bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative Biology of Two Natural Variants of the IncQ-2 Family Plasmids, pRAS3.1 and pRAS3.2
Authors: Loftie-Eaton Wesley , Rawlings Douglas E. 
Published: August 2009

ABSTRACTPlasmids pRAS3.1 and pRAS3.2 are two closely related, natural variants of the IncQ-2 plasmid family that have identical plasmid backbones except for two differences. Plasmid pRAS3.1 has five 6-bp repeat sequences in the promoter region of themobBgene and four 22-bp iterons in itsoriVregion, whereas pRAS3.2 has only four 6-bp repeats and three 22-bp iterons. Plasmid pRAS3.1 was found to have a higher copy number than pRAS3.2, and we show that the extra 6-bp repeat results in an increase inmobBand downstreammobA/repBexpression. Placement ofrepB(primase) behind an arabinose-inducible promoter intransresulted in an increase inrepBexpression and an approximately twofold increase in the copy number of plasmids with identical numbers of 22-bp iterons. The pRAS3 plasmids were shown to have a previously unrecognized toxin-antitoxin plasmid stability module within their replicons. The ability of the pRAS3 plasmids to mobilize theoriTregions of two other plasmids of the IncQ-2 family, pTF-FC2 and pTC-F14, suggested that the mobilization proteins pRAS3 are relaxed and can mobilizeoriTregions with substantially different sequences. Plasmids pRAS3.1 and pRAS3.2 were highly incompatible with plasmids pTF-FC2 and pTC-F14, and this incompatibility was removed on inactivation of an open reading frame situated downstream of themobCDEmobilization genes rather than being due to the 22-bporiV-associated iterons. We propose that the pRAS3 plasmids represent a third, γ incompatibility group within the IncQ-2 family plasmids.
Characterization of Hydrogen Peroxide-Induced DNA Release by
Streptococcus sanguinis
and
Streptococcus gordonii
Authors: Kreth Jens , Vu Hung , Zhang Yongshu , Herzberg Mark C. 
Published: August 2009

ABSTRACT

Extracellular DNA (eDNA) is produced by several bacterial species and appears to contribute to biofilm development and cell-cell adhesion. We present data showing that the oral commensals
Streptococcus sanguinis
and
Streptococcus gordonii
release DNA in a process induced by pyruvate oxidase-dependent production of hydrogen peroxide (H
2
O
2
). Surprisingly,
S. sanguinis
and
S. gordonii
cell integrity appears unaffected by conditions that cause autolysis in other eDNA-producing bacteria. Exogenous H
2
O
2
causes release of DNA from
S. sanguinis
and
S. gordonii
but does not result in obvious lysis of cells. Under DNA-releasing conditions, cell walls appear functionally intact and ribosomes are retained over time. During DNA release, intracellular RNA and ATP are not coreleased. Hence, the release mechanism appears to be highly specific for DNA. Release of DNA without detectable autolysis is suggested to be an adaptation to the competitive oral biofilm environment, where autolysis could create open spaces for competitors to invade. Since eDNA promotes cell-to-cell adhesion, release appears to support oral biofilm formation and facilitates exchange of genetic material among competent strains.
Rbf Promotes Biofilm Formation byStaphylococcus aureusvia Repression oficaR, a Negative Regulator oficaADBC
Authors: Cue David , Lei Mei G. , Luong Thanh T. , Kuechenmeister Lisa , Dunman Paul M. , O'Donnell Sinead , Rowe Sarah , O'Gara James P. , Lee Chia Y. 
Published: August 2009

ABSTRACTWe previously reported the identification of a gene,rbf, involved in the regulation of biofilm formation byStaphylococcus aureus8325-4. In an effort to study the mechanism of regulation, microarrays were used to compare the transcription profiles of the wild-type strain with anrbfmutant and anrbfoverexpression strain of the clinical isolate UAMS-1. Among the genes affected byrbfoverexpression are those of the intercellular adhesion (ica) locus; however, expression of these genes was not affected by anrbfdeletion in the chromosome. TheicaADBCgenes are responsible for production of poly-N-acetylglucosamine (PNAG), a major constituent of biofilm. TheicaRgene encodes a negative regulator oficaADBC. In UAMS-1 carrying an Rbf-encoding plasmid, Rbf was found to repressicaRtranscription with a concomitant increase inicaADBCexpression and increased PNAG and biofilm production relative to isogenic strains lacking the plasmid. Sequencing of therbfgene from UAMS-1 showed that there was a 2-bp insertion affecting the 50th codon of therbfopen reading frame, suggesting thatrbfis a pseudogene in UAMS-1. This finding explains why deletion ofrbfhad no effect on biofilm formation in UAMS-1. To further characterize the Rbf regulation on biofilm we compared biofilm formation,icaAandicaRtranscription, and PNAG production in 8325-4 and its isogenicrbfandicaRsingle mutants and anrbf icaRdouble mutant. Our results are consistent with a model whereinrbfrepresses synthesis oficaR, which in turn results in derepression oficaADBCand increased PNAG production. Furthermore, purifiedrbfdid not bind to theicaRoricaApromoter region, suggesting thatrbfcontrols expression of an unknown factor(s) that repressesicaR. The role ofrbfin controlling theS. aureusbiofilm phenotype was further demonstrated in a clinical strain, MW2.
SYNCHRONY-BREAKING PERIOD-DOUBLING BIFURCATIONS FOR THREE-CELL HOMOGENEOUS COUPLED MAPS
Authors: COMANICI ADELA 
Published: August 2009

Network architecture can lead to robust synchrony in coupled maps and to codimension one bifurcations from synchronous fixed-points at which the associated Jacobian is nilpotent. We discuss the codimension one synchrony-breaking period-doubling bifurcations for three-cell coupled maps. Interesting phenomena occur for all these coupled maps — a branch of period-2 points with amplitude growing as |λ|⅙ for coupled networks of feed-forward type, as well as multiple (two) branches of period-2 points with amplitude growing as |λ|½ for coupled networks of feed-forward type. We also discuss how some results related to patterns of synchrony that are valid for coupled vector fields are also valid for coupled maps.
ON TWO-DIMENSIONAL DYNAMICAL SYSTEMS ASSOCIATED WITH MEMBRANE KINETICS UNDERLYING CARDIAC ARRHYTHMIAS
Authors: BAKER B. M. , KIDWELL M. E. , KLINE R. P. , POPOVICI I. 
Published: August 2009

We study the orbits, stability and coexistence of orbits in the two-dimensional dynamical system introduced by Kline and Baker to model cardiac rhythmic response to periodic stimulation — as a function of (a) kinetic parameters (two amplitudes, two rate constants) and (b) stimulus period. The original paper focused mostly on the one-dimensional version of this model (one amplitude, one rate constant), whose orbits, stability properties, and bifurcations were analyzed via the theory of skew-tent (hence unimodal) maps; the principal family of orbits were so-called "n-escalators", with n a positive integer. The two-dimensional analog (motivated by experimental results) has led to the current study of continuous, piecewise smooth maps of a polygonal planar region into itself, whose dynamical behavior includes the coexistence of stable orbits. Our principal results show (1) how the amplitude parameters control which escalators can come into existence, (2) escalator bifurcation behavior as the stimulus period is lowered — leading to a "1/n bifurcation law", and (3) the existence of basins of attraction via the coexistence of three orbits (two of them stable, one unstable) at the first (largest stimulus period) bifurcation. We consider the latter result our most important, as it is conjectured to be connected with arrhythmia.
A NONLINEAR DYNAMICS PERSPECTIVE OF WOLFRAM'S NEW KIND OF SCIENCE. PART X: PERIOD-1 RULES
Authors: CHUA LEON O. , PAZIENZA GIOVANNI E. , SHIN JINWOOK 
Published: August 2009

This stage of our journey through the universe of one-dimensional binary Cellular Automata is devoted to period-1 rules, constituting the first of the six groups in which we systematized the 88 globally-independent CA rules.The first part of this article is mainly dedicated to reviewing the terminology and the empirical results found in the previous papers of our quest. We also introduce the concept of the ω-limit orbit with the purpose of linking our work to the classical theory of nonlinear dynamical systems. Moreover, we present the basin tree diagrams of all period-1 rules — except for rule [Formula: see text], which is trivial — along with their Boolean cubes and time-1 characteristic functions.In the second part, we prove a theorem demonstrating that all rules belonging to group 1 have robust period-1 rules for any finite, and infinite, bit-string length L. This is the first time we give analytical results on the behavior of CA local rules for large values of L and, consequently, for bi-infinite bit strings.The theoretical treatment is complemented by two remarkable practical results: an explicit formula for generating isomorphic basin trees, and an algorithm for creating new periodic orbits by concatenation. We also provide several examples of both of them, showing how they help to avoid tedious simulations.
Lazy evaluation and delimited control
Authors: Garcia Ronald , Lumsdaine Andrew , Sabry Amr 
Published: August 2009

The call-by-need lambda calculus provides an equational framework for reasoning syntactically about lazy evaluation. This paper examines its operational characteristics.
By a series of reasoning steps, we systematically unpack the standard-order reduction relation of the calculus and discover a novel abstract machine definition which, like the calculus, goes "under lambdas." We prove that machine evaluation is equivalent to standard-order evaluation.
Unlike traditional abstract machines, delimited control plays a significant role in the machine's behavior. In particular, the machine replaces the manipulation of a heap using store-based effects with disciplined management of the evaluation stack using control-based effects. In short, state is replaced with control.
To further articulate this observation, we present a simulation of call-by-need in a call-by-value language using delimited control operations.
The third homomorphism theorem on trees
Authors: Morihata Akimasa , Matsuzaki Kiminori , Hu Zhenjiang , Takeichi Masato 
Published: August 2009

Parallel programs on lists have been intensively studied. It is well known that associativity provides a good characterization for divide-and-conquer parallel programs. In particular, the third homomorphism theorem is not only useful for systematic development of parallel programs on lists, but it is also suitable for automatic parallelization. The theorem states that if two sequential programs iterate the same list leftward and rightward, respectively, and compute the same value, then there exists a divide-and-conquer parallel program that computes the same value as the sequential programs.
While there have been many studies on lists, few have been done for characterizing and developing of parallel programs on trees. Naive divide-and-conquer programs, which divide a tree at the root and compute independent subtrees in parallel, take time that is proportional to the height of the input tree and have poor scalability with respect to the number of processors when the input tree is ill-balanced.
In this paper, we develop a method for systematically constructing scalable divide-and-conquer parallel programs on trees, in which two sequential programs lead to a scalable divide-andconquer parallel program. We focus on paths instead of trees so as to utilize rich results on lists and demonstrate that associativity provides good characterization for scalable divide-and-conquer parallel programs on trees. Moreover, we generalize the third homomorphism theorem from lists to trees.We demonstrate the effectiveness of our method with various examples. Our results, being generalizations of known results for lists, are generic in the sense that they work well for all polynomial data structures.
Feedback-directed barrier optimization in a strongly isolated STM
Authors: Bronson Nathan G. , Kozyrakis Christos , Olukotun Kunle 
Published: August 2009

Speed improvements in today's processors have largely been delivered in the form of multiple cores, increasing the importance of abstractions that ease parallel programming. Software transactional memory (STM) addresses many of the complications of concurrency by providing a simple and composable model for safe access to shared data structures. Software transactions extend a language with an atomic primitive that declares that the effects of a block of code should not be interleaved with actions executing concurrently on other threads. Adding barriers to shared memory accesses provides atomicity, consistency and isolation.
Strongly isolated STMs preserve the safety properties of transactions for all memory operations in a program, not just those inside an atomic block. Isolation barriers are added to non-transactional loads and stores in such a system to prevent those accesses from observing or corrupting a partially completed transaction. Strong isolation is especially important when integrating transactions into an existing language and memory model. Isolation barriers have a prohibitive performance overhead, however, so most STM proposals have chosen not to provide strong isolation.
In this paper we reduce the costs of strong isolation by customizing isolation barriers for their observed usage. The customized barriers provide accelerated execution by blocking threads whose accesses do not follow the expected pattern. We use hot swap to tighten or loosen the hypothesized pattern, while preserving strong isolation. We introduce a family of optimization hypotheses that balance verification cost against generality.
We demonstrate the feasibility of dynamic barrier optimization by implementing it in a bytecode-rewriting Java STM. Feedback-directed customization reduces the overhead of strong isolation from 505% to 38% across 11 non-transactional benchmarks; persistent feedback data further reduces the overhead to 16%. Dynamic optimization accelerates a multi-threaded transactional benchmark by 31% for weakly-isolated execution and 34% for strongly-isolated execution.
Semi-sparse flow-sensitive pointer analysis
Authors: Hardekopf Ben , Lin Calvin 
Published: August 2009

Pointer analysis is a prerequisite for many program analyses, and the effectiveness of these analyses depends on the precision of the pointer information they receive. Two major axes of pointer analysis precision are flow-sensitivity and context-sensitivity, and while there has been significant recent progress regarding scalable context-sensitive pointer analysis, relatively little progress has been made in improving the scalability of flow-sensitive pointer analysis.
This paper presents a new interprocedural, flow-sensitive pointer analysis algorithm that combines two ideas-semi-sparse analysis and a novel use of BDDs-that arise from a careful understanding of the unique challenges that face flow-sensitive pointer analysis. We evaluate our algorithm on 12 C benchmarks ranging from 11K to 474K lines of code. Our fastest algorithm is on average 197x faster and uses 4.6x less memory than the state of the art, and it can analyze programs that are an order of magnitude larger than the previous state of the art.
The semantics of x86-CC multiprocessor machine code
Authors: Sarkar Susmit , Sewell Peter , Nardelli Francesco Zappa , Owens Scott , Ridge Tom , Braibant Thomas , Myreen Magnus O. , Alglave Jade 
Published: August 2009

Multiprocessors are now dominant, but real multiprocessors do not provide the sequentially consistent memory that is assumed by most work on semantics and verification. Instead, they have subtle relaxed (or weak) memory models, usually described only in ambiguous prose, leading to widespread confusion.
We develop a rigorous and accurate semantics for x86 multiprocessor programs, from instruction decoding to relaxed memory model, mechanised in HOL. We test the semantics against actual processors and the vendor litmus-test examples, and give an equivalent abstract-machine characterisation of our axiomatic memory model. For programs that are (in some precise sense) data-race free, we prove in HOL that their behaviour is sequentially consistent. We also contrast the x86 model with some aspects of Power and ARM behaviour.
This provides a solid intuition for low-level programming, and a sound foundation for future work on verification, static analysis, and compilation of low-level concurrent code.
Parallel thinking
Authors: Blelloch Guy E. 
Published: August 2009

Assuming that the multicore revolution plays out the way the microprocessor industry expects, it seems that within a decade most programming will involve parallelism at some level. One needs to ask how this affects the the way we teach computer science, or even how we have people think about computation. With regards to teaching there seem to be three basic choices: (1) we only train a small number of experts in parallel computation who develop a collection of libraries, and everyone else just uses them; (2) we leave our core curriculum pretty much as is, but add some advanced courses on parallelism or perhaps tack on a few lectures at the end of existing courses; or (3) we start teaching parallelism from the start and embed it throughout the curriculum with the idea of getting students to think about parallelism as the most natural form of computation and sequential computation as a special case.
This talk will examine some of the implications of the third option. It will argue that thinking about parallelism, when treated in an appropriate way, might be as easy or easier that thinking sequentially. A key prerequisite, however, is to identify what the core ideas in parallelism are and how they might be layered and integrated with existing concepts. Another more difficult issue is how to cleanly integrate these ideas among courses. After all much of the success of sequential computation follows from the concept of a random access machine and its ability to serve as a simple, albeit imperfect, interface between programming languages, algorithm analysis, and hardware design. The talk will go through an initial list of some core ideas in parallelism, and an approach to integrating these ideas between parallel algorithms, programming languages, and, to some extent, hardware. This requires, however, moving away from the concept of a machine model as a interface for thinking about computation.
Opportunities beyond single-core microprocessors
Authors: Hill Mark D. 
Published: August 2009

Designers of future hardware and software face many challenges. Performance scaling of sequential cores is not what it once was. The best architectures for many cores, or equivalents, are not clear. Software, especially on clients, does not make abundant parallelism clear. Computer use and disposal is not so green. Smarter phones must not burn your pocket. Transistors and wires are getting less reliable. CMOS may run out of steam for technical or economic reasons. And the list goes on.
But in challenges, optimists find opportunities. This panel will be about opportunities. I have invited experts with experience in academia, industry, and government to discuss the great possibilities ahead. I have asked them to identify two or three topics, where, at most, one is part of their current work. Then we will have a discussion.
Efficient, portable implementation of asynchronous multi-place programs
Authors: Bikshandi Ganesh , Castanos Jose G. , Kodali Sreedhar B. , Nandivada V. Krishna , Peshansky Igor , Saraswat Vijay A. , Sur Sayantan , Varma Pradeep , Wen Tong 
Published: August 2009

The X10 programming language is organized around the notion of places (an encapsulation of data and activities operating on the data), partitioned global address space (PGAS), and asynchronous computation and communication.
This paper introduces an expressive subset of X10, Flat X10, designed to permit efficient execution across multiple single-threaded places with a simple runtime and without compromising on the productivity of X10. We present the design, implementation and evaluation of a compiler and runtime system for Flat X10. The Flat X10 compiler translates programs into C++ SPMD programs communicating using an active messaging infrastructure. It uses novel techniques to transform explicitly parallel programs into SPMD programs. The runtime system is based on IBM's LAPI (Low-level API) and is easily portable to other libraries such as GASNet and ARMCI.
Our implementation realizes performance comparable to hand-written MPI programs for well-known HPC benchmarks such as Random Access, Stream, and FFT, on a Federation-based cluster of Power5 SMPs (with hundreds of processors) and the Blue Gene (with thousands of processors). Submissions based on the work presented in this paper were co-winners of the 2007 and 2008 HPC Challenge Type II Awards.
A compiler and runtime system for enabling data mining applications on gpus
Authors: Ma Wenjing , Agrawal Gagan 
Published: August 2009

With increasing need for accelerating data mining and scientific data analysis on large data sets, and less chance to improve processor performance by simply increasing clock frequencies, multi-core architectures and accelerators like FPGAs and GPUs have become popular. A recent development in using GPU for general computing has been the release of CUDA (Compute Unified Device Architecture) by NVIDIA. CUDA allows GPU programming with Clanguage-like features, thus easing the development of non-graphics applications on a GPU. However, several challenges still remain in programming the GPUs with CUDA, because CUDA involves explicit parallel programming and management of its complex memory hierarchy, as well as allocating device memory, moving data between CPU anddevice memory, and specification of thread grid configurations.
In this paper, we offer a solution for the programmers to generate CUDA code by specifying the sequential reduction loop(s) with some information about the parameters. With program analysis and code generation, the applications are mapped to a GPU. Several additional optimizations are also performed by the middleware.
We have evaluated our system using three popular data miningapplications, k-means clustering, EM clustering, and Principal Component Analysis (PCA). The speedup that each of these applications achieve over a sequential CPU version ranges between 20 and 50.
Wave Driving in the Tropical Lower Stratosphere as Simulated by WACCM. Part II: ENSO-Induced Changes for Northern Winter
Authors: Taguchi Masakazu 
Published: August 2009

Abstract
This study investigates ENSO-induced changes in the tropical lower stratosphere for northern winter as simulated by the Whole Atmosphere Community Climate Model (WACCM). A comparison is made between two 3650-day perpetual January experiments forced with La Niña– and El Niño–like sea surface temperature conditions over the equatorial Pacific. The present analysis includes an extension of the diagnostic framework used for the climatological annual cycle in Part I. A comprehensive description of the ENSO-induced changes, together with their heat and zonal momentum budget diagnoses, demonstrates that the changes are consistently characterized by cooling, locally accelerated Brewer–Dobson circulation (upwelling and poleward flow) and strengthened tropical/subtropical wave driving for the El Niño–like condition. The cooling broadly peaks near the equator with general hemispheric symmetry, and the strengthenings in the poleward flow and wave driving take place in both hemispheres. An important role in the strengthened wave driving is played by changes in tropical/subtropical stationary waves. The changes notably include a dumbbell-shaped height pattern over the Pacific or a modulation of equatorial Rossby waves in response to redistributed convective heating with the ENSO-like perturbation.