bluuebunny/crossref_metadata_2025_split huggingface dataset:
A mechanical proof of Segall's PIF algorithm
Authors: Hesselink Wim H. 
Published: February 2005

Abstract
We describe the construction of a distributed algorithm with asynchronous communication together with a mechanically verified proof of correctness. For this purpose we treat Segall's PIF algorithm (propagation of information with feedback). The proofs are based on invariants, and variant functions for termination. The theorem prover NQTHM is used to deal with the many case distinctions due to asynchronous distributed computation. Emphasis is on the modelling assumptions, the treatment of nondeterminacy, the forms of termination detection, and the proof obligations for a complete mechanical proof. Finally, a comparison is made with (the proof of) the minimum spanning tree algorithm of Gallager, Humblet, and Spira, for which the technique was developed.
Towards a practitioners' approach to Abadi and Lamport's method
Authors: Engelhardt Kai , de Roever Willem -Paul 
Published: February 2005

AbstractOur own basic intuitions are presented when introducing the method developed by Abadi and Lamport in [AbL88a] for proving refinement between specifications of nondeterministic programs correct to people unacquainted with it. The example we use to illustrate this method is a nontrivial communication protocol that provides a mechanism analogous to message passing between migrating processes within a fixed finite network of nodes due to Kleinman, Moscowitz, Pnueli and Shapiro [KMP91]. Especially the cruel last step of a three step refinement proof of that protocol gives rise to a deeper understanding of, and some small enhancements to, Abadi and Lamport's 1988 method.
Specifying distributed CICS in Z: Accessing local and remote resources
Authors: Houston Iain S. C. , Josephs Mark B. 
Published: February 2005

Abstract
The CICS/ESA Intercommunication Guide is a source of information about distributed CICS systems. Among other things, it describes how an application program running on one system can issue a command that will be shipped to a remote system. A resource manager located at the remote system will execute the command and ship back a response.
This paper presents a formal specification of the above interaction between application programs and resource managers. Some familiarity with the Z specification language is assumed. The structure of the specification illustrates how it is possible to address separately, and later combine, different aspects of a complex system, including its distributed nature.
Priority as extremal probability
Authors: Smolka Scott A. , Steffen Bernhard 
Published: February 2005

Abstract

We extend the stratified model of probabilistic processes to obtain a very general notion of
process priority.
The main idea is to allow probability guards of value 0 to be associated with alternatives of a probabilistic summation expression. Such alternatives can be chosen only if the non-zero alternatives are precluded by contextual constraints. We refer to this model as one of “extremal probability” and to its signature as
PCCS
ζ
. We provide
PCCS
ζ
with a structural operational semantics and a notion
of probabilistic bisimulation
, which is shown to be a congruence. Of particular interest is the abstraction
PCCS
π
of
PCCS
ζ
in which all non-zero probability guards are identified.
PCCS
π
represents a customized framework for reasoning about priority, and covers all features of process algebras proposed for reasoning about priority that we know of.
A criterion for atomicity
Authors: Anderson James H. , Gouda Mohamed G. 
Published: February 2005

Abstract

Most proof methods for reasoning about concurrent programs are based upon the
interleaving semantics
of concurrent computation: a concurrent program is executed in a stepwise fashion, with only one enabled action being executed at each step. Interleaving semantics, in effect, requires that a concurrent program be executed as a nondeterministic sequential program. This is clearly an abstraction of the way in which concurrent programs are actually executed. To ensure that this is a reasonable abstraction, interleaving semantics should only be used to reason about programs with “simple” actions; we call such programs “atomic”. In this paper, we formally characterise the class of atomic programs. We adopt the criterion that a program is
atomic
if it can be implemented in a wait-free, serialisable manner by a primitive program. A program is
primitive
if each of its actions has at most one occurrence of a shared bit, and each shared bit is read by at most one process and written by at most one process. It follows from our results that the traditionally accepted atomicity criterion, which allows each action to have at most one occurrence of a shared variable, can be relaxed, allowing programs to have more powerful actions. For example, according to our criterion, an action can read any finite number of shared variables, provided it writes no shared variable.
Reasoning about Prolog programs: From modes through types to assertions
Authors: Apt Krzysztof R. , Marchiori Elena 
Published: February 2005

Abstract
We provide here a systematic comparative study of the relative strength and expressive power of a number of methods for program analysis of Prolog. Among others we show that these methods can be arranged in the following hierarchy: mode analysis ⇒ type analysis ⇒ monotonic properties ⇒ nonmonotonic run-time properties. We also discuss a method allowing us to prove global run-time properties.
The weakest precondition calculus: Recursion and duality
Authors: Bonsangue Marcello M. , Kok Joost N. 
Published: February 2005

Abstract
An extension of Dijkstra's guarded command language is studied, including unbounded demonic choice and a backtrack operator. We consider three orderings on this language: a refinement ordering defined by Back, a new deadlock ordering, and an approximation ordering of Nelson. The deadlock ordering is in between the two other orderings. All operators are monotonic in Nelson's ordering, but backtracking is not monotonic in Back's ordering and sequential composition is not monotonic for the deadlock ordering. At first sight recursion can only be added using Nelson's ordering. We show that, under certain circumstances, least fixed points for non-monotonic functions can be obtained by iteration from the least element. This permits the addition of recursion even using Back's ordering or the deadlock ordering in a fully compositional way. In order to give a semantic characterization of the three orderings that relates initial states to possible outcomes of the computation, the relation between predicate transformers and discrete power domains is studied. We consider (two versions of) the Smyth power domain and the Egli-Milner power domain.
Extending hoare logic to real-time
Authors: Hooman Jozef 
Published: February 2005

AbstractClassical Hoare triples are modified to specify and design distributed real-time systems. The assertion language is extended with primitives to express the timing of observable actions. Further the interpretation of triples is adapted such that both terminating and nonterminating computations can be specified. To verify that a concurrent program, with message passing along asynchronous channels, satisfies a real-time specification, we formulate a compositional proof system for our extended Hoare logic. The use of compositionality during top-down design is illustrated by a process control example of a chemical batch processing system.
Model-checking discrete duration calculus
Authors: Hansen Michael R. 
Published: February 2005

AbstractDuration Calculus was introduced in [ZHR91] as a logic to specify and reason about requirements for real-time systems. It is an extension of Interval Temporal Logic [Mos85] where one can reason about integrated constraints over time-dependent and Boolean valued states without explicit mention of absolute time. Several major case studies, e.g. the gas burner system in [RRH93], have shown that Duration Calculus provides a high level of abstraction for both expressing and reasoning about specifications. Using Timed Automata [A1D92] one can express how real-time systems can be constructed at a level of detail which is close to an actual implementation. We consider in the paper the correctness of Timed Automata with respect to Duration Calculus formulae. For a subset of Duration Calculus, we show that one can automatically verify whether a Timed Automaton ℳ is correct with respect to a formulaD, abbreviated ℳ ⊨D, i.e. one can domodel-checking. The subset we consider is expressive enough to formalize the requirements to the gas burner system given in [RRH93]; but only for a discrete time domain. Model-checking is done by reducing the correctness problem ℳ ⊨D to the inclusion problem of regular languages.
Retargeting a hardware compiler using protocol converters
Authors: Brown Geoffrey , Luk Wayne , O'Leary John 
Published: February 2005

AbstractWe show how to retarget a compiler for occam-like programs from generating two-phase delay-insensitive circuits to generating four-phase speed independent circuits. The specifications of the two-phase circuit elements for our compiler are used to produce a set of equivalent specifications for four-phase circuit elements using a set of protocol converters. Automatic tools have been used in checking that our four-phase implementations satisfy their specifications.
Superposition refinement of reactive systems
Authors: Back R. J. R. , Sere K. 
Published: February 2005

Abstract
Superposition refinement enhances an algorithm by superposing one computation mechanism onto another mechanism, in a way that preserves the behavior of the original mechanism. Superposition seems to be particularly well suited to the development of parallel and distributed programs: an originally simple sequential algorithm can be extended with mechanisms that distribute control and state information to many processes, thus permitting efficient parallel execution of the algorithm. We will show in this paper how superposition of reactive systems is expressed in the refinement calculus. We illustrate the power of this method by a case study, showing how a distributed broadcasting system is derived through a sequence of superposition refinements.
A static view of localities
Authors: Aceto Luca 
Published: February 2005

Abstract
This paper proposes alternative, effective characterizations for nets of automata of the location equivalence and preorder presented by Boudol et al. in the companion paper [BCHK]. Contrary to the technical development in the above given reference, where locations are dynamically associated to the subparts of a process in the operational semantics, the equivalence and preorder we propose are based on a static association of locations to the parallel components of a net. Following this static approach, it is possible to give these “distributed nets” a standard operational semantics which associates with each net a finite labelled transition system. Using this operational semantics for distributed nets, we introduce effective notions of equivalence and preorder which are shown to coincide with those proposed in [BCHK].
Community outreach for untreated schizophrenia in rural India: a follow-up study of symptoms, disability, family burden and costs
Authors: SRINIVASA MURTHY R. , KISHORE KUMAR K. V. , CHISHOLM D. , THOMAS T. , SEKAR K. , CHANDRASHEKAR C. R. 
Published: February 2005

Background. In resource-poor countries, there remains an alarming treatment gap for people with schizophrenia, particularly those living in rural areas. Decentralization of mental health services, including community-based outreach programmes, represents one obvious strategy for bringing appropriate care to these communities. This study set out to assess the costs and effects of such a programme in rural Karnataka in India.Method. Eight rural communities were visited by an outreach team, who identified cases of drug-naive or currently untreated schizophrenia. Recruited cases were provided with appropriate psychotropic medication and psychosocial support, and after obtaining informed consent were assessed every 3 months over one and a half years on symptomatology, disability, family burden, resource use and costs. A repeated-measures analysis was carried out to test for significant change in these outcome measures over this period.Results. A total of 100 cases of untreated schizophrenia were recruited, of whom 28% had never received antipsychotic medication and the remaining 72% had not been on medication for the past 6 months. Summary scores for psychotic symptoms, disability and family burden were all reduced significantly, with particular improvement observed at the first follow-up assessment. Increases in treatment and community outreach costs over the follow-up period were accompanied by reductions in the costs of informal-care sector visits and family care-giving time.Conclusions. Efforts to organize community-based care such as outreach services for people with schizophrenia living in more remote areas of resource-constrained countries can bring substantial benefits to patients and families alike.
Childhood physical and sexual abuse and subsequent depressive and anxiety disorders for two American Indian tribes
Authors: LIBBY ANNE M. , ORTON HEATHER D. , NOVINS DOUGLAS K. , BEALS JANETTE , MANSON SPERO M. 
Published: February 2005

Background. This study examined the relationship of childhood abuse, both physical and sexual, with subsequent lifetime depressive and anxiety disorders – depression or dysthymia, post-traumatic stress disorder (PTSD), and panic or generalized anxiety disorder (GAD) – among American Indians (AIs).Method. Three thousand and eighty-four AIs from two tribes – Southwest and Northern Plains – participated in a large-scale, community-based study. Participants were asked about traumatic events and family history, and were administered standard diagnostic measures of depressive/anxiety disorders.Results. Prevalence of childhood physical abuse was approximately 7% for both tribes. The Southwest tribe had higher prevalence of depressive and anxiety disorders, with rates of PTSD being the highest. Childhood physical abuse was significant in bivariate models of depressive/anxiety disorders, and remained so in the multivariate models.Conclusions. Childhood physical abuse was a significant predictor of all disorder groups for males in both tribes except for panic/GAD for the Northern Plains tribe in multivariate models; females showed a more varied pattern. Childhood sexual abuse did not significantly differ for males and females, and was an independent predictor of PTSD for both tribes, controlling for childhood physical abuse and other factors, and was significant for the other disorder groups only in the Southwest. Additional covariates that increased the odds of depressive/anxiety disorders were adult physical or sexual victimization, chronic illness, lifetime alcohol or drug disorder, and parental problems with depression, alcohol, or violence. Results provided empirical evidence of childhood and later life risk factors and expanded the population at risk to include males.
Steady-state kinetics and inhibition of anaerobically purified human homogentisate 1,2-dioxygenase
Authors: VELDHUIZEN Edwin J. A. , VAILLANCOURT Frédéric H. , WHITING Cheryl J. , HSIAO Marvin M.-Y. , GINGRAS Geneviève , XIAO Yufang , TANGUAY Robert M. , BOUKOUVALAS John , ELTIS Lindsay D. 
Published: February 2005

HGO (homogentisate 1,2-dioxygenase; EC 1.13.11.5) catalyses the O2-dependent cleavage of HGA (homogentisate) to maleylacetoacetate in the catabolism of tyrosine. Anaerobic purification of heterologously expressed Fe(II)-containing human HGO yielded an enzyme preparation with a specific activity of 28.3± 0.6 μmol·min−1·mg−1 (20 mM Mes, 80 mM NaCl, pH 6.2, 25 °C), which is almost twice that of the most active preparation described to date. Moreover, the addition of reducing agents or other additives did not increase the specific activity, in contrast with previous reports. The apparent specificity of HGO for HGA was highest at pH 6.2 and the steady-state cleavage of HGA fit a compulsory-order ternary-complex mechanism (Km value of 28.6±6.2 μM for HGA, Km value of 1240±160 μM for O2). Free HGO was subject to inactivation in the presence of O2 and during the steady-state cleavage of HGA. Both cases involved the oxidation of the active site Fe(II). 3-Cl HGA, a potential inhibitor of HGO, and its isosteric analogue, 3-Me HGO, were synthesized. At saturating substrate concentrations, HGO cleaved 3-Me and 3-Cl HGA 10 and 100 times slower than HGA respectively. The apparent specificity of HGO for HGA was approx. two orders of magnitude higher than for either 3-Me or 3-Cl HGA. Interestingly, 3-Cl HGA inactivated HGO only twice as rapidly as HGA. This contrasts with what has been observed in mechanistically related dioxygenases, which are rapidly inactivated by chlorinated substrate analogues, such as 3-hydroxyanthranilate dioxygenase by 4-Cl 3-hydroxyanthranilate.
Structure–Function Analysis of Cf-9, a Receptor-Like Protein with Extracytoplasmic Leucine-Rich Repeatsw⃞
Authors: van der Hoorn Renier A.L. , Wulff Brande B.H. , Rivas Susana , Durrant Marcus C. , van der Ploeg Anke , de Wit Pierre J.G.M. , Jones Jonathan D.G. 
Published: February 2005

AbstractThe tomato (Lycopersicon pimpinellifolium) resistance protein Cf-9 belongs to a large class of plant proteins with extracytoplasmic Leu-rich repeats (eLRRs). eLRR proteins play key roles in plant defense and development, mainly as receptor-like proteins or receptor-like kinases, conferring recognition of various pathogen molecules and plant hormones. We report here a large-scale structure–function analysis of an eLRR protein. A total of 66 site-directed mutants of Cf-9 were analyzed for activity in Avr9 recognition and for protein stability and the results interpreted with the help of a homology model of the Cf-9 structure. Conserved Trp and Cys pairs in the N-terminal LRR-flanking domain appear to be important for Cf-9 activity and are probably exposed at the putative concave inner surface of the Cf-9 protein, where recognition specificity also resides. Removal of each of the 22 putative N-linked glycosylation sites (PGS) revealed that many PGSs contribute to Cf-9 activity and that the PGSs in the putative α-helices of the LRR modules are essential. Immunoblot analysis and mass spectrometry showed that all but one of the PGSs are N-glycosylated. Introduction of glycosylation at the putative concave β-sheet surface blocks Cf-9 activity, in some cases probably by disturbing specific recognition, and in another case by steric hindrance with existing N-glycans. The glycosylation pattern and several other features are conserved in other eLRR proteins, where similar mutations show similar phenotypes.
RIN13 Is a Positive Regulator of the Plant Disease Resistance Protein RPM1
Authors: Al-Daoude Antonious , de Torres Zabala Marta , Ko Jong-Hyun , Grant Murray 
Published: February 2005

AbstractThe RPM1 protein confers resistance to Pseudomonas syringae pv tomato DC3000 expressing either of the Type III effector proteins AvrRpm1 or AvrB. Here, we describe the isolation and functional characterization of RPM1 Interacting Protein 13 (RIN13), a resistance protein interactor shown to positively enhance resistance function. Ectopic expression of RIN13 (RIN13s) enhanced bacterial restriction mechanisms but paradoxically abolished the normally rapid hypersensitive response (HR) controlled by RPM1. In contrast with wild-type plants, leaves expressing RIN13s did not undergo electrolyte leakage or accumulate H2O2 after bacterial delivery of AvrRpm1. Overexpression of RIN13 also altered the transcription profile observed during a normal HR. By contrast, RIN13 knockout plants had the same ion leakage signatures and HR timing of wild-type plants in response to DC3000(avrRpm1) but failed to suppress bacterial growth. The modified phenotypes seen in the RIN13s/as plants were specific to recognition of AvrRpm1 or AvrB, and wild-type responses were observed after challenge with other incompatible pathogens or the virulent DC3000 isolate. Our results suggest that cell death is not necessary to confer resistance, and engineering enhanced resistance without activation of programmed cell death is a real possibility.
Role of β-Oxidation in Jasmonate Biosynthesis and Systemic Wound Signaling in Tomato
Authors: Li Chuanyou , Schilmiller Anthony L. , Liu Guanghui , Lee Gyu In , Jayanty Sastry , Sageman Carolyn , Vrebalov Julia , Giovannoni James J. , Yagi Kaori , Kobayashi Yuichi , Howe Gregg A. 
Published: February 2005

Abstract
Jasmonic acid (JA) is a lipid-derived signal that regulates plant defense responses to biotic stress. Here, we report the characterization of a JA-deficient mutant of tomato (Lycopersicon esculentum) that lacks local and systemic expression of defensive proteinase inhibitors (PIs) in response to wounding. Map-based cloning studies demonstrated that this phenotype results from loss of function of an acyl-CoA oxidase (ACX1A) that catalyzes the first step in the peroxisomal β-oxidation stage of JA biosynthesis. Recombinant ACX1A exhibited a preference for C12 and C14 straight-chain acyl-CoAs and also was active in the metabolism of C18 cyclopentanoid-CoA precursors of JA. The overall growth, development, and reproduction of acx1 plants were similar to wild-type plants. However, the mutant was compromised in its defense against tobacco hornworm (Manduca sexta) attack. Grafting experiments showed that loss of ACX1A function disrupts the production of the transmissible signal for wound-induced PI expression but does not affect the recognition of this signal in undamaged responding leaves. We conclude that ACX1A is essential for the β-oxidation stage of JA biosynthesis and that JA or its derivatives is required both for antiherbivore resistance and the production of the systemic wound signal. These findings support a role for peroxisomes in the production of lipid-based signaling molecules that promote systemic defense responses.
Identification and Dynamics of Two Classes of Aurora-Like Kinases in Arabidopsis and Other Plants
Authors: Demidov Dmitri , Van Damme Daniël , Geelen Danny , Blattner Frank R. , Houben Andreas 
Published: February 2005

AbstractAurora-like kinases play key roles in chromosome segregation and cytokinesis in yeast, plant, and animal systems. Here, we characterize three Arabidopsis thaliana protein kinases, designated AtAurora1, AtAurora2, and AtAurora3, which share high amino acid identities with the Ser/Thr kinase domain of yeast Ipl1 and animal Auroras. Structure and expression of AtAurora1 and AtAurora2 suggest that these genes arose by a recent gene duplication, whereas the diversification of plant α and β Aurora kinases predates the origin of land plants. The transcripts and proteins of all three kinases are most abundant in tissues containing dividing cells. Intracellular localization of green fluorescent protein–tagged AtAuroras revealed an AtAurora-type specific association mainly with dynamic mitotic structures, such as microtubule spindles and centromeres, and with the emerging cell plate of dividing tobacco (Nicotiana tabacum) BY-2 cells. Immunolabeling using AtAurora antibodies yielded specific signals at the centromeres that are coincident with histone H3 that is phosphorylated at Ser position10 during mitosis. An in vitro kinase assay demonstrated that AtAurora1 preferentially phosphorylates histone H3 at Ser 10 but not at Ser 28 or Thr 3, 11, and 32. The phylogenetic analysis of available Aurora sequences from different eukaryotic origins suggests that, although a plant Aurora gene has been duplicated early in the evolution of plants, the paralogs nevertheless maintained a role in cell cycle–related signal transduction pathways.