bluuebunny/crossref_metadata_2025 huggingface dataset:
Antibodies to Capsular Polysaccharide and Clumping Factor A Prevent Mastitis and the Emergence of Unencapsulated and Small-Colony Variants ofStaphylococcus aureusin Mice
Authors: Tuchscherr Lorena P. N. , Buzzola Fernanda R. , Alvarez Lucía P. , Lee Jean C. , Sordelli Daniel O.
Published: September 2008

The pathogenesis ofStaphylococcus aureusinfections is influenced by multiple virulence factors that are expressed under variable conditions, and this has complicated the design of an effective vaccine. Clinical trials that targeted the capsule or clumping factor A (ClfA) failed to protect the recipients against staphylococcal infections. We passively immunized lactating mice with rabbit antibodies toS. aureuscapsular polysaccharide (CP) serotype 5 (CP5) or CP8 or with monoclonal antibodies to ClfA. Mice immunized with antibodies to CP5 or CP8 or with ClfA had significantly reduced tissue bacterial burdens 4 days after intramammary challenge with encapsulatedS. aureusstrains. After several passages in mice passively immunized with CP-specific antiserum, increasing numbers of stable unencapsulated variants ofS. aureuswere cultured from the infected mammary glands. Greater numbers of these unencapsulatedS. aureusvariants than of the corresponding encapsulated parental strains were internalized in vitro in MAC-T bovine cells. Furthermore, small-colony variants (SCVs) were recovered from the infected mammary glands after several passages in mice passively immunized with CP-specific antiserum. A combination of antibodies effectively sterilized mammary glands in a significant number of passively immunized mice. More importantly, passive immunization with antibodies to both CP and ClfA fully inhibited the emergence of unencapsulated “escape mutants” and significantly reduced the appearance of SCVs. A vaccine formulation comprising CP conjugates plus a surface-associated protein adhesin may be more effective than either antigen alone for prevention ofS. aureusinfections.
Immunogenicity of Recombinant Attenuated
Salmonella enterica
Serovar Typhimurium Vaccine Strains Carrying a Gene That Encodes
Eimeria tenella
Antigen SO7
Authors: Konjufca Vjollca , Jenkins Mark , Wang Shifeng , Juarez-Rodriguez Maria Dolores , Curtiss Roy
Published: September 2008

Recombinant attenuated
Salmonella
vaccines against avian coccidiosis were developed to deliver
Eimeria
species antigens to the lymphoid tissues of chickens via the type 3 secretion system (T3SS) and the type 2 secretion system (T2SS) of
Salmonella
. For antigen delivery via the T3SS, the
Eimeria tenella
gene encoding sporozoite antigen SO7 was cloned downstream of the translocation domain of the
Salmonella enterica
serovar Typhimurium
sopE
gene in the parental pYA3868 and pYA3870 vectors to generate pYA4156 and pYA4157. Newly constructed T3SS vectors were introduced into host strain χ8879 (Δ
phoP233
Δ
sptP1033
::
xylE
Δ
asdA16
), an attenuated derivative of the highly virulent UK-1 strain. The SopE-SO7 fusion protein was secreted by the T3SS of
Salmonella
. The vector pYA4184 was constructed for delivery of the SO7 antigen via the T2SS. The SO7 protein was toxic to
Salmonella
when larger amounts were synthesized; thus, the synthesis of this protein was placed under the control of the
lacI
repressor gene, whose expression in turn was dependent on the amount of available arabinose in the medium. The pYA4184 vector was introduced into host strain χ9242 (Δ
phoP233
Δ
asdA16
Δ
araBAD23
Δ
relA198
::
araC
P
BAD
lacI
TT [TT is the T4
ipIII
transcription terminator]). In addition to SO7, for immunization and challenge studies we used the EAMZ250 antigen of
Eimeria acervulina
, which was previously shown to confer partial protection against
E. acervulina
challenge when it was delivered via the T3SS. Immunization of chickens with a combination of the SO7 and EAMZ250 antigens delivered via the T3SS induced superior protection against challenge by
E. acervulina
. In contrast, chickens immunized with SO7 that was delivered via the T2SS of
Salmonella
were better protected from challenge by
E. tenella
.
An In Vivo and In Vitro Model of
Plasmodium falciparum
Rosetting and Autoagglutination Mediated by
varO
, a Group A
var
Gene Encoding a Frequent Serotype
Authors: Vigan-Womas Inès , Guillotte Micheline , Le Scanf Cécile , Igonet Sébastien , Petres Stéphane , Juillerat Alexandre , Badaut Cyril , Nato Farida , Schneider Achim , Lavergne Anne , Contamin Hugues , Tall Adama , Baril Laurence , Bentley Graham A. , Mercereau-Puijalon Odile
Published: September 2008

In the
Saimiri sciureus
monkey, erythrocytes infected with the varO antigenic variant of the
Plasmodium falciparum
Palo Alto 89F5 clone bind uninfected red blood cells (rosetting), form autoagglutinates, and have a high multiplication rate, three phenotypic characteristics that are associated with severe malaria in human patients. We report here that varO parasites express a
var
gene having the characteristics of group A
var
genes, and we show that the varO Duffy binding-like 1α
1
(DBL1α
1
) domain is implicated in the rosetting of both
S. sciureus
and human erythrocytes. The soluble varO N-terminal sequence (NTS)-DBL1α
1
recombinant domain, produced in a baculovirus-insect cell system, induced high titers of antibodies that reacted with varO-infected red blood cells and disrupted varO rosettes. varO parasites were culture adapted in vitro using human erythrocytes. They formed rosettes and autoagglutinates, and they had the same surface serotype and expressed the same
varO
gene as the monkey-propagated parasites. To develop an in vitro model with highly homogeneous varO parasites, rosette purification was combined with positive selection by panning with a varO NTS-DBL1α
1
-specific mouse monoclonal antibody. The single-variant, clonal parasites were used to analyze seroprevalence for varO at the village level in a setting where malaria is holoendemic (Dielmo, Senegal). We found 93.6% (95% confidence interval, 89.7 to 96.4%) seroprevalence for varO surface-reacting antibodies and 86.7% (95% confidence interval, 82.8 to 91.6%) seroprevalence for the recombinant NTS-DBL1α
1
domain, and virtually all permanent residents had seroconverted by the age of 5 years. These data imply that the varO model is a relevant in vivo and in vitro model for rosetting and autoagglutination that can be used for rational development of vaccine candidates and therapeutic strategies aimed at preventing malaria pathology.
Targeted Mutagenesis in PathogenicLeptospiraSpecies: Disruption of the LigB Gene Does Not Affect Virulence in Animal Models of Leptospirosis
Authors: Croda Julio , Figueira Claudio Pereira , Wunder Elsio A. , Santos Cleiton S. , Reis Mitermayer G. , Ko Albert I. , Picardeau Mathieu
Published: September 2008

The pathogenic mechanisms ofLeptospira interrogans, the causal agent of leptospirosis, remain largely unknown. This is mainly due to the lack of tools for genetically manipulating pathogenicLeptospiraspecies. Thus, homologous recombination between introduced DNA and the corresponding chromosomal locus has never been demonstrated for this pathogen. Leptospiral immunoglobulin-like repeat (Lig) proteins were previously identified as putativeLeptospiravirulence factors. In this study, aligBmutant was constructed by allelic exchange inL. interrogans; in this mutant a spectinomycin resistance (Spcr) gene replaced a portion of theligBcoding sequence. Gene disruption was confirmed by PCR, immunoblot analysis, and immunofluorescence studies. TheligBmutant did not show decrease virulence compared to the wild-type strain in the hamster model of leptospirosis. In addition, inoculation of rats with theligBmutant induced persistent colonization of the kidneys. Finally, LigB was not required to mediate bacterial adherence to cultured cells. Taken together, our data provide the first evidence of site-directed homologous recombination in pathogenicLeptospiraspecies. Furthermore, our data suggest that LigB does not play a major role in dissemination of the pathogen in the host and in the development of acute disease manifestations or persistent renal colonization.
The
Toxoplasma gondii
Dense Granule Protein GRA7 Is Phosphorylated upon Invasion and Forms an Unexpected Association with the Rhoptry Proteins ROP2 and ROP4
Authors: Dunn Joe Dan , Ravindran Sandeep , Kim Seon-Kyeong , Boothroyd John C.
Published: September 2008

The obligate intracellular parasite
Toxoplasma gondii
infects warm-blooded animals throughout the world and is an opportunistic pathogen of humans. As it invades a host cell,
Toxoplasma
forms a novel organelle, the parasitophorous vacuole, in which it resides during its intracellular development. The parasite modifies the parasitophorous vacuole and its host cell with numerous proteins delivered from rhoptries and dense granules, which are secretory organelles unique to the phylum
Apicomplexa
. For the majority of these proteins, little is known other than their localization. Here we show that the dense granule protein GRA7 is phosphorylated but only in the presence of host cells. Within 10 min of invasion, GRA7 is present in strand-like structures in the host cytosol that contain rhoptry proteins. GRA7 strands also contain GRA1 and GRA3. Independently of its phosphorylation state, GRA7 associates with the rhoptry proteins ROP2 and ROP4 in infected host cells. This is the first report of interactions between proteins secreted from rhoptries and dense granules.
Higher fasting plasma glucose levels within the normoglycaemic range and rotator cuff tears
Authors: Longo U G , Franceschi F , Ruzzini L , Spiezia F , Maffulli N , Denaro V
Published: September 2008

Objective:

To determine the plasma glucose levels in non-diabetic patients with rotator cuff tear.

Design:

Frequency-matched case–control study.

Setting:

University Teaching Hospital.

Participants:

The study included 194 subjects who were operated on at our institution. Group 1 included 97 consecutive patients (36 men and 61 women; mean age: 62.9 years, range 37 to 82) who underwent arthroscopic repair of a rotator cuff tear in 2007 and 2008. Group 2 (control group) included 97 patients (36 men and 61 women; mean age: 61.6 years, range 36 to 80) who underwent arthroscopic meniscectomy for a meniscal tear in the same period, and had no evidence of shoulder pathology. These patients were frequency-matched by age (within 3 years) and gender with patients of Group 1.

Main outcome measure:

Measurement of fasting plasma glucose levels.

Results:

Patients with rotator cuff tears (Group 1) showed statistically significantly higher fasting plasma glucose levels within the normoglycaemic range (p = 0.007) than patients with meniscal tear (Group 2).

Conclusions:

The present study suggests that normal, but in the high range of normal, increasing plasma glucose levels may be a risk factor for rotator cuff tear. An enhanced understanding of these factors holds the promise of new approaches to the prevention and management of rotator cuff tears.
A THEORETICAL APPROACH FOR PARETO–ZIPF LAW
Authors: TUNCAY ÇAĞLAR
Published: September 2008

We suggest an analytical approach for the Pareto–Zipf law, where we assume random multiplicative noise and fragmentation processes for the growth of the number of citizens of each city and the number of the cities, respectively.
A COMPARISON OF SPLINES INTERPOLATIONS WITH STANDARD FINITE DIFFERENCE METHODS FOR ONE-DIMENSIONAL ADVECTION-DIFFUSION EQUATION
Authors: THONGMOON MONTRI , TANGMANEE SUWON , MCKIBBIN ROBERT
Published: September 2008

Four types of numerical methods namely: Natural Cubic Spline, Special A-D Cubic Spline, FTCS and Crank–Nicolson are applied to both advection and diffusion terms of the one-dimensional advection-diffusion equations with constant coefficients. The numerical results from two examples are tested with the known analytical solution. The errors are compared when using different Peclet numbers.
FRACTIONAL BROWNIAN MOTION WITH STOCHASTIC VARIANCE: MODELING ABSOLUTE RETURNS IN STOCK MARKETS
Authors: ROMAN H. E. , PORTO M.
Published: September 2008

We discuss a model for simulating a long-time memory in time series characterized in addition by a stochastic variance. The model is based on a combination of fractional Brownian motion (FBM) concepts, for dealing with the long-time memory, with an autoregressive scheme with conditional heteroskedasticity (ARCH), responsible for the stochastic variance of the series, and is denoted as FBMARCH. Unlike well-known fractionally integrated autoregressive models, FBMARCH admits finite second moments. The resulting probability distribution functions have power-law tails with exponents similar to ARCH models. This idea is applied to the description of long-time autocorrelations of absolute returns ubiquitously observed in stock markets.
STRUCTURES AND ENERGETIC OF PALLADIUM-COBALT BINARY CLUSTERS
Authors: ARSLAN HAYDAR
Published: September 2008

The structure and energetic of Palladium-Cobalt clusters (N = 11–20) have been studied extensively by a Monte Carlo method based on Sutton–Chen many-body potential. The basin-hopping algorithm was used to determine the global minima of bimetallic clusters. The structural changes with cluster size were observed. Most of the structures had built on icosahedral packing. Second energy difference analyzes were performed to investigate the relative stability of a cluster with respect to its size and composition is discussed.
STABILIZATION ANALYSIS AND MODIFIED KdV EQUATION OF LATTICE MODELS WITH CONSIDERATION OF RELATIVE CURRENT
Authors: LI ZHIPENG , LI XINGLI , LIU FUQIANG
Published: September 2008

In this paper, the lattice model which depends not only on the difference of the optimal current and the local current but also on the relative current is presented and analyzed in detail. We derive the stability condition of the extended model by considering a small perturbation around the homogeneous flow solution with finding that the improvement in the stability of the traffic flow is obtained by taking into account the relative current, which is also confirmed by direct simulations. Moreover, from the nonlinear analysis to the extended models, the relative current dependence of the propagating kink solutions for traffic jam is obtained by deriving the modified KdV equation near the critical point by using the reductive perturbation method.
ASSESSMENT OF MAGNETOHYDRODYNAMIC LATTICE BOLTZMANN SCHEMES IN TURBULENCE AND RECTANGULAR JETS
Authors: RILEY BENJAMIN M. , RICHARD JACQUES C. , GIRIMAJI SHARATH S.
Published: September 2008

Two lattice Boltzmann method (LBM) formulations are possible to account for the effect of the magnetic field on the velocity field in magnetohydrodynamic (MHD) flows. In the body-force formulation (BFF), the magnetic field effects manifest as an external acceleration. In the extended equilibrium formulation (EEF), the effect appears through a modified equilibrium distribution function. Further, for the velocity field itself, the available choices are the single-relaxation time (SRT) and multi-relaxation time (MRT) models. Thus, for MHD-LBM, there are four possible permutations: SRT-BFF, SRT-EEF, MRT-BFF and MRT-EEF. Numerical implementation of the first three have already been presented in the literature. In this work, we, (i) develop the numerical implementation of MRT-EEF and (ii) perform an assessment of the four possible approaches. Our results indicate that the MRT-EEF is the most robust and accurate of the MHD-LBM computational schemes examined.
DYNAMICS BEHAVIORS OF SCALE-FREE NETWORKS WITH ELASTIC DEMAND
Authors: LI YAN-LAI , SUN HUI-JUN , WU JIAN-JUN
Published: September 2008

Many real-world networks, such as transportation networks and Internet, have the scale-free properties. It is important to study the bearing capacity of such networks. Considering the elastic demand condition, we analyze load distributions and bearing capacities with different parameters through artificially created scale-free networks. The simulation results show that the load distribution follows a power-law form, which means some ordered pairs, playing the dominant role in the transportation network, have higher demand than other pairs. We found that, with the decrease of perceptual error, the total and average ordered pair demand will decrease and then stay in a steady state. However, with the increase of the network size, the average demand of each ordered pair will decrease, which is particularly interesting for the network design problem.
QUANTUM CORNER — TRANSFER MATRIX DMRG
Authors: BARTEL ERIK , SCHADSCHNEIDER ANDREAS
Published: September 2008

We propose a new method for the calculation of thermodynamic properties of one-dimensional quantum systems by combining the TMRG approach with the corner transfer-matrix method. The corner transfer-matrix DMRG method brings reasonable advantage over TMRG for classical systems. We have modified the concept for the calculation of thermal properties of one-dimensional quantum systems. The novel QCTMRG algorithm is implemented and used to study two simple test cases, the classical Ising chain and the isotropic Heisenberg model. In a discussion, the advantages and challenges are illuminated.
DECAY CONSTANTS OF S AND P WAVE MESONS
Authors: WANG GUO-LI
Published: September 2008

The decay constants of S wave and P wave heavy mesons are computed by means of the relativistic (instantaneous) Salpeter equation.
PROBING NEW PHYSICS FROM TOP QUARK FCNC PROCESS AT LHC: A MINI REVIEW
Authors: YANG JIN MIN
Published: September 2008

Since the top quark FCNC processes are extremely supressed in the Standard Model (SM) but could be greatly enhanced in some new physics models, they could serve as a smoking gun for new physics hunting at the LHC. In this brief review we summarize the new physics predictions for various top quark FCNC processes at the LHC by focusing on two typical models: the minimal supersymmetric model (MSSM) and the topcolor-assisted technicolor (TC2) model. The conclusion is: (1) Both new physics models can greatly enhance the SM predictions by several orders; (2) The TC2 model allows for largest enhancement, and for each channel the maximal prediction is much larger than in the MSSM; (3) Compared with the 3σ sensitivity at the LHC, only a couple of channels are accessible for the MSSM while most channles are accesible for the TC2 model.
HORIZONTAL SYMMETRY
Authors: LAM C. S.
Published: September 2008

The relation between fermion mixing and horizontal symmetry is discussed.
THE MINIMAL TYPE-I SEESAW MODEL AND FLAVOR-DEPENDENT LEPTOGENESIS
Authors: XING ZHI-ZHONG , ZHOU SHUN
Published: September 2008

In this talk, we first give a brief review of the so-called minimal seesaw models and then concentrate on the minimal type-I seesaw model with two almost degenerate right-handed Majorana neutrinos of [Formula: see text]. A specific texture of the neutrino Yukawa coupling matrix is proposed to achieve the nearly tri-bimaximal neutrino mixing pattern. This ansatz predicts (1) θ23 = π/4, |δ| = π/2 and sin 2θ12 = (1 − 2tan2θ13)/3 in the m1 = 0 case; and (2) θ23 = π/4 and θ13 = 8 = 0 in the m3 = 0 case. In both cases, the cosmological baryon number asymmetry can be explained via the resonant leptogenesis mechanism. Finally, we demonstrate the significance of flavor-dependent effects in our leptogenesis scenario.
SUMMARY
Authors: NG J. N.
Published: September 2008

Some of the highlights of the conference are described with emphasis to the connection to LHC. The standard Cabibbo-Kobayashi-Maskawa paradigm for flavor physics in the quark sector is now well established. On the other hand the origin of neutrino masses is still under active investigations. A look into the near future is also given.
Thailand Capital Flight through Trade with the US During Times of Political and Economic Instability
Authors: Chunhachinda Pornchai , de Boyrie Maria E. , Pak Simon J.
Published: September 2008

This paper investigates capital flight from Thailand to the US through trade misinvoicing during the period from 1990 to 2005. The evidence indicates that capital flight from Thailand to the US, valued over US$16,189 million, had been done through under-invoicing exports to the US rather than over-invoicing imports from the US. The major incentive for the movement of capital is investment, followed by political events in Thailand, and the most significant determinants of capital flight are the US T-bill rate, the deposit rate in Thailand, and the degree of overvaluation of the Thai Baht. Interestingly, the 1997 Asian economic crisis did not play a significant role in the capital movement through trade.
Investment and Capital Market Imperfections: Some Evidence from a Developing Economy, India
Authors: Bhaduri Saumitra N.
Published: September 2008

This paper presents a switching regression model of investment decision where the probability of a firm facing financial constraint is endogenously determined. The approach, therefore, obviates the use of a priori criteria to exogenously identify the financially constrained firms, and thereby addresses the potential misclassification problem faced in the existing literature. A sample of 576 Indian manufacturing firms, collected across 15 broad industries is used for this study. The study establishes that financially constrained firms exhibit a much higher investment-cash flow sensitivity than those identified to be unconstrained. It also probes into the possible determinants of financial constraints, and finds empirical support for its hypothesis that young, liquidity constrained and low dividend payout firms are more likely to face financial constraints, when compared to their respective counterparts. This paper also provides some insight into the impact of the ongoing liberalization program on the financial constraints faced by the Indian firms.
Low-latency adaptive streaming over tcp
Authors: Goel Ashvin , Krasic Charles , Walpole Jonathan
Published: September 2008

Media streaming over TCP has become increasingly popular because TCP's congestion control provides remarkable stability to the Internet. Streaming over TCP requires adapting to bandwidth availability, but unforunately, TCP can introduce significant latency at the application level, which causes unresponsive and poor adaptation. This article shows that this latency is not inherent in TCP but occurs as a result of throughput-optimized TCP implementations. We show that this latency can be minimized by dynamically tuning TCP's send buffer. Our evaluation shows that this approach leads to better application-level adaptation and it allows supporting interactive and other low-latency applications over TCP.
Data placement and prefetching with accurate bit rate control for interactive media server
Authors: Lim Seung-Ho , Jeong Yo-Won , Park Kyu Ho
Published: September 2008

An interactive Media Server should support unrestricted control to viewers with their service level agreements. It is important to manage video data effectively to facilitate efficient retrieval. In this paper, we propose an efficient placement algorithm as part of an effective retrieval scheme to increase the number of clients who can be provided with interactive service. The proposed management schemes are incorporated with a bit count control method that is based on repeated tuning of quantization parameters to adjust the actual bit count to the target bit count. The encoder using this method can generate coded frames whose sizes are synchronized with the RAID stripe size, so that when various fast-forward levels are accessed we can reduce the seek and rotational latency and enhance the disk throughput of each disk in the RAID system. Experimental results demonstrate that the proposed schemes can significantly improve the average service time and guarantee more users service of quality, and the interactive media server can thereby efficiently service a large number of clients.
Rethink the sync
Authors: Nightingale Edmund B. , Veeraraghavan Kaushik , Chen Peter M. , Flinn Jason
Published: September 2008

We introduce
external synchrony
, a new model for local file I/O that provides the reliability and simplicity of synchronous I/O, yet also closely approximates the performance of asynchronous I/O. An external observer cannot distinguish the output of a computer with an externally synchronous file system from the output of a computer with a synchronous file system. No application modification is required to use an externally synchronous file system. In fact, application developers can program to the simpler synchronous I/O abstraction and still receive excellent performance. We have implemented an externally synchronous file system for Linux, called xsyncfs. Xsyncfs provides the same durability and ordering-guarantees as those provided by a
synchronously
mounted ext3 file system. Yet even for I/O-intensive benchmarks, xsyncfs performance is within 7% of ext3 mounted
asynchronously
. Compared to ext3 mounted synchronously, xsyncfs is up to two orders of magnitude faster.
A stateless approach to connection-oriented protocols
Authors: Shieh Alan , Myers Andrew C. , Sirer Emin Gün
Published: September 2008

Traditional operating system interfaces and network protocol implementations force some system state to be kept on both sides of a connection. This state ties the connection to its endpoints, impedes transparent failover, permits denial-of-service attacks, and limits scalability. This article introduces a novel TCP-like transport protocol and a new interface to replace sockets that together enable all state to be kept on one endpoint, allowing the other endpoint, typically the server, to operate without any per-connection state. Called
Trickles
, this approach enables servers to scale well with increasing numbers of clients, consume fewer resources, and better resist denial-of-service attacks. Measurements on a full implementation in Linux indicate that Trickles achieves performance comparable to TCP/IP, interacts well with other flows, and scales well. Trickles also enables qualitatively different kinds of networked services. Services can be geographically replicated and contacted through an anycast primitive for improved availability and performance. Widely-deployed practices that currently have client-observable side effects, such as periodic server reboots, connection redirection, and failover, can be made transparent, and perform well, under Trickles. The protocol is secure against tampering and replay attacks, and the client interface is backward-compatible, requiring no changes to sockets-based client applications.
The softer side of
Communications
Authors: Delman Scott E.
Published: September 2008

Much has already been written about the expanded editorial scope of the new
Communications.
For most of these changes we have Editor-in-Chief Moshe Y. Vardi and his distinguished Editorial Board to thank.
Clean elections
Authors: Farivar Cyrus
Published: September 2008

With end-to-end auditable voting, a voter can verify whether his or her vote was tallied correctly and whether all of the votes were properly tabulated.
Historical reflectionsWill the future of software be open source?
Authors: Campbell-Kelly Martin
Published: September 2008

Tracing the course of influential computing developments and considering possible paths to new paradigms.
Computing ethicsComputer experts
Authors: Johnson Deborah G.
Published: September 2008

Considering the responsibilities of those who build systems fundamental to significant social functions, institutions, and values.
From the front linesDOA with SOA
Authors: Bell Alex E.
Published: September 2008

Diagnosing the symptoms of failing to accommodate critical software architecture properties that often result in the demise of projects.
Point/counterpointThe U.S. should ban paperless electronic voting machines
Authors: Dill David L. , Castro Daniel
Published: September 2008

Debating the public policy issues involved in proposed efforts toward improving voting systems while considering the range of technical and societal challenges.
Document design matters
Authors: Wilde Erik , Glushko Robert J.
Published: September 2008

How do we apply the concept of resource orientation by designing representations to support interactions?
A closer look at GPUs
Authors: Fatahalian Kayvon , Houston Mike
Published: September 2008

As the line between GPUs and CPUs begins to blur, it's important to understand what makes GPUs tick.
Crossroads for Canadian CS enrollment
Authors: Slonim Jacob , Scully Sam , McAllister Michael
Published: September 2008

What should be done to reverse falling CS enrollment in the Canadian education system?
The many facets of natural computing
Authors: Kari Lila , Rozenberg Grzegorz
Published: September 2008

Natural computing builds a bridge between computer science and natural sciences.
Q&AA complex thinker
Authors: Hoffmann Leah
Published: September 2008

Daphne Koller discusses probabilistic relational modeling, artificial intelligence, and her new work with biologists.
Defunctionalized interpreters for programming languages
Authors: Danvy Olivier
Published: September 2008

This document illustrates how functional implementations of formal semantics (structural operational semantics, reduction semantics, small-step and big-step abstract machines, natural semantics, and denotational semantics) can be transformed into each other. These transformations were foreshadowed by Reynolds in "Definitional Interpreters for Higher-Order Programming Languages" for functional implementations of denotational semantics, natural semantics, and big-step abstract machines using closure conversion, CPS transformation, and defunctionalization. Over the last few years, the author and his students have further observed that functional implementations of small-step and of big-step abstract machines are related using fusion by fixed-point promotion and that functional implementations of reduction semantics and of small-step abstract machines are related using refocusing and transition compression. It furthermore appears that functional implementations of structural operational semantics and of reduction semantics are related as well, also using CPS transformation and defunctionalization. This further relation provides an element of answer to Felleisen's conjecture that any structural operational semantics can be expressed as a reduction semantics: for deterministic languages, a reduction semantics is a structural operational semantics in continuation style, where the reduction context is a defunctionalized continuation. As the defunctionalized counterpart of the continuation of a one-step reduction function, a reduction context represents the rest of the reduction, just as an evaluation context represents the rest of the evaluation since it is the defunctionalized counterpart of the continuation of an evaluation function.
Typed iterators for XML
Authors: Castagna Giuseppe , Nguyen Kim
Published: September 2008

XML transformations are very sensitive to types: XML types describe the tags and attributes of XML elements as well as the number, kind, and order of their sub-elements. Therefore, operations, even simple ones, that modify these features may affect the types of documents. Operations on XML documents are performed by iterators that, to be useful, need to be typed by a kind of polymorphism that goes beyond what currently exists. For this reason these
iterators
are not programmed but, rather, hard-coded in the languages. However, this approach soon reaches its limits, as the hard-coded iterators cannot cover fairly standard usage scenarios.

As a solution to this problem we propose a generic language to define iterators for XML data. This language can either be used as a compilation target (e.g., for XPATH) or it can be grafted on any statically typed host programming language (as long as this has product types) to endow it with XML processing capabilities. We show that our language mostly offers the required degree of polymorphism, study its formal properties, and show its expressiveness and practical impact by providing several usage examples and encodings.
AURA
Authors: Jia Limin , Vaughan Jeffrey A. , Mazurak Karl , Zhao Jianzhou , Zarko Luke , Schorr Joseph , Zdancewic Steve
Published: September 2008

This paper presents AURA, a programming language for access control that treats ordinary programming constructs (e.g., integers and recursive functions) and authorization logic constructs (e.g., principals and access control policies) in a uniform way. AURA is based on polymorphic DCC and uses dependent types to permit assertions that refer directly to AURA values while keeping computation out of the assertion level to ensure tractability. The main technical results of this paper include fully mechanically verified proofs of the decidability and soundness for AURA's type system, and a prototype typechecker and interpreter.
The power of Pi
Authors: Oury Nicolas , Swierstra Wouter
Published: September 2008

This paper exhibits the power of programming with dependent types by dint of embedding three domain-specific languages: Cryptol, a language for cryptographic protocols; a small data description language; and relational algebra. Each example demonstrates particular design patterns inherent to dependently-typed programming. Documenting these techniques paves the way for further research in domain-specific embedded type systems.
Type checking with open type functions
Authors: Schrijvers Tom , Peyton Jones Simon , Chakravarty Manuel , Sulzmann Martin
Published: September 2008

We report on an extension of Haskell with open type-level functions and equality constraints that unifies earlier work on GADTs, functional dependencies, and associated types. The contribution of the paper is that we identify and characterise the key technical challenge of
entailment checking
; and we give a novel, decidable, sound, and complete algorithm to solve it, together with some practically-important variants. Our system is implemented in GHC, and is already in active use.
From ML to ML
F
Authors: Rémy Didier , Yakobowski Boris
Published: September 2008

ML
F
is a type system that seamlessly merges ML-style type inference with System-F polymorphism. We propose a system of graphic (type) constraints that can be used to perform type inference in both ML or ML
F
. We show that this constraint system is a small extension of the formalism of graphic types, originally introduced to represent ML
F
types. We give a few semantic preserving transformations on constraints and propose a strategy for applying them to solve constraints. We show that the resulting algorithm has optimal complexity for ML
F
type inference, and argue that, as for ML, this complexity is linear under reasonable assumptions.
Experience report
Authors: Jones Mark P.
Published: September 2008

This paper describes our experience using a functional language, Haskell, to build an embedded, domain-specific language (DSL) for component configuration in large-scale, real-time, embedded systems. Prior to the introduction of the DSL, engineers would describe the steps needed to configure a particular system in a handwritten XML document. In this paper, we outline the application domain, give a brief overview of the DSL that we developed, and provide concrete data to demonstrate its effectiveness. In particular, we show that the DSL has several significant benefits over the original, XML-based approach including reduced code size, increased modularity and scalability, and detection and prevention of common defects. For example, using the DSL, we were able to produce clear and intuitive descriptions of component configurations that were sometimes less than 1/30 of the size of the original XML.
Transactional events for ML
Authors: Effinger-Dean Laura , Kehrt Matthew , Grossman Dan
Published: September 2008

Transactional events (TE) are an approach to concurrent programming that enriches the first-class synchronous message-passing of Concurrent ML (CML) with a combinator that allows multiple messages to be passed as part of one all-or-nothing synchronization. Donnelly and Fluet (2006) designed and implemented TE as a Haskell library and demonstrated that it enables elegant solutions to programming patterns that are awkward or impossible in CML. However, both the definition and the implementation of TE relied fundamentally on the code in a synchronization not using mutable memory, an unreasonable assumption for mostly functional languages like ML where functional interfaces may have impure implementations.

We present a definition and implementation of TE that supports ML-style references and nested synchronizations, both of which were previously unnecessary due to Haskell's more restrictive type system. As in prior work, we have a high-level semantics that makes nondeterministic choices such that synchronizations succeed whenever possible and a low-level semantics that uses search to implement the high-level semantics soundly and completely. The key design trade-off in the semantics is to allow updates to mutable memory without requiring the implementation to consider all possible thread interleavings. Our solution uses first-class heaps and allows interleavings only when a message is sent or received. We have used Coq to prove the high- and low-level semantics equivalent.

We have implemented our approach by modifying the Objective Caml run-time system. By modifying the run-time system, rather than relying solely on a library, we can eliminate the potential for nonterminating computations within unsuccessful synchronizations to run forever.
Implicitly-threaded parallelism in Manticore
Authors: Fluet Matthew , Rainey Mike , Reppy John , Shaw Adam
Published: September 2008

The increasing availability of commodity multicore processors is making parallel computing available to the masses. Traditional parallel languages are largely intended for large-scale scientific computing and tend not to be well-suited to programming the applications one typically finds on a desktop system. Thus we need new parallel-language designs that address a broader spectrum of applications. In this paper, we present Manticore, a language for building parallel applications on commodity multicore hardware including a diverse collection of parallel constructs for different granularities of work. We focus on the implicitly-threaded parallel constructs in our high-level functional language. We concentrate on those elements that distinguish our design from related ones, namely, a novel parallel binding form, a nondeterministic parallel case form, and exceptions in the presence of data parallelism. These features differentiate the present work from related work on functional data parallel language designs, which has focused largely on parallel problems with regular structure and the compiler transformations --- most notably, flattening --- that make such designs feasible. We describe our implementation strategies and present some detailed examples utilizing various mechanisms of our language.
Parametric higher-order abstract syntax for mechanized semantics
Authors: Chlipala Adam
Published: September 2008

We present
parametric higher-order abstract syntax (PHOAS)
, a new approach to formalizing the syntax of programming languages in computer proof assistants based on type theory. Like higher-order abstract syntax (HOAS), PHOAS uses the meta language's binding constructs to represent the object language's binding constructs. Unlike HOAS, PHOAS types are definable in general-purpose type theories that support traditional functional programming, like Coq's Calculus of Inductive Constructions. We walk through how Coq can be used to develop certified, executable program transformations over several statically-typed functional programming languages formalized with PHOAS; that is, each transformation has a machine-checked proof of type preservation and semantic preservation. Our examples include CPS translation and closure conversion for simply-typed lambda calculus, CPS translation for System F, and translation from a language with ML-style pattern matching to a simpler language with no variable-arity binding constructs. By avoiding the syntactic hassle associated with first-order representation techniques, we achieve a very high degree of proof automation.
Efficient nondestructive equality checking for trees and graphs
Authors: Adams Michael D. , Dybvig R. Kent
Published: September 2008

The Revised
6
Report on Scheme requires its generic equivalence predicate, equal?, to terminate even on cyclic inputs. While the terminating equal? can be implemented via a DFA-equivalence or union-find algorithm, these algorithms usually require an additional pointer to be stored in each object, are not suitable for multithreaded code due to their destructive nature, and may be unacceptably slow for the small acyclic values that are the most likely inputs to the predicate.

This paper presents a variant of the union-find algorithm for equal? that addresses these issues. It performs well on large and small, cyclic and acyclic inputs by interleaving a low-overhead algorithm that terminates only for acyclic inputs with a more general algorithm that handles cyclic inputs. The algorithm terminates for all inputs while never being more than a small factor slower than whichever of the acyclic or union-find algorithms would have been faster. Several intermediate algorithms are also presented, each of which might be suitable for use in a particular application, though only the final algorithm is suitable for use in a library procedure, like equal?, that must work acceptably well for all inputs.
Functional pearl
Authors: Hinze Ralf
Published: September 2008

Streams, infinite sequences of elements, live in a coworld: they are given by a coinductive data type, operations on streams are implemented by corecursive programs, and proofs are conducted using coinduction. But there is more to it: suitably restricted, stream equations possess
unique solutions
, a fact that is not very widely appreciated. We show that this property gives rise to a simple and attractive proof technique essentially bringing equational reasoning to the coworld. In fact, we redevelop the theory of recurrences, finite calculus and generating functions using streams and stream operators building on the cornerstone of unique solutions. The development is constructive: streams and stream operators are implemented in Haskell, usually by one-liners. The resulting calculus or library, if you wish, is elegant and fun to use. Finally, we rephrase the proof of uniqueness using generalised algebraic data types.
Data-flow testing of declarative programs
Authors: Fischer Sebastian , Kuchen Herbert
Published: September 2008

We propose a novel notion of data-flow coverage for testing declarative programs. Moreover, we extend an automatic test-case generator such that it can achieve data-flow coverage. The coverage information is obtained by instrumenting a program such that it collects coverage information during its execution. Finally, we show the benefits of data-flow based testing for a couple of example applications.
Functional translation of a calculus of capabilities
Authors: Charguéraud Arthur , Pottier François
Published: September 2008

Reasoning about imperative programs requires the ability to track aliasing and ownership properties. We present a type system that provides this ability, by using regions, capabilities, and singleton types. It is designed for a high-level calculus with higher-order functions, algebraic data structures, and references (mutable memory cells). The type system has polymorphism, yet does not require a value restriction, because capabilities act as explicit store typings.

We exhibit a type-directed, type-preserving, and meaning-preserving translation of this imperative calculus into a pure calculus. Like the monadic translation, this is a store-passing translation. Here, however, the store is partitioned into multiple fragments, which are threaded through a computation only if they are relevant to it. Furthermore, the decomposition of the store into fragments can evolve dynamically to reflect ownership transfers.

The translation offers deep insight about the inner workings and soundness of the type system. If coupled with a semantic model of its target calculus, it leads to a semantic model of its imperative source calculus. Furthermore, it provides a foundation for our long-term objective of designing a system for specifying and certifying imperative programs with dynamic memory allocation.
Paradise
Authors: Augustsson Lennart , Mansell Howard , Sittampalam Ganesh
Published: September 2008

We have implemented a two-stage language, Paradise, for building reusable components which are used to price financial products. Paradise is embedded in Haskell and makes heavy use of type-class based overloading, allowing the second stage to be compiled into a variety of backend platforms.

Paradise has enabled us to begin moving away from implementation directly in monolithic Excel spreadsheets and towards a more modular and retargetable approach.
Ynot
Authors: Nanevski Aleksandar , Morrisett Greg , Shinnar Avraham , Govereau Paul , Birkedal Lars
Published: September 2008

We describe an axiomatic extension to the Coq proof assistant, that supports writing, reasoning about, and extracting higher-order, dependently-typed programs with
side-effects
. Coq already includes a powerful functional language that supports dependent types, but that language is limited to pure, total functions. The key contribution of our extension, which we call Ynot, is the added support for computations that may have effects such as non-termination, accessing a mutable store, and throwing/catching exceptions.

The axioms of Ynot form a small trusted computing base which has been formally justified in our previous work on Hoare Type Theory (HTT). We show how these axioms can be combined with the powerful type and abstraction mechanisms of Coq to build higher-level reasoning mechanisms which in turn can be used to build realistic, verified software components. To substantiate this claim, we describe here a representative series of modules that implement imperative finite maps, including support for a higher-order (effectful) iterator. The implementations range from simple (e.g., association lists) to complex (e.g., hash tables) but share a common interface which abstracts the implementation details and ensures that the modules properly implement the finite map abstraction.
A scheduling framework for general-purpose parallel languages
Authors: Fluet Matthew , Rainey Mike , Reppy John
Published: September 2008

The trend in microprocessor design toward multicore and manycore processors means that future performance gains in software will largely come from harnessing parallelism. To realize such gains, we need languages and implementations that can enable parallelism at many different levels. For example, an application might use both explicit threads to implement course-grain parallelism for independent tasks and implicit threads for fine-grain data-parallel computation over a large array. An important aspect of this requirement is supporting a wide range of different scheduling mechanisms for parallel computation.

In this paper, we describe the scheduling framework that we have designed and implemented for Manticore, a strict parallel functional language. We take a micro-kernel approach in our design: the compiler and runtime support a small collection of scheduling primitives upon which complex scheduling policies can be implemented. This framework is extremely flexible and can support a wide range of different scheduling policies. It also supports the nesting of schedulers, which is key to both supporting multiple scheduling policies in the same application and to hierarchies of speculative parallel computations.

In addition to describing our framework, we also illustrate its expressiveness with several popular scheduling techniques. We present a (mostly) modular approach to extending our schedulers to support cancellation. This mechanism is essential for implementing eager and speculative parallelism. We finally evaluate our framework with a series of benchmarks and an analysis.