1, MMAP[K]/PH[K]/1, MMAP[K]/SM[K]/1, SM[K]/PH[K]/1 (many in both discrete- and continuous-time), where state-of-the-art solution techniques are used to solve these models efficiently.

The Matlab version of the SMCSolver and Q-MAM tool is available at http://win.ua.ac.be/?vanhoudt/ while the Fortran 90 version of the SMCSolver tool with the GUI can be downloaded from http://bezout.dm.unipi.it/SMCSolver.
Selective resource characterization for evaluation of system dynamics
Authors: Casolari Sara , Colajanni Michele , Tosi Stefania
Published: April 2012

Management decisions to achieve peak performance operations, scalability and availability in distributed systems require a continuous statistical characterization of data sets coming from server and network monitors. Due to the increasing sizes of data centers and their continuous dynamic changes, the traditional approaches that work on all data sets in a centralized way are impractical. We propose a strategy for data processing that is able to limit the analysis of the large sets of collected measures to a smaller subset of significant information for a twofold purpose: to classify the collected data sets in few classes characterized by similar statistical behaviors, to evaluate the dynamics of the overall system and its most relevant changes. The proposed strategy works at the level of server resources and of significant aggregation of servers of the overall distributed system. Several experimental results demonstrate the feasibility of the proposed strategy that is validated in real contexts.
Dynamic aspects and behaviors of complex systems in performance and reliability assessment
Authors: Distefano Salvatore , Puliafito Antonio , Trivedi Kishor S.
Published: April 2012

Reliability and performance evaluation are important, often mandatory, steps in designing and analyzing (critical) systems. In such cases, accurate models are required to adequately take into account interference or dependent behaviors affecting the system, its parts and the external environment, especially if the system experiences high complexity. The techniques and tools to adopt in the evaluation have to adequately fit the problem considered. The main goal of this paper is to identify the dynamic-dependent aspects that can affect the reliability and performance of a system. Starting from the concept of dependence at the basis of system decomposition, an analytic framework and some of the most important dynamic-dependent aspects and behaviors are characterized in terms of both dynamic reliability and performance.
Compositional synthesis of temporal fault trees from state machines
Authors: Mahmud Nidhal , Walker Martin , Papadopoulos Yiannis
Published: April 2012

Dependability analysis of a dynamic system which is embedded with several complex interrelated components raises two main problems. First, it is difficult to represent in a single coherent and complete picture how the system and its constituent parts behave in conditions of failure. Second, the analysis can be unmanageable due to a considerable number of failure events, which increases with the number of components involved. To remedy this problem, in this paper we outline an analysis approach that converts failure behavioural models (state machines) to temporal fault trees (TFTs), which can then be analysed using Pandora -- a recent technique for introducing temporal logic to fault trees. The approach is compositional and potentially more scalable, as it relies on the synthesis of large system TFTs from smaller component TFTs. We show, by using a Generic Triple Redundant (GTR) system, how the approach enables a more accurate and full analysis of an increasingly complex system.
Heuristics for QoS maintenance
Authors: de Nitto Personà Vittoria
Published: April 2012

The fluctuation in resource availability demands for adaptive behavior in wireless environments. The problem is exacerbated by the differentiated services with different quality demands. We present the MATS+ scheme, an adaptive bandwidth allocation and admission control algorithm for mobile integrated services networks. This extends the recently proposed MATS scheme [11] to include non-real time classes and a per-class utilization control. We define an analytical model and performance metrics to evaluate the proposed scheme. The efficiency and flexibility of the analytical model allows conducting several experiments in a real word scenario by changing different system parameters. From the obtained results we define an interesting heuristics to initialize the scheme guaranteeing QoS requirements and to maintain the QoS while adapting to environment changing conditions.
Biologically relevant association rules for classification of microarray data
Authors: Antonie Luiza , Bessonov Kyrylo
Published: April 2012

In this paper we investigate a method for classifying microarray data using association rules. Associative classifiers, classification systems based on association rules, show good performance level while being easy to read and understand. This feature is especially attractive for biological data where experts can read and validate the association rules. Relevant features are selected using Support Vector Machines with Recursive Feature Elimination. These features are discretized according to their relative expression levels (upregulated, downregulated or no change) and then they are used to build an associative classifier. The proposed combination proves highly accurate for the studied microarray data collection. In addition, the classification rules discovered and employed in the classification process prove to be biologically relevant.
CTS 2011 Workshop Report: the Fourth International Workshop on Computational Transportation Science
Authors: Thakuriah Piyushimita , Geers D. Glenn , Liang Steve
Published: April 2012

The 2011 ACM SIGSPATIAL GIS Conference hosted the Fourth International Workshop on Computational Transportation Science which was held on 1 November 2011. We hope to hold a Fifth Workshop in 2012.
Highlights on ACM HPDGIS 2011: the Second International ACM SIGSPATIAL Workshop on High Performance and Distributed Geographic Information Systems (HPDGIS) 2011
Authors: Wang Shaowen , Padmanabhan Anand , Wilkins-Diehr Nancy , Shi Xuan , Vatsavai Ranga Raju
Published: April 2012

The ACM SIGSPATIAL HPDGIS 2011 workshop was held in Chicago, Illinois, USA on November 1, 2011 in conjunction with the 19th ACM SIGSPATIAL International Conference on Advances in Geographic Information System, and was a great success. High performance computing and distributed systems have become prominent elements in the landscape of communication, computing, and information technologies due to the increasingly computationally and data intensive nature of geospatial problems in numerous fields and significant requirements for service-oriented computing and collaborative problem solving. Efficient handling of massive spatial databases, shared and role-based access to distributed data, and high-end computing services are fundamental to the real-time and near-real-time responses required by many GIS and associated decision support applications. The second international ACM SIGSPATIAL HPDGIS workshop was hence designed to bring together researchers and practitioners to map out the fundamental research areas centered on advances in high performance computing, distributed systems, and their applications to Geographic Information Systems (GIS) and spatial analysis. The primary objective of the workshop series is to provide an overarching forum in which participants discuss the state-of- the-art, share research progress and activities, and establish future directions for research and education in HPDGIS.
ISA 2011 Workshop Report: a report on the Third International Workshop on Indoor Spatial Awareness
Authors: Kulik Lars , Güting Ralf Hartmut , Lu Hua
Published: April 2012

Large indoor spaces such as office complexes and shopping malls have become an important part of our daily lives and research into indoor space is increasingly attracting attention from academia and industry. Indoor space differs from outdoor space in several important aspects such as layout, topology, constraints, or access restrictions. Techniques that are successful for outdoor spaces, for example GPS positioning, do not work well in indoor environments and require new approaches. Similarly, giving directions in outdoor spaces usually requires only two dimensions, whereas indoor navigation often involves the third dimension as office buildings and shopping malls typically have several floors.
LBSN 2011 Workshop Report: the Third ACM SIGSPATIAL International Workshop on Location-Based Social Networks (LBSN 2011)
Authors: Zheng Yu , Mokbel Mohamed F.
Published: April 2012

Social networks have been prevalent on the Internet, attracting many professionals from a variety of fields. By adding a location dimension, we can bring online social networks back to the physical world and share our real-life experiences in the virtual world conveniently. In Location Based Social Networks (LBSN), people cannot only track and share location-related information with each other via either mobile devices or desktop computers, but also leverage collaborative social knowledge learned from user-generated and location-related contents. As location is one of the most important properties in people's daily lives, LBSN will bridge the gap between online societies and the physical world and enable a lot of novel applications changing the way we live, such as travel planning, location/friend recommendations, community discovery, human mobility modeling and user activity analysis. The technology derived from LBSN, e.g., location trajectory mining and retrieval, can also be applied to a multitude of other research areas including biology, sociology, geography, and climatology, etc. The objective of this workshop is to provide professionals, researchers, and technologists with a single forum where they can discuss and share the state-of-the-art of LBSN development and applications, present their ideas and contributions, and set future directions in emerging innovative research for location based social networks.
Highlights from QuEST 2011: 2nd SIGSPATIAL ACM GIS 2011 International Workshop on Querying and Mining Uncertain Spatio-Temporal Data
Authors: Kröger Peer , Renz Matthias
Published: April 2012

Querying and mining uncertain data has received a lot of attention from the research community in recent years due to the enormous increase of geographically referenced data occasioned by developments in IT, digital mapping and remote sensing. The global expansion of Geo Information Systems emphasizes the importance of developing data driven inductive approaches to geographical analysis and modeling. An important problem is that collected data often is inherently imprecise and may contain incomplete, inaccurate or outdated information. Such data arises particular in dynamic environments. Traditional querying and mining approaches are often inapplicable or may extract misleading or plain wrong information when applied to uncertain data.
Comprehensive kernel instrumentation via dynamic binary translation
Authors: Feiner Peter , Brown Angela Demke , Goel Ashvin
Published: April 2012

Dynamic binary translation (DBT) is a powerful technique that enables fine-grained monitoring and manipulation of an existing program binary. At the user level, it has been employed extensively to develop various analysis, bug-finding, and security tools. Such tools are currently not available for operating system (OS) binaries since no comprehensive DBT framework exists for the OS kernel. To address this problem, we have developed a DBT framework that runs as a Linux kernel module, based on the user-level DynamoRIO framework. Our approach is unique in that it controls all kernel execution, including interrupt and exception handlers and device drivers, enabling comprehensive instrumentation of the OS without imposing any overhead on user-level code. In this paper, we discuss the key challenges in designing and building an in-kernel DBT framework and how the design differs from user-space. We use our framework to build several sample instrumentations, including simple instruction counting as well as an implementation of shadow memory for the kernel. Using the shadow memory, we build a kernel stack overflow protection tool and a memory addressability checking tool. Qualitatively, the system is fast enough and stable enough to run the normal desktop workload of one of the authors for several weeks.
Bottleneck identification and scheduling in multithreaded applications
Authors: Joao José A. , Suleman M. Aater , Mutlu Onur , Patt Yale N.
Published: April 2012

Performance of multithreaded applications is limited by a variety of bottlenecks, e.g. critical sections, barriers and slow pipeline stages. These bottlenecks serialize execution, waste valuable execution cycles, and limit scalability of applications. This paper proposes Bottleneck Identification and Scheduling in Multithreaded Applications (BIS), a cooperative software-hardware mechanism to identify and accelerate the most critical bottlenecks. BIS identifies which bottlenecks are likely to reduce performance by measuring the number of cycles threads have to wait for each bottleneck, and accelerates those bottlenecks using one or more fast cores on an Asymmetric Chip Multi-Processor (ACMP). Unlike previous work that targets specific bottlenecks, BIS can identify and accelerate bottlenecks regardless of their type. We compare BIS to four previous approaches and show that it outperforms the best of them by 15% on average. BIS' performance improvement increases as the number of cores and the number of fast cores in the system increase.
Optimal task assignment in multithreaded processors
Authors: Radojković Petar , Čakarević Vladimir , Moretó Miquel , Verdú Javier , Pajuelo Alex , Cazorla Francisco J. , Nemirovsky Mario , Valero Mateo
Published: April 2012

The introduction of massively multithreaded (MMT) processors, comprised of a large number of cores with many shared resources, has made task scheduling, in particular task to hardware thread assignment, one of the most promising ways to improve system performance. However, finding an optimal task assignment for a workload running on MMT processors is an NP-complete problem. Due to the fact that the performance of the best possible task assignment is unknown, the room for improvement of current task-assignment algorithms cannot be determined. This is a major problem for the industry because it could lead to: (1)~A waste of resources if excessive effort is devoted to improving a task assignment algorithm that already provides a performance that is close to the optimal one, or (2)~significant performance loss if insufficient effort is devoted to improving poorly-performing task assignment algorithms.

In this paper, we present a method based on Extreme Value Theory that allows the prediction of the performance of the optimal task assignment in MMT processors. We further show that executing a sample of several hundred or several thousand
random
task assignments is enough to obtain, with very high confidence, an assignment with a performance that is close to the optimal one. We validate our method with an industrial case study for a set of multithreaded network applications running on an UltraSPARC~T2 processor.
CRUISE
Authors: Jaleel Aamer , Najaf-abadi Hashem H. , Subramaniam Samantika , Steely Simon C. , Emer Joel
Published: April 2012

When several applications are co-scheduled to run on a system with multiple shared LLCs, there is opportunity to improve system performance. This opportunity can be exploited by the hardware, software, or a combination of both hardware and software. The software, i.e., an operating system or hypervisor, can improve system performance by co-scheduling jobs on LLCs to minimize shared cache contention. The hardware can improve system throughput through better replacement policies by allocating more cache resources to applications that benefit from the cache and less to those applications that do not. This study presents a detailed analysis on the interactions between intelligent scheduling and smart cache replacement policies. We find that smart cache replacement reduces the burden on software to provide intelligent scheduling decisions. However, under smart cache replacement, there is still room to improve performance from better application co-scheduling. We find that co-scheduling decisions are a function of the underlying LLC replacement policy. We propose Cache Replacement and Utility-aware Scheduling (CRUISE)-a hardware/software co-designed approach for shared cache management. For 4-core and 8-core CMPs, we find that CRUISE approaches the performance of an ideal job co-scheduling policy under different LLC replacement policies.