bluuebunny/crossref_metadata_2025 huggingface dataset:
TIC: A timed calculus
Authors: Quemada Juan , de Frutos David , Azcorra Arturo
Published: February 2005

TIC is a timed algebraic calculus which combines ideas from asynchronous and synchronous calculi. Time is introduced by assigning explicit time restrictions to the events of an asynchronous calculus. The semantics is defined in an operational way. Interleaving of behaviours is defined in such a way that a proper merge of events in time is achieved. Weak timed bisimulation is also defined. Examples are presented to show the applicability of the calculus to the study of timed behaviours.
Proof by analogy in mural
Authors: Vadera Sunil
Published: February 2005

An important advantage of using a formal method of developing software is that one can prove that development steps are correct with respect to their specification. Conducting proofs by hand, however, can be time consuming to the extent that designers have to judge whether a proof of a particular obligation is worth conducting. Even if hand proofs are worth conducting, how do we know that they are correct?

One approach to overcoming this problem is to use an automatic theorem proving system to develop and check our proofs. However, in order to enable present day theorem provers to check proofs, one has to conduct them in much more detail than hand proofs. Carrying out more detailed proofs is of course more time consuming.

This paper describes the use of proof by analogy in an attempt to reduce the time spent on proofs. We develop and implement a proof follower based on analogy and present an example to illustrate its characteristics. The example shows that even when the follower fails to complete a proof, it can provide a hint that enables the user to complete a proof.
Interpreting Message Flow Graphs
Authors: Ladkin Peter B. , Leue Stefan
Published: February 2005

We give a semantics for Message Flow Graphs (MFGs), which play the role for interprocess communication that Program Dependence Graphs play for control flow in parallel processes. MFGs have been used to analyse parallel code, and are closely related to Message Sequence Charts and Time Sequence Diagrams in telecommunications systems. Our requirements are firstly, to determine unambiguously exactly what execution traces are specified by an MFG, and secondly, to use a finite-state interpretation. Our methods function for both asynchronous and synchronous communications. From a set of MFGs, we define a transition system of global states, and from that a Büchi automaton by considering safety and liveness properties of the system. In order easily to describe liveness properties, we interpret the traces of the transition system as a model of Manna-Pnueli temporal logic. Finally, we describe the expressive power of MFGs by mimicking an arbitrary Büchi automaton by means of a set of MFGs.
Safety, liveness and fairness in temporal logic
Authors: Sistla A. Prasad
Published: February 2005

In this paper we present syntactic characterization of temporal formulas that express various properties of interest in the verification of concurrent programs. Such a characterization helps us in choosing the right techniques for proving correctness with respect to these properties. The properties that we consider include safety properties, liveness properties and fairness properties. We also present algorithms for checking if a given temporal formula expresses any of these properties.
Processes with probabilities, priority and time
Authors: Tofts Chris
Published: February 2005

A probabilistic calculus, derived from Milner's SCCS, WSCCS is presented. We define a notion of bisimulation for probabilistic processes and show that it is a congruence. A simple equational characterisation is shown to be both sound and complete for finite processes. We present many examples including some extended ones. The larger examples show both the expressive power of WSCCS and the availability of simple proof methods for some complex systems.
Temporal theories as modularisation units for concurrent system specification
Authors: Fiadeiro J. , Maibaum T.
Published: February 2005

In this paper, we bring together the use of temporal logic for specifying concurrent systems, in the tradition initiated by A. Pnueli, and the use of tools from category theory as a means for structuring specifications as combinations of theories in the style developed by R. Burstall and J. Goguen. As a result, we obtain a framework in which systems of interconnected components can be described by assembling the specifications of their components around a diagram, using theory morphisms to specify how the components interact. This view of temporal theories as specification units naturally brings modularity to the description and analysis of systems. Moreover, it becomes possible to import into the area of formal development of reactive systems the wide body of specification techniques that have been defined for structuring specifications independently of the underlying logic, and that have been applied with great success in the area of Abstract Data Types. Finally, as a discipline of design, we use the object-oriented paradigm according to which components keep private data and interact by sharing actions, with a view towards providing formal tools for the specification of concurrent objects.
Weakest preconditions for progress
Authors: Lukkien Johan J. , van de Snepscheut Jan L. A.
Published: February 2005

Predicate transformers that map the postcondition and all intermediate conditions of a command to a precondition are introduced. They can be used to specify certain progress properties of sequential programs.
Discrete time process algebra
Authors: Baeten J. C. M. , Bergstra J. A.
Published: February 2005

The axiom system ACP of [BeK84a] was extended with real time features in [BaB91]. Here we proceed to define a discrete time extension of ACP, along the lines of ATP [NiS94]. We present versions based on relative timing and on absolute timing. Both approaches are integrated using parametric timing. The time free ACP theory is embedded in the discrete time theory.
Hoare's logic and VDM
Authors: Coenen J.
Published: February 2005

A relational framework which unifies Hoare's logic and VDM is presented. Within this framework a partial correctness version of VDM is defined. It is argued that this partial correctness version of VDM is intuitive and consistent with the original total correctness version. Furthermore it is shown how both partial and total correctness formulae and specifications can be translated from Hoare's logic into VDM and vice versa. VDM's satisfiability requirement is briefly discussed, and a similar condition for Hoare's logic is defined.:
The consistency theorem for free type definitions in Z
Authors: Spivey Michael
Published: February 2005

Successive editions of the author's reference manual for the Z specification language [ZRM89, ZRM92] gave different sufficient conditions for the consistency of free type definitions. Both were expressed in terms of the settheoretic constructions present in the type definition. Whilst the first edition specified that these constructions should be
continuous
, in the sense that they preserve limits of ascending chains of sets, the second edition specified that they should be
finitary
, i.e., that the result of each construction should be the union of a set of finite approximations. This short note clarifies the relationship between these two conditions.
Modular structuring of VDM specifications in VVSL
Authors: Middelburg C. A.
Published: February 2005

VVSL is a language for writing modularly structured VDM specifications. Its modularisation mechanism permits two modules to have parts of their state in common, including hidden parts. Firstly, this paper gives an overview of the structuring sublanguage of VVSL and a concise description of its semantic foundations: DA (a general algebraic model of modules) and
λπ
-calculus (a variant of classical lambda calculus). The paper also presents a variation on a “challenge problem” of Fitzgerald and Jones as an example of the use of VVSL's structuring language. Finally, their modular structuring style and the suggested language features to support it are commented upon.
When is partial trace equivalence adequate?
Authors: Bloom Bard
Published: February 2005

Two processes arepartial trace equivalentiff they can perform the same sequences of actions in isolation. Partial trace equivalence is perhaps the simplest possible notion of process equivalence. In general, it is too simple: it is not usually an adequate semantics. We investigate the circumstances under which it is adequate, which are surprisingly rich. We give two substantial classes of languages for which partial traces are adequate. In one class, partial trace equivalence suffices for total correctness, and operations such as true sequencing are possible; but all processes are determinate and silent moves are not possible. The other class — which includes many standard process calculi, such as CCS and CSP — admits indeterminacy and silent moves, but partial traces only suffice for partial correctness and true sequencing is not definable.
A theory of processes with localities
Authors: Boudol G. , Castellani I. , Hennessy M. , Kiehn A.
Published: February 2005

We study a notion of observation for concurrent processes which allows the observer to see the distributed nature of processes, giving explicit names for the location of actions. A general notion of bisimulation related to this observation of distributed systems is introduced. Our main result is that these bisimulation relations, particularized to a process algebra extending CCS, are completely axiomatizable. We discuss in detail two instances of location bisimulations, namely the location equivalence and the location preorder.
Transferrin binding capacity as a marker of differentiation and maturation of rat erythroid cells fractionated by counter current distribution in aqueous polymer two-phase systems
Authors: Sancho P. , Mendieta J. , García-Pérez A. I. , Luque J.
Published: February 2005

Rat bone marrow cell populations, containing different proportions of erythroid cells, have been fractionated by counter-current distribution in the non-charge-sensitive dextran/polyethyleneglycol two-phase systems on the basis of hydrophobic cell surface properties. Cell fractions with a low distribution coefficient, which contain non-erythroid cells and early erythoblasts, showed a low transferrin binding capacity and a low haemoglobin/cell ratio whereas cell fractions with a high distribution coefficient, which contain intermediate-late erythroblasts and mature red cells, showed an elevated transferrin binding capacity and the highest haemoglobin/cell ratio. These results support transferrin binding capacity as a good marker parameter for the erythroid bone marrow cell differentiation and maturation processes.
Chlorpromazine and other psychoactive drug induced alterations of a membrane bound enzyme in rat brain
Authors: Nag Maitreyi , Nandi Namita
Published: February 2005

Psychoactive drugs like chlorpromazine (CPZ), imipramine, lithium and amphetamine in one way or another affect behaviour. The drug responses are presumably mediated by inducing a change in the activity of membrane bound enzymes. CPZ is very potent in inhibiting the alkaline phosphatase activity in rat brain. The combined effect of CPZ with other drugs shows that CPZ and imipramine together inhibit the enzyme activity significantly greater than the individual inhibition either by CPZ or by imipramine alone. Effective inhibition of the alkaline phosphatase activity with a single drug or combined drugs may lead to a change in neuronal permeability through glucocorticoids thereby affecting mood.
Image, context and transition: smoking in mid‐to‐late adolescence
Authors: Wiltshire Susan , Amos Amanda , Haw Sally , McNeill Ann
Published: February 2005

This paper explores 16–19‐year‐old Scottish smokers’ experiences and attitudes towards smoking and their understandings of the ways in which this transitional period impacts on their smoking behaviour. The study involved 49 qualitative interviews conducted mostly in friendship pairs. Interviewees also completed a brief smoking questionnaire. The paper highlights the salience of social context in smoking initiation and maintenance, and the role of smoking across a range of social spheres. Interviewees described how transitions from school to work, further education or un/employment, impacted on their smoking. Smoking was perceived to be an important ‘lubricant’ for social relations, and marker of an acceptable identity in familiar and new contexts which acted to reinforce and increase smoking. In contrast, smoking restrictions at home, work and/or educational settings were felt to moderate consumption. This has implications for cessation programmes for older adolescents who have been relatively ignored by tobacco control. The study also suggests that if smoke‐free policies were extended to all workplaces, this would have a particular impact on smoking amongst older adolescents by hindering the transition from social to regular smoking.
The significance of economy in the Russian bi-lateral treaty process
Authors: Dusseault David , Hansen Martin Ejnar , Mikhailov Slava
Published: February 2005

In his recent article, Söderlund [Söderlund, P.J., 2003. The significance of structural power resources in the Russian bi-lateral treaty process 1994–1998. Communist and Post-Communist Studies 36, 311–324] tests structural factors that influence the order in which the Russian regions gained a bi-lateral agreement with the federal centre, emphasizing the importance of ethnicity, religion and economy. We replicate his results, and provide an extension where we argue instead that the only significant determinants of the bi-lateral process have been economic issues. Our results are substantiated by an improved methodology that addresses several debatable choices made by the author in the original article.
Biological contamination studies of lunar landing sites: implications for future planetary protection and life detection on the Moon and Mars
Authors: Glavin D.P. , Dworkin J.P. , Lupisella M. , Kminek G. , Rummel J.D.
Published: February 2005

Chemical and microbiological studies of the impact of terrestrial contamination of the lunar surface during the Apollo missions could provide valuable data to help refine future Mars surface exploration plans and planetary protection requirements for a human mission to Mars. NASA and ESA have outlined new visions for solar system exploration that will include a series of lunar robotic missions to prepare for and support a human return to the Moon, and future human exploration of Mars and other destinations. Under the Committee on Space Research's (COSPAR's) current planetary protection policy for the Moon, no decontamination procedures are required for outbound lunar spacecraft. Nonetheless, future in situ investigations of a variety of locations on the Moon by highly sensitive instruments designed to search for biologically derived organic compounds would help assess the contamination of the Moon by lunar spacecraft and Apollo astronauts. These studies could also provide valuable ‘ground truth’ data for Mars sample return missions and help define planetary protection requirements for future Mars bound spacecraft carrying life detection experiments.
Buds from the tree of life: linking compartmentalized prokaryotes and eukaryotes by a non-hyperthermophile common ancestor and implications for understanding Archaean microbial communities
Authors: Fuerst John A. , Nisbet Euan G.
Published: February 2005

The origin of the first nucleated eukaryote and the nature of the last common ancestor of the three domains of life are major questions in the evolutionary biology of cellular life on Earth, the solutions to which may be linked. Planctomycetes are unusual compartmentalized bacteria that include a membrane-bounded nucleoid. The possibility that they constitute a very deep branch of the domain Bacteria suggests a model for the evolution of the three domains of life from a last common ancestor that was a mesophile or moderate thermophile with a compartmentalized eukaryote-like cell plan. Planctomycetes and some members of the domain Archaea may have retained cell compartmentalization present in an original eukaryote-like last common ancestor of the three domains of life. The implications of this model for possible habitats of the early evolution of domains of cellular life and for interpretation of geological evidence relating to those habitats and the early emergence of life are examined here.
Semi‐rational engineering of a coral fluorescent protein into an efficient highlighter
Authors: Tsutsui Hidekazu , Karasawa Satoshi , Shimizu Hideaki , Nukina Nobuyuki , Miyawaki Atsushi
Published: February 2005

Kaede is a natural photoconvertible fluorescent protein found in the coral Trachyphyllia geoffroyi. It contains a tripeptide, His 62‐Tyr 63‐Gly 64, which acts as a green chromophore that is photoconvertible to red following (ultra‐) violet irradiation. Here, we report the molecular cloning and crystal structure determination of a new fluorescent protein, KikG, from the coral Favia favus, and its in vitro evolution conferring green‐to‐red photoconvertibility. Substitution of the His 62‐Tyr 63‐Gly 64 sequence into the native protein provided only negligible photoconversion. On the basis of the crystal structure, semi‐rational mutagenesis of the amino acids surrounding the chromophore was performed, leading to the generation of an efficient highlighter, KikGR. Within mammalian cells, KikGR is more efficiently photoconverted and is several‐fold brighter in both the green and red states than Kaede. In addition, KikGR was successfully photoconverted using two‐photon excitation microscopy at 760 nm, ensuring optical cell labelling with better spatial discrimination in thick and highly scattering tissues.
Diet and foraging behaviour of the semi-aquatic Varanus mertensi (Reptilia:Varanidae)
Authors: Mayes P. J. , Thompson G. G. , Withers P. C.
Published: February 2005

We report on the aquatic and terrestrial foraging behaviour and diet of the semi-aquatic Varanus mertensi. Foraging behaviour of V. mertensi is similar to that of other large terrestrial varanids: slow, methodical forwards movement with the head swaying from side to side with regular tongue flicks. Both olfactory and visual cues are used to detect prey. Foraging in the water is remarkably similar to that in the terrestrial environment, with this species using both visual and olfactory cues. Like other varanids, this species is able to use previous experiences to maximise its chance of locating prey. V. mertensi consume a large number of freshwater crabs (Holthuisana sp.) and a variety of small invertebrate and vertebrate prey across their distribution. Dietary differences across geographic regions are minor. Its diet is sufficiently catholic to enable it to adapt to seasonal and spatial differences in prey availability, one reason for its widespread distribution in the wet–dry tropics of Australia. Stomach contents differ from those of scats, with soft-bodied prey items being absent from scat samples.
Skinks currently assigned to Carlia aerata (Scincidae:Lygosominae) of north-eastern Queensland: a preliminary study of cryptic diversity and two new species
Authors: Couper Patrick J. , Worthington Wilmer Jessica , Roberts Lewis , Amey Andrew P. , Zug George R.
Published: February 2005

A preliminary investigation of genetic diversity in Carlia aerata, by sequencing the mitochondrial ND4 gene, revealed the presence of two cryptic species, described herein. The sequence data was added to an existing phylogeny to discern molecular relationships. Interestingly, genetic affinities lie not with C. aerata, the species to which they key. Instead, one has affinities with C. tanneri, the other with C. foliorum. This casts doubt on the validity of morphological characters alone to infer relationships within this genus. Despite low levels of genetic divergence from sister taxa, the new species can be diagnosed from these by morphological characters that exhibit little or no intraspecific variation. The addition of these new species to the gene tree did not enhance resolution of the phylogenetic relationships at the deeper nodes of the Carlia tree. The discovery of these two new cryptic species provides further support for a previously suggested rapid mid-Miocene diversification of Carlia that may have resulted from the successful expansion of a rainforest-dwelling ancestor into the expanding woodlands associated with Miocene climate fluctuations.
Using evolutionary Expectation Maximization to estimate indel rates
Authors: Holmes Ian
Published: February 2005

Motivation

The Expectation Maximization (EM) algorithm, in the form of the Baum–Welch algorithm (for hidden Markov models) or the Inside-Outside algorithm (for stochastic context-free grammars), is a powerful way to estimate the parameters of stochastic grammars for biological sequence analysis. To use this algorithm for multiple-sequence evolutionary modelling, it would be useful to apply the EM algorithm to estimate not only the probability parameters of the stochastic grammar, but also the instantaneous mutation rates of the underlying evolutionary model (to facilitate the development of stochastic grammars based on phylogenetic trees, also known as Statistical Alignment). Recently, we showed how to do this for the point substitution component of the evolutionary process; here, we extend these results to the indel process.

Results

We present an algorithm for maximum-likelihood estimation of insertion and deletion rates from multiple sequence alignments, using EM, under the single-residue indel model owing to Thorne, Kishino and Felsenstein (the ‘TKF91’ model). The algorithm converges extremely rapidly, gives accurate results on simulated data that are an improvement over parsimonious estimates (which are shown to underestimate the true indel rate), and gives plausible results on experimental data (coronavirus envelope domains). Owing to the algorithm's close similarity to the Baum–Welch algorithm for training hidden Markov models, it can be used in an ‘unsupervised’ fashion to estimate rates for unaligned sequences, or estimate several sets of rates for sequences with heterogenous rates.

Availability

Software implementing the algorithm and the benchmark is available under GPL from http://www.biowiki.org/

Contact

ihh@berkeley.edu
Recovery from DSM‐IV alcohol dependence: United States, 2001–2002
Authors: Dawson Deborah A. , Grant Bridget F. , Stinson Frederick S. , Chou Patricia S. , Huang Boji , Ruan W. June
Published: February 2005

Aims  To investigate the prevalence and correlates of recovery from Diagnostic and Statistical Manual version IV (DSM‐IV) alcohol dependence by examining the past‐year status of individuals who met the criteria for prior‐to‐past‐year (PPY) dependence.

Design  Cross‐sectional, retrospective survey of a nationally representative sample of US adults 18 years of age and over (first wave of a planned longitudinal survey).

Methods  This analysis is based on data from the 2001–02 National Epidemiologic Survey on Alcohol and Related Conditions (NESARC), in which data were collected in personal interviews conducted with one randomly selected adult in each sample household. A subset of the NESARC sample (total n = 43 093), consisting of 4422 US adults 18 years of age and over classified with PPY DSM‐IV alcohol dependence, were evaluated with respect to their past‐year recovery status: past‐year dependence, partial remission, full remission, asymptomatic risk drinking, abstinent recovery (AR) and non‐abstinent recovery (NR). Correlates of past‐year status were examined in bivariate analyses and using multivariate logistic regression models.

Findings  Of people classified with PPY alcohol dependence, 25.0% were still classified as dependent in the past year; 27.3% were classified as being in partial remission; 11.8% were asymptomatic risk drinkers who demonstrated a pattern of drinking that put them at risk of relapse; 17.7% were low‐risk drinkers; and 18.2% were abstainers. Only 25.5% of people with PPY dependence ever received treatment. Being married was associated positively with the odds of both AR and NR, and ethanol intake was negatively associated with both. Severity of dependence increased the odds of AR but decreased the odds of NR. The odds of AR (but not NR) increased with age and female gender but were decreased by the presence of a personality disorder. Treatment history modified the effects of college attendance/graduation, age at onset and interval since onset on the odds of recovery.

Conclusions  There is a substantial level of recovery from alcohol dependence. Information on factors associated with recovery may be useful in targeting appropriate treatment modalities.
Outcome criteria in smoking cessation trials: proposal for a common standard
Authors: West Robert , Hajek Peter , Stead Lindsay , Stapleton John
Published: February 2005

Smoking cessation treatment is now integrated into many health‐care systems and a major research effort is under way to improve current success rates. Until now results from randomized clinical trials have been reported in many different ways, leading to problems of interpretation. We propose six standard criteria comprising the ‘Russell Standard’ (RS). These criteria are applicable to trials of cessation aids where participants have a defined target quit date and there is face‐to‐face contact with researchers or clinic staff, as follows. (1) Follow‐up for 6 months (RS6) or 12 months (RS12) from the target quit date or the end of a predefined ‘grace period’; (2) self‐report of smoking abstinence over the whole follow‐up period allowing up to five cigarettes in total; (3) biochemical verification of abstinence at least at the 6‐month or 12‐month follow‐up point; (4) use of an ‘intention‐to‐treat’ approach in which data from all randomized smokers are included in the analysis unless they have died or moved to an untraceable address (participants who are included in the analysis are counted as smokers if their smoking status at the final follow‐up cannot be determined); (5) following‐up ‘protocol violators’ and using their true smoking status in the analysis; and (6) collecting follow‐up data blind to smokers’ allocation to trial group. We believe that these criteria provide the best compromise between practicability and surrogacy for long‐term cessation and will enable meaningful comparison between studies. There may be good reasons why other outcome criteria would also be reported, and studies that involve interventions with special groups or where there is no designated target quit date or face to face contact would need to adapt these criteria accordingly.
Eradication of Helicobacter pylori increases platelet count in patients with idiopathic thrombocytopenic purpura in Japan
Authors: Inaba T. , Mizuno M. , Take S. , Suwaki K. , Honda T. , Kawai K. , Fujita M. , Tamura T. , Yokota K. , Oguma K. , Okada H. , Shiratori Y.
Published: February 2005

Background  The effect of Helicobacter pylori eradication on the platelet count in patients with thrombocytopenic purpura is controversial. In this multicentre study, we prospectively assessed the effect of H. pylori eradication therapy in idiopathic thrombocytopenic purpura patients.

Materials and methods  Thirty‐five consecutive patients with chronic idiopathic thrombocytopenic purpura (11 males and 24 females, a median age of 57) were assessed for H. pylori infection by use of a urea breath test. All patients received 1‐week triple therapy (amoxicillin, clarithromycin, and lansoprazole) to eradicate H. pylori. At 6 months, idiopathic thrombocytopenic purpura patients with a platelet count recovery of greater than 100 × 109 L−1 were defined as idiopathic thrombocytopenic purpura responders.

Results  Helicobacter pylori infection was observed in 25 (71%) of the 35 patients. All infected patients were cured. Eleven patients were identified as idiopathic thrombocytopenic purpura responders; 24 were considered nonresponders. Platelet counts improved by more than 100 × 109 L−1 in 11 (44%) of the 25 patients cured of H. pylori infection, while none of the 10 patients H. pylori‐negative patients experienced the same improvement (P = 0·015). Univariate analysis showed that H. pylori infection and its eradication were significant factors associated with platelet recovery (P = 0·015).

Conclusions  Helicobacter pylori infection played a role in the pathogenesis of idiopathic thrombocytopenic purpura in approximately 30% of all patients assessed and 45% of the patients with H. pylori infection. Eradication of H. pylori in idiopathic thrombocytopenic purpura patients led to improved disease activity.
Quantification of dose perturbation by plaque in vascular brachytherapy
Authors: Wexberg P. , Kirisits C. , Berger D. , Sulzbacher I. , Maurer G. , Potter R. , Georg D. , Glogar D.
Published: February 2005

Background  Dose prescription and reporting in vascular brachytherapy (VBT) is based on the assumption that the vessel wall is water equivalent, which does not consider a possible dose perturbation by plaque. As the extent of this perturbation is unknown, we aimed to quantify dose attenuation by atherosclerotic plaque for beta‐ and gamma‐radiation.

Material and methods  The dose delivered from Strontium‐90/Yttrium‐90 (90Sr/Y) and Iridium‐192 (192Ir) sources with and without human peripheral arteries (90Sr/Y: n = 38, 192Ir: n = 7) surrounding the respective delivery catheter was determined with radiochromic films. Plaque and vessel wall thickness were measured using light microscopy. From the ratio‐attenuated doseunattenuated dose (dose perturbation factor: DPF) we determined averaged attenuation coefficients for atherosclerotic plaque (µP) and the residual part of the vessel wall (µW) by regression analysis based on the function DPF = exp(–µP * plaque thickness –µW * residual wall thickness).

Results  Attenuation in case of 192Ir was less than the measurement uncertainties. For beta‐radiation correlation was found by discrimination between calcified and noncalcified plaque. Classifying noncalcified plaque as normal arterial tissue, the regression coefficient was r = 0·845 at µP= 0·5356 mm−1 and µW = 0·0663 mm−1.

Conclusions  Vascular brachytherapy with beta radiation in calcified arteries results in significant dose attenuation within the vessel wall, which can be calculated on knowing the vascular morphometry. Thus, plaque thickness should be taken into account in treatment planning and retrospective analyses.
A variant Cri du Chat phenotype and autism spectrum disorder in a subject withde novocryptic microdeletions involving 5p15.2 and 3p24.3‐25 detected using whole genomic array CGH
Authors: Harvard C , Malenfant P , Koochek M , Creighton S , Mickelson ECR , Holden JJA , Lewis MES , Rajcan‐Separovic E
Published: February 2005

Cri du Chat syndrome (CdCs) is a well‐defined clinical entity, with an incidence of 1/15,000 to 1/50,000. The critical region for CdCs has been mapped to 5p15, with the hallmark cat‐like cry sublocalized to 5p15.3 and the remaining clinical features to 5p15.2. We report findings in a subject with ade novot(5;7)(p15.2;p12.2) and an inv(3)(p24q24), who was found to have a cryptic microdeletion in the critical region for CdCs detected using a 1‐Mb genomic microarray. In addition to 5p deletion, the proband had ade novosingle clone loss at the 3p breakpoint of inv(3)(p24q24) and a familial single clone deletion at 18q12. Deletions were confirmed using microsatellite analysis and fluorescencein situhybridization. The 5p deletion encompasses approximately 3 Mb, mapping to the border between bands 5p15.2 and 5p15.31. The single clone deletion on chromosome 3 maps to 3p24.3‐3p25, for which there is no known phenotype. The clinical features of our proband differ from the characteristic CdC phenotype, which may reflect the combined effect of the twode novomicrodeletions and/or may further refine the critical region for CdCs. Typical features of CdCs that are present in the proband include moderate intellectual disability, speech, and motor delay as well as dysmorphic features (e.g. broad and high nasal root, hypertelorism, and coarse facies). Expected CdCs features that are not present are growth delay, microcephaly, round facies, micrognathia, epicanthal folds, and the signature high‐pitched cry. Behavioral traits in this subject included autism spectrum disorder, attention‐deficit hyperactivity disorder, and unmanageable behavior including aggression, tantrums, irritability, and self‐destructive behavior. Several of these behaviors have been previously reported in patients with 5p deletion syndrome. Although most agree on the cat‐cry critical region (5p15.3), there is discrepancy in the precise location and size of the region associated with the more severe manifestations of CdCs. The clinical description of this proband and the characterization of his 5p deletion may help to further refine the phenotype–genotype associations in CdCs and autism spectrum disorder.
Clinical practice guidelines: barriers to durability after effective early implementation
Authors: Brand C. , Landgren F. , Hutchinson A. , Jones C. , MacGregor L. , Campbell D.
Published: February 2005

Background:  Clinical practice guidelines in general (General‐CPG) may reduce variation in clinician performance and improve patient outcomes. Short‐term evaluation is now routine, but demonstration of early successful implementation does not necessarily ensure longer‐term effectiveness.

Aim:  To assess adherence to chronic obstructive pulmonary disease (COPD)‐CPG recommendations at the Royal Melbourne Hospital (RMH), 2 years after successful implementation. To identify barriers to sustained success of General‐CPG.

Methods:  A multi‐faceted evaluation was performed to document: (i) current adherence to COPD management recommendations (medical record audit); (ii) awareness of attitudes towards and barriers for the use of COPD‐CPG and General‐CPG (staff survey, focus groups and key informant interviews) and (iii) access to and quality of available General‐CPG (internet review and random sample General‐CPG evaluation.

Results:  Adherence to COPD‐CPG recommendations was highly variable. Adherence was higher in the Emergency Department than the general wards and for specific therapeutic recommendations. It was lower for non‐pharmacological therapy and for recommendations relating to processes of care. Most health professionals were in favour of General‐CPG. Barriers to use of General‐CPG were in keeping with previous literature reports. Organizational issues including high levels of staff turnover and lack of integration of General‐CPG into hospital quality frameworks were highlighted as major barriers. Hospital intranet access and presentation of General‐CPG identified lack of consistency in terminology and presentation.

Conclusion:  Short‐term effectiveness of COPD‐CPG implementation did not ensure sustained success. Departmental organizational behaviours and organizational system barriers are major factors influencing durability. (Intern Med J 2005; 35: 162–169)
Medical history from the viewpoint of the patient
Authors: Wiltshire J.
Published: February 2005

Abstract

The patient narrative is now an established literary form, but has been largely disregarded within medicine. Medical history in general also pays only passing attention to the testimonies of individual patients. The patient narrative is not a merely contemporary development, however, but has many precursors in the past. This article outlines a project to bring medical history and the patient narrative into relationship and thereby to give the patient an intellectual history. (Intern Med J 2005; 35: 193–194)
Prolonged neglect following unilateral disruption of a prefrontal cortical–dorsal striatal system
Authors: Christakou Anastasia , Robbins Trevor W. , Everitt Barry J.
Published: February 2005

We investigated the potential function of the system formed by connections between the medial prefrontal cortex and the dorsomedial striatum in aspects of attentional function in the rat. It has been reported previously that disconnection of the same corticostriatal circuit produced marked deficits in performance of a serial, choice reaction‐time task while sparing the acquisition of an appetitive Pavlovian approach behaviour in an autoshaping task (Christakou et al., 2001). Here, we hypothesized that unilateral disruption of the same circuit would lead to hemispatial inattention, contrasting with the global attention deficit following complete disconnection of the system. Combined unilateral lesions of the medial prefrontal cortex (mPFC) and the medial caudate–putamen (mCPu) within the same hemisphere produced a severe and long‐lasting contralesional neglect syndrome while sparing the acquisition of autoshaping. These results provide further evidence for the involvement of the medial prefrontal‐dorsomedial striatal circuit in aspects of attentional function, as well as insight into the nature of neglect deficits following lesions at different levels within corticostriatal circuitry.
A role for synGAP in regulating neuronal apoptosis
Authors: Knuesel Irene , Elliott Abigail , Chen Hong‐Jung , Mansuy Isabelle M. , Kennedy Mary B.
Published: February 2005

The brain‐specific Ras/Rap GTPase‐activating protein synGAP is a major component of the postsynaptic density at glutamatergic synapses. It is a target for phosphorylation by Ca2+/calmodulin‐dependent protein kinase II, which up‐regulates its GTPase‐activating activity. Thus, SynGAP may play an important role in coupling N‐methyl‐d‐aspartate‐type glutamate receptor activation to signaling pathways downstream of Ras or Rap. Homozygous deletion of synGAP is lethal within the first few days after birth. Therefore, to study the functions of synGAP, we used the cre/loxP recombination system to produce conditional mice mutants in which gradual loss of synGAP begins at ∼ 1 week, and usually becomes maximal by 3 weeks, after birth. The resulting phenotypes fall into two groups. In a small group, the level of synGAP protein is reduced to 20–25% of wild type, and they die at 2–3 weeks of age. In a larger group, the levels remain higher than ∼ 40% of wild type, and they survive and remain healthy. In all mutants, however, an abnormally high number of neurons in the hippocampus and cortex undergo apoptosis, as detected by caspase‐3 activation. The effect is cell autonomous, occurring only in neuronal types in which the synGAP gene is eliminated. The level of caspase‐3 activation in neurons correlates inversely with the level of synGAP protein measured at 2 and 8 weeks after birth, indicating that neuronal apoptosis is enhanced by reduction of synGAP. These data show that synGAP plays a role in regulation of the onset of apoptotic neuronal death.
Descending respiratory polysynaptic inputs to cervical and thoracic motoneurons diminish during early postnatal maturation in rat spinal cord
Authors: Juvin Laurent , Morin Didier
Published: February 2005

Isolated brainstem‐spinal cord preparations were used to explore the coexistence of a direct and an indirect descending drive from the brainstem respiratory centre to cervical and thoracic respiratory motoneurons in the neonatal Sprague–Dawley rat. Polysynaptic spinal relay pathways from the respiratory centre were suppressed by selectively perfusing the cord with mephenesin (1 mm) or a solution enriched with Ca2+ and Mg2+. At birth, both direct and spinally relayed pathways are functional and contribute equally to the global descending respiratory drive. However, during the first postnatal week, significant maturational changes appear in the way the respiratory centre controls its target respiratory motoneurons in the cervical and thoracic spinal cord, with the direct respiratory drive becoming progressively predominant with maturation (from 50% to around 75% of the global descending command). The relative contributions of the monosynaptic and the polysynaptic spinal pathways may therefore have important implications for effective respiratory control during early postnatal development.
The broad‐scale ecology of energy expenditure of endotherms
Authors: Anderson Kristina J. , Jetz Walter
Published: February 2005

Energy expenditure in animals scales allometrically with body mass, but residual variation is not well understood. We examine the existing data on field metabolic rates (FMR) in endotherms for the potential role of environmental conditions. Across latitude, mass‐corrected FMR of 248 bird and mammal populations fall between two constraint lines: a lower bound that increases towards the poles and is driven by environmental factors and an upper bound that is invariant with latitude and may represent physiological limitations. This triangular pattern can be explained statistically with a multipredictor model that combines environmental conditions and species biology (including phylogeny). Lower environmental temperature and longer day length increase FMR, while taxonomy and diet explain much of the remaining variation. Combined, these effects appear to form a diversity of ‘metabolic niches’ that overall decreases from the tropics to the poles. The potential of factors related to latitude acting as constraints on the ecology and evolution of metabolic strategies in endotherms is discussed.
A framework for fostering a community of practice: scaffolding learners through an evolving continuum
Authors: Hung David , Chee Tan Seng , Hedberg John G , Thiam Seng Koh
Published: February 2005

This paper proposes a framework of an evolving community of practitioners along a simulation, participation, and codetermined interactions continuum. Simulation, participation, and codetermined interactions are three models of learning, which describe how learners can be brought through a scaffolded process within a community experience. The framework also focuses on the processes rather than on the outcomes or products of a community. In this paper, we describe a case study of a group of heads of Information and Communications Technology (ICT) in schools being scaffolded through an experiential workshop to achieve learning outcomes such as ICT‐based project work (as product) and other constructivist dispositions of learning (as processes). The proposed framework is intended to be sufficiently broad so that learners are supported from simulation to codetermined interactions where autonomy of learners’ co‐construction efforts are encouraged and experienced.
New and Emerging Contradiction Elimination Tools
Authors: Mann Darrell
Published: February 2005

The paper discusses a systematic programme of patent and science‐based research that has culminated in the production of a range of new matrices for the TRIZ toolkit, in particular, the creation of new generic matrices aimed at technical, business and software applications. The new technical matrix tool updates both the form and content of the original matrix, expanding the list of parameters it contains, increasing the inventive principle recommendations for each contradiction, and also making it easier for users to connect their specific problem to the generic framework. The paper also discusses the creation of a number of company and industry‐specific matrix tools based on the mass of research data collected, and discusses the likely future evolution of the contradiction elimination toolkit.
Direct in situ detection of cells in deep‐sea sediment cores from the Peru Margin (ODP Leg 201, Site 1229)
Authors: MAUCLAIRE L. , ZEPP K. , MEISTER P. , MCKENZIE J.
Published: February 2005

Microbiological investigations of deep‐sea sediments recovered from the Peru Margin during the ODP Leg 201 (Hole 1229A, 1–110 mbsf) demonstrated that microoganisms were a consistent component throughout the profile. Optimization of the dilution factor and DAPI‐staining procedures for direct cell counts allowed the determination of the abundance of the entire microbial community, which was about 108 cells per g dry sediment. Microbial diversity in discrete samples taken from the 110‐m profile was analysed using horseradish‐peroxydase‐rRNA‐probes. In general, the majority of the detected cells belonged to the Eubacteria kingdom with a dominance of sulphate‐reducing bacteria. The composition of the suflate‐reducing community varied with depth. Desulfobacteriaceae were dominant in the uppermost sulphate‐reducing zone and Desulfovibrionaceae at deeper depths in the upward diffusing sulphate‐rich brines. Both sulphate‐reducing groups were also detected in the methanogenic zone. Similarly, Archaea were detected throughout the profile, not only in the methanogenic zone but also in the upper and lower sulphate‐reducing zones.
Biosynthetic pathways, gene replacement and the antiquity of life
Authors: RAYMOND JASON , BLANKENSHIP ROBERT E.
Published: February 2005

The appearance of oxygen in the Earth's atmosphere, a by‐product of oxygenic photosynthesis invented by primitive cyanobacteria, stands as one of the major events in the history of life on Earth. While independent lines of geological data suggest that oxygen first began to accumulate in the atmosphere c. 2.2 billion years ago, a growing body of biomarker data purports to push this date back fully 500 million years, based on the presumption that an oxygen‐dependent biochemistry was functional at this time. Here, we present a cautionary tale in the extension of modern biochemistry into Archean biota, identifying a suite of examples of evolutionary convergence where an enzyme catalysing a highly specific, O2‐requiring reaction has an oxygen‐independent counterpart, able to carry out the same reaction under anoxic conditions. The anaerobic enzyme has almost certainly been replaced in many reactions by the more efficient and irreversible aerobic version that uses O2. We suggest that the unambiguous interpretation of Archean biomarkers demands a rigorous understanding of modern biochemistry and its extensibility into ancient organisms.
Iron reduction in the metal‐rich guts of wood‐feeding termites
Authors: VU AMY THI , NGUYEN NHA CAO , LEADBETTER JARED R.
Published: February 2005

Termites play important roles in lignocellulose and humus turnover in diverse terrestrial ecosystems, and are significant sources of global atmospheric methane and carbon dioxide. All known termite species engage in obligate, complex nutritional symbioses with their gut microbes to carry out such processes. Several hundred microbial species, representing a broad phylogenetic and physiological diversity, are found within the well‐bounded, microliter‐in‐scale gut ecosystem of a given termite. However, most of these species have never been obtained in laboratory culture, and little can be said about their functional roles in the gut community or symbiosis. Herein, an unappreciated facet of the gut chemistry and microbiology of wood‐feeding termites is revealed: the redox metabolism of iron. Gut fluids from field‐collected termites contained millimolar amounts of ferrous iron and other heavy metals. When iron(III) hydroxides were amended to a filter paper diet of Zootermopsis nevadensis, a dampwood termite collected in the San Gabriel Mountains of Southern California, the specimens accumulated high levels of iron(II) in their guts. Additionally, iron was reduced at rapid initial rates in anoxic gut homogenates prepared from field‐collected Z. nevadensis specimens. A Clostridium sp. and a Desulfovibrio sp. were isolated from dilution‐to‐extinction enrichments of Z. nevadensis gut contents and were found to reduce iron(III), as did the termite gut spirochete Treponema primitia. The iron in the guts of wood‐feeding termites may influence the pathways of carbon‐ and electron‐flow, as well as microbial community composition in these tiny ecosystems of global importance.