bluuebunny/crossref_metadata_2025 huggingface dataset:
Non‐parametric bootstrap confidence intervals for the intraclass correlation coefficient
Authors: Ukoumunne Obioha C. , Davison Anthony C. , Gulliford Martin C. , Chinn Susan
Published: December 2003

The intraclass correlation coefficient ρplays a key role in the design of cluster randomized trials. Estimates of ρ obtained from previous cluster trials and used to inform sample size calculation in planned trials may be imprecise due to the typically small numbers of clusters in such studies. It may be useful to quantify this imprecision. This study used simulation to compare different methods for assigning bootstrap confidence intervals to ρfor continuous outcomes from a balanced design. Data were simulated for combinations of numbers of clusters (10, 30, 50), intraclass correlation coefficients (0.001, 0.01, 0.05, 0.3) and outcome distributions (normal, non‐normal continuous). The basic, bootstrap‐t, percentile, bias corrected and bias corrected accelerated bootstrap intervals were compared with new methods using the basic and bootstrap‐t intervals applied to a variance stabilizing transformation of ρ. The standard bootstrap methods provided coverage levels for 95 per cent intervals that were markedly lower than the nominal level for data sets with only 10 clusters, and only provided close to 95 per cent coverage when there were 50 clusters. Application of the bootstrap‐t method to the variance stabilizing transformation of ρimproved upon the performance of the standard bootstrap methods, providing close to nominal coverage. Copyright © 2003 John Wiley & Sons, Ltd.
Estimating the incidence of subclinical infections withLegionella Pneumoniausing data augmentation: analysis of an outbreak in The Netherlands
Authors: Nagelkerke Nico J. D. , Boshuizen Hendriek C. , de Melker Hester E. , Schellekens Joop F. P. , Peeters Marcel F. , Spaendonck Marina Conyn‐van
Published: December 2003

Infections withLegionellabacteria can cause a potentially lethal form of pneumonia known as legionnaires' disease. In 1999 a major outbreak, causing 31 deaths, occurred among visitors and exhibitors of a consumer fair in The Netherlands. The epidemiology of subclinical infections is largely unknown, as there is no reliable method to diagnose such infections. To explore the incidence of subclinical infections, IgG and IgM antibody levels among exhibitors were compared to those among a representative sample of the Dutch population. As exhibitors were assumed to comprise both infected and uninfected individuals, their antibody levels were modelled as a mixture distribution. As infected individuals are expected to cluster around a point source, the spatial aspect of the spread of infections was taken into account. To estimate the distribution of antibody levels among infected individuals and to impute infection status among exhibitors, data augmentation was used. Subclinical infection appeared to be very common and its frequency declined with the distance from the putative source of the outbreak. Copyright © 2003 John Wiley & Sons, Ltd.
Power comparison of two‐sided exact tests for association in 2 × 2 contingency tables using standard, mid p and randomized test versions
Authors: Lydersen Stian , Laake Petter
Published: December 2003

Exact Pearson's chi square, likelihood ratio (LR), and Fisher's tests are obtained from the conditional distribution of its test statistic, given therow and column sums of the contingency table. The power and obtained significance level of the standard, mid p, and randomized versions of these tests are compared for two‐sided tests in 2 × 2 tables, using binomial and multinomial sampling. The mid p type I error probabilities seldom exceed thenominal significance level. The mid p and randomized test versions have approximately the same power, and higher power than the standard test version. The power of the Pearson's chi square, LR and Fisher's test differ, and they differ in approximately the same way for standard, mid p and randomized test versions for any given set of parameters. There is no general ranking between the three tests. In many cases, Pearson's chi square and Fisher's tests have almost equal power, and higher power than LR. In a few cases, perhaps characterized by poorly balanced designs, LR performs best. Fisher's test seems to be slightly more robust even if the design is poor. Copyright © 2003 John Wiley & Sons, Ltd.
Sample size re‐estimation in group‐sequential response‐adaptive clinical trials
Authors: C. Morgan Caroline
Published: December 2003

In clinical trials where the variances of the response variables are unknown, in accurate estimates of these can affect the type II error rate considerably. More accurate estimates of the variances may be obtained by taking a look at the data available part way through the trial and re‐calculating the required sample size based on these new estimates. The main impetus for sample size re‐estimation came from a two‐stage procedure developed by Stein in 1945 and the literature is now replete with variations on this approach. In this paper, existing sample size re‐estimation methods for both fixed sample and sequential clinical trial models will be reviewed. These will then be extended for use in group‐sequential response‐adaptive designs. In particular, a test for a recently developed group‐sequential response‐adaptive design, which compares two treatments with immediate normally distributed responses and unknown variances, is presented based on a modified version of Stein's test. The principal modifications involve updating the required sample size at each interim analysis and calculating thetest statistic based on the current estimates of the variances. Hence, all the available information is used at each stage. Simulation is used to assess to what extent the updating of the required sample size at each interim analysis in the new test helps to attain the nominal error rates. The test is compared to modified versions of a simple test and a Stein‐type group sequential t‐test studied in the recent literature. These tests calculate the required sample sizes based on less accurate estimates of the variances. The type I error rate is close to the nominal value and the power is more accurately maintained in the new test. Copyright © 2003 John Wiley & Sons, Ltd.
Intervention effects in observational survival studies with an application in total hip replacements
Authors: Friede Tim , Henderson Robin
Published: December 2003

Time to revision is a common and clinically relevant endpoint for studies of patients with total hip replacement. Because failures occur rarely within the first years after replacement, new surgical techniques and materials are often implemented without evidence of their effectiveness from randomized trials. Observational data may be available but this relies on the use of historical controls which has been heavily criticized. Instead the use of change‐point methods has been suggested to detect changes caused by successfully implemented interventions. In the setting of a proportional hazards model we develop a semi‐parametric changepoint method to detect changes in baseline hazard. The procedure is motivated by and applied to a clinical study in patients with total hip replacements, where the effect of a new cement type is of interest. Power properties of the proposed method are investigated. Copyright © 2003 John Wiley & Sons, Ltd.
Editorial
Authors: Cooke John , Denvir Tim
Published: December 2003

In June 1999, the first International Workshop on Integrated Formal Methods was held at York University in the UK. The primary aim of the workshop was the combination of behavioural and state-based formalisms to yield practical solutions to industrial problems.

The workshop proceedings were edited by Keijiro Araki, Andy Galloway and Kenji Taguchi and are available as “IFM99” (ISBN 1-85233-107-0, published by Springer). After the workshop, selected authors were invited to develop journal versions of their papers, incorporating further extensions, corrections and revisions. This was arranged by Andy Galloway who then passed the papers to the journal for refereeing. And here we must record our sincere thanks to Andy. Without his efforts this issue of the journal would simply not have been possible.

Following reports from referees and senior colleagues from the editorial board (and the withdrawal of one submission for publication in a book) five papers were accepted for publication here. We hope that those rejected will be further revised and resubmitted; they contained good work but required further development.

The common theme is, predictably, the marrying of component specification with control of the interconnecting system, and the first 4 papers all present variations on the theme of Z + CSP. Sühl adds an additional structuring mechanism to Z and CSP and targets his application area as real-time embedded systems, whereas Derrick and Boiten use Object-Z to give partial specifications (viewpoints) which are then combined using CSP. Smith and Hayes describe Real-time Object-Z, which results from the integration of Object-Z with timed traces, and Mahony and Dong investigate the necessary formal underpinning required to combine Timed CSP and Object-Z by means of a trace model.

The final paper, by Große-Rhode, introduces and illustrates a mechanism for checking the compatibility of different partial specifications and for coping with composite specifications in which different formalisms have been used.

Whether or not this area of formal methods research merely allows us to integrate different, more ‘appropriate’, specification languages or gives rise to new hybrid languages remains to be seen. What is certain is that there are still many problems to be tackled and technology to be transferred.
An Overview of the Integrated Formalism RT-Z
Authors: Sühl Carsten
Published: December 2003

We present an integration of the formal specification languages Z and timed CSP, called RT-Z, incorporating their combined strengths in a coherent frame. To cope with complex systems, RT-Z is equipped with structuring constructs built on top of the integration, because both Z and timed CSP lack appropriate facilities. The formal semantics of RT-Z, based on the denotational semantics of Z and timed CSP, is a prerequisite for preciseness and mathematical rigour. RT-Z is intended to be used in the requirements definition and design phases of the system and software development process. The envisaged application area is the development of real-time embedded systems.
POP, A Broad-Spectrum Programming Language, 1967–2002
Authors: Popplestone Robin
Published: December 2003

This paper discusses the POP-2 language and Multipop time-sharing system developed during the second half of the 1960s. POP-2's expressiveness spanned numeric and symbolic programming and supported experiments in logic of programming languages (by Boyer and Moore) and programming language concepts (for example, Michie's memoisation). The paper also discusses how the goals of POP-2 might be achieved in a successor language.
Shallow Linear Action Graphs and their Embeddings
Authors: Leifer James J. , Milner Robin
Published: December 2003

Action calculi, which generalise process calculi such as Petri nets, π-calculusand ambient calculus, have been presented in terms ofaction graphs. We here offerlinearaction graphs as a primitive basis for action calculi. This paper presents the category of embeddings of undirected linear action graphs without nesting, using a novel form of graphical reasoning which simplifies some otherwise complex manipulations in regular algebra. The results are adapted in a few lines to directed graphs. This work is part of a long-term search for a uniform behavioural theory for process calculi.
Testing Conditions for Communicating Stream X-machine Systems
Authors: Ipate Florentin , Holcombe Mike
Published: December 2003

X-machines were proposed by Holcombe as a possible specification language and since then a number of further investigations have demonstrated that the model is intuitive and easy to use. In particular,
stream X-machines
(
SXM
), a particular class of X-machines, have been found to be extremely useful in practice. Furthermore, a method of testing systems specified as SXMs exists and is proved to detect all faults of the implementation provided that the system meets certain
“design for test conditions”
. Recently, a
system of communicating SXMs
was introduced as a means of modelling parallel processing. This paper proves that each communicating machine component can be transformed in a straightforward manner so that the entire system will behave like a single stream X-machine - the equivalent SXM of the system. The paper goes on to investigate the applicability of the SXM testing method to a system of communicating SXMs and identifies a class of communicating SXMs for which the equivalent SXM of the system meets the “design for test conditions”.
Distributing Finite Automata Through Petri Net Synthesis
Authors: Badouel Éric , Caillaud Benoît , Darondeau P.
Published: December 2003

The synthesis problem for Petri nets consists in deciding constructively the existence of a Petri net with sequential state graph isomorphic to a given graph. If events are attached to locations, one may set as an additional requirement that the synthesised net should be distributable; i.e. such that events at different locations have no common input place, whence distributed conflicts are avoided. Distributable nets are easily implemented by finite families of automata (one per location) communicating with each other by asynchronous message passing. We show that the general Petri net synthesis problem and its distributed version may both be solved in time polynomial in the size of the given graph. We report on some preliminary experiments of Petri net synthesis applied to the distribution of reactive automata using the tool

SYNET

.
Editorial
Authors: COOKE JOHN
Published: December 2003

At the time of writing this editorial, subscribers will have just received their copies of the triple issue honouring the work of Rod Burstall. Coordinating this collection was a substantial undertaking; and thanks go to all concerned, particularly to David Rydeheard and Don Sannella and the behind the scenes production staff. We (the journal editors) hope you agree that it was well worth waiting for the fascinating collection.

The production and scheduling of that set of papers, and other incidental but cumulative factors, have contributed to recent issues being late. We hope soon to be back close to our planned, evenly timed, publication timetable; however it also seems timely to mention, and to reiterate, some changes which are afoot.

As of this issue (14.1) we shall revert to our initial publication frequency of 4 issues per year, but these will be larger than in earlier volumes and will retain the large page format adopted in Volume 12. [A reminder for authors who use LaTeX to use the new class files.] We are now receiving, and publishing, long papers (but still with the option of including supplementary material on the web) and, except in special issues, strive to achieve a reasonable coverage of topics within the given constraints.

Although normally skipped over, readers of the journal front matter might notice periodic changes to the editorial board. These usually go unmentioned; our editors (who are working editors, not merely ‘names’) seek no reward or praise. Readers will also notice the recently modernised BCS-FACS logo and a declaration that the journal (although truly international in scope) was founded by (BCS-)FACS, some even to this day refer to it as ‘the FACS journal’, and we are very happy for this to continue.

Bringing these two threads together gets me to the point of this digression. Dan Simpson founded the BCS specialist group on Formal Aspects of Computing Science some 25 years ago. Without his radical suggestion that the BCS had a specialist group that actually addressed Computer Science, there would have been no FACS and no FACS journal. Dan has recently finished his spell as Dean in the Faculty of IT at Brighton University and he has also resigned as a member of our editorial board. As you can see, he was active to the very end being responsible for progressing 2 of the 3 papers in this issue. I gather he now intends to concern himself with other matters; I would counsel a less stressful life and more Bob Dylan music.

He has been a friend and colleague of many of those associated with the FACS group and its journal; on their behalf may I offer a big ‘thank you’ for all that you have done for us and offer our best wishes for whatever endeavours you are about to embark upon. Very many years ago, at a conference, I heard someone respond in debate “I didn't see who said that but it sounded like Mr Simpson from Teesside … .” – well it's no longer ‘Mr’ nor ‘Teesside’ but I can't believe that we really have seen or heard the last of this Yorkshire lad.

Thanks, goodbye and good luck.
A Mechanically Proved and Incremental Development of IEEE 1394 Tree Identify Protocol
Authors: Abrial Jean-Raymond , Cansell Dominique , Méry Dominique
Published: December 2003

The IEEE 1394 tree identify protocol illustrates the adequacy of the
event-driven approach
used together with the B Method. This approach provides a complete framework for developing mathematical models of distributed algorithms. A specific development is made of a series of more and more refined models. Each model is made of a number of static properties (the invariant) and dynamic parts (the guarded events). The internal consistency of each model as well as its correctness with regard to its previous abstraction are proved with the proof engine of Atelier B, which is the tool associated with B. In the case of IEEE 1394 tree identify protocol, the initial model is very primitive: it provides the basic properties of the graph (symmetry, acyclicity, connectivity), and its dynamic parts essentially contain a single event which
elects the leader
in one shot. Further refinements introduce more events, showing how each node of the graph non-deterministically participates in the leader election. At some stage in the development, message passing is introduced. This raises a specific potential contention problem, whose solution is given. The last stage of the refinement completely localises the events by making them take decisions based on local data only.
Minimal, rigid foliations by curves on $\mathbb{CP}^n$
Authors: Loray Frank , Rebelo Julio C.
Published: December 2003

We prove the existence of
minimal
and
rigid
singular holomorphic foliations by curves on the projective space

\mathbb{CP}^n

for every dimension

n≥ 2

and every degree

d ≥ 2

. Precisely, we construct a foliation

\mathcal F

which is induced by a homogeneous vector field of degree

d

, has a finite singular set and all the regular leaves are dense in the whole of

\mathbb{CP}^n

. Moreover,

\mathcal F

satisfies many additional properties expected from chaotic dynamics and is rigid in the following sense: if

\mathcal F

is conjugate to another holomorphic foliation by a homeomorphism sufficiently close to the identity, then these foliations are also conjugate by a projective transformation. Finally, all these properties are persistent for small perturbations of

\mathcal F

.

This is done by considering pseudo-groups generated on the unit ball

\mathbb{B}^n ⊂ \mathbb{C}^n

by small perturbations of elements in

\mathrm{Diff}(\mathbb{C}^n,0)

. Under open conditions on the generators, we prove the existence of many pseudo-flows in their closure (for the

C^0

-topology) acting transitively on the ball. Dynamical features as minimality, ergodicity, positive entropy and rigidity may easily be derived from this approach. Finally, some of these pseudo-groups are realized in the transverse dynamics of polynomial vector fields in

\mathbb{CP}^n

.
Canonical contact forms on spherical CR manifolds
Authors: WANG WEI
Published: December 2003

We construct the CR invariant canonical contact form can(J) on scalar positive spherical CR manifold (M,J), which is the CR analogue of canonical metric on locally conformally flat manifold constructed by Habermann and Jost. We also construct another canonical contact form on the Kleinian manifold OHgr(Gamma)/Gamma, where Gamma is a convex cocompact subgroup of AutCRS2n+1=PU(n+1,1) and OHgr(Gamma) is the discontinuity domain of Gamma. This contact form can be used to prove that OHgr(Gamma)/Gamma is scalar positive (respectively, scalar negative, or scalar vanishing) if and only if the critical exponent delta(Gamma)n, or delta(Gamma)=n). This generalizes Nayatanirsquos result for convex cocompact subgroups of SO(n+1,1). We also discuss the connected sum of spherical CR manifolds.
Rigidity and gluing for Morse and Novikov complexes
Authors: Cornea Octav , Ranicki Andrew
Published: December 2003

We obtain rigidity and gluing results for the Morse complex of a real-valued Morse function as well as for the Novikov complex of a circle-valued Morse function. A rigidity result is also proved for the Floer complex of a hamiltonian defined on a closed symplectic manifold (M,ohgr) with c1|pgr2(M)=[ohgr]|pgr2(M)=0. The rigidity results for these complexes show that the complex of a fixed generic function/hamiltonian is a retract of the Morse (respectively Novikov or Floer) complex of any other sufficiently C0 close generic function/hamiltonian. The gluing result is a type of Mayer-Vietoris formula for the Morse complex. It is used to express algebraically the Novikov complex up to isomorphism in terms of the Morse complex of a fundamental domain. Morse cobordisms are used to compare various Morse-type complexes without the need of bifurcation theory.
Functions with prescribed singularities
Authors: Alberti Giovanni , Baldo S. , Orlandi Giandomenico
Published: December 2003

The distributional k-dimensional Jacobian of a map u in the Sobolev space W1,k-1 which takes values in the the sphere Sk-1 can be viewed as the boundary of a rectifiable current of codimension k carried by (part of) the singularity of u which is topologically relevant. The main purpose of this paper is to investigate the range of the Jacobian operator; in particular, we show that any boundary M of codimension k can be realized as Jacobian of a Sobolev map valued in Sk-1. In case M is polyhedral, the map we construct is smooth outside M plus an additional polyhedral set of lower dimension, and can be used in the constructive part of the proof of a Gamma-convergence result for functionals of Ginzburg-Landau type, as described in [2].
Handle attaching in symplectic homology and the Chord Conjecture
Authors: Cieliebak Kai
Published: December 2003

Arnold conjectured that every Legendrian knot in the standard contact structure on the 3-sphere possesses a characteristic chord with respect to any contact form. I confirm this conjecture if the know has Thurston-Bennequin invariant m1. More generally, existence of chords is proved for a standard Legendrian unknot on the boundary of a subcritical Stein manifold of any dimension. There is also a multiplicity result which implies in some situations existence of infinitely many chords. The proof relies on the behaviour of symplectic homology under handle attaching. The main observation is that symplectic homology only changes in the presence of chords.
Regularity of minimizers of the calculus of variations in Carnot groups via hypoellipticity of systems of Hörmander type
Authors: Capogna Luca , Garofalo Nicola
Published: December 2003

We prove the hypoellipticity for systems of Hörmander type with constant coefficients in Carnot groups of step 2. This result is used to implement blow-up methods and prove partial regularity for local minimizers of non-convex functionals, and for solutions of non-linear systems which appear in the study of non-isotropic metric structures with scalings. We also establish estimates of the Hausdorff dimension of the singular set.
The lateral line of zebrafish: a model system for the analysis of morphogenesis and neural development in vertebrates
Authors: Dambly‐Chaudière Christine , Sapède Dora , Soubiran Fabien , Decorde Kelly , Gompel Nicolas , Ghysen Alain
Published: December 2003

Abstract The lateral line of the zebrafish has many of the advantages that made the sensory organs of Drosophila a very productive model system: 1) it comprises a set of discrete sense organs (neuromasts) arranged in a defined, species‐specific pattern, such that each organ can be individually recognized; 2) the neuromasts are superficial and easy to visualize, and the innervating neurons are easy to label; 3) the sensory projection is simple yet reproducibly organized. Here we describe some of the tools that can be used to investigate the development of this system, and we illustrate their usefulness with specific exemples. We conclude that the lateral line is uniquely suited among vertebrate sensory systems for a molecular, cellular and genetic analysis of pattern formation and of neural development.
Does angiotensin‐converting enzyme gene polymorphism affect blood pressure? Findings after 6 years of follow‐up in healthy subjects
Authors: Di Pasquale Pietro , Cannizzaro Sergio , Paterna Salvatore
Published: December 2003

Background:

There has been an increase in research into the association between angiotensin‐converting enzyme (ACE) gene deletion polymorphism and cardiovascular disease, with conflicting results. The present prospective long‐term study was conducted to evaluate whether the DD genotype could also be associated with a higher prevalence of hypertension in healthy subjects, over 6 years of follow‐up.

Methods:

Population: 684 healthy volunteers (aged, 25–55 years): normotensive and free of cardiovascular diseases, with acceptable echocardiographic window. All subjects had to have a normal electrocardiogram (ECG) and echocardiogram (ECHO) at entry.

Study protocol:

All subjects underwent a complete physical examination, 12‐lead ECG and ECHO, and venous blood samples were drawn for DNA analysis and cholesterol. All subjects had a clinical evaluation each year for the 6 year duration of the study.

Results:

All 684 subjects completed 6 years of follow‐up. We identified three genetically distinct groups. The ACE‐DD group (n=225, 80F/145M, mean age 43.4±7.6 years) had 42 hypertensive subjects (18.3%), 5 heart failure (HF) subjects and 6 subjects with acute coronary syndromes (ACS). There was no association between family history, smoking habit, hypercholesterolemia and events. The ACE‐ID group (n=335, 116F/219M, mean age 43.6±7 years) had 16 hypertensive subjects (4.7%) and 3 subjects with ACS. The ACE‐II group (n=124, 45F/79M, mean age 42.5±6.9 years) had 2 hypertensive subjects (1.6%) and 1 HF subject. The incidence of hypertension and cardiovascular events was significantly higher in the ACE‐DD group (53 cases, 23%) than in the ACE‐ID and ACE‐II groups (20 and 3 cases, 5.9 and 2.4%, respectively), P=0.0001. The higher incidence of hypertension was observed in the older age groups (36–45 and 46–55 years) with ACE‐DD and ACE‐ID genotypes.

Conclusion:

Our data suggest that ACE‐DD polymorphism is associated with a higher incidence of hypertension in baseline healthy subjects, irrespective of other risk factors. The higher incidence of hypertension was apparent predominantly in the older age groups.
Self‐inflicted cesarean section with maternal and fetal survival
Authors: Molina‐Sosa A. , Galvan‐Espinosa H. , Gabriel‐Guzman J. , Valle R.F.
Published: December 2003

An unusual case of self‐inflicted cesarean section with maternal and child survival is presented. No similar event was found in an Internet literature search. Because of a lack of medical assistance and a history of fetal death in utero, a 40‐year‐old multiparous woman unable to deliver herself alone vaginally sliced her abdomen and uterus and delivered her child. She was transferred to a hospital where she underwent repair of the incisions and had to remain hospitalized. Mother and child survived the event. Unusual and extraordinary measures to preserve their offspring sometimes moves women to extreme decisions endangering their own lives. Social, educational, and health measures should be instituted all over the world, particularly in rural areas of developing countries, to avoid such extreme events.
Inhibitor‐induced structural change of the active site of human poly(ADP‐ribose) polymerase
Authors: Kinoshita Takayoshi , Nakanishi Isao , Warizaya Masaichi , Iwashita Akinori , Kido Yoshiyuki , Hattori Kouji , Fujii Takashi
Published: December 2003

The crystal structure of human recombinant poly(ADP‐ribose) polymerase (PARP) complexed with a potent inhibitor, FR257517, was solved at 3.0 Å resolution. The fluorophenyl part of the inhibitor induces an amazing conformational change in the active site of PARP by motion of the side chain of the amino acid, Arg878, which forms the bottom of the active site. Consequently, a corn‐shaped hydrophobic subsite, which consists of the side chains of Leu769, Ile879, Pro881, and the methylene chain of Arg878, newly emerges from the well‐known active site.
Cytokines regulate the affinity of soluble CD44 for hyaluronan
Authors: Cichy Joanna , Puré Ellen
Published: December 2003

CD44, a receptor for the extracellular matrix glycosaminoglycan hyaluronan, has been implicated in many adhesion‐dependent cellular processes including tumor growth and metastasis. Soluble CD44 has been identified in the serum of normal individuals. Furthermore, tumor progression is often associated with marked increases in plasma levels of soluble CD44. Release of soluble CD44 by proteolytic cleavage (shedding) of membrane‐anchored CD44 is likely to alter cellular responses to the environment due to modification of the cell surface and the potential for soluble CD44 to influence CD44‐mediated hyaluronan binding to cell surfaces. Cellular activation is typically required to induce hyaluronan binding to cell surface CD44 but the affinity of endogenous soluble CD44 for hyaluronan remains unknown. In this study, we demonstrate that oncostatin M and transforming growth factor β1 (TGF‐β1) which stimulate hyaluronan binding to HTB58 lung epithelial‐derived tumor cells, also induce the release of soluble CD44. Interestingly, soluble CD44 released by oncostatin M‐treated cells retained the ligand‐binding properties of the membrane‐anchored receptor. In contrast, soluble CD44 released from TGF‐β1‐treated HTB58 cells differed in its hyaluronan‐binding capacity from cell surface CD44 expressed on TGF‐β1‐stimulated cells. These data indicate that the mechanisms that regulate the generation of soluble CD44 may also govern the binding of the released receptor to hyaluronan and therefore determine the impact on CD44‐dependent physiologic and pathologic processes.
Identification and characterization of a novel Δ6‐fatty acid desaturase gene from Rhizopus arrhizus
Authors: Zhang Qi , Li Mingchun , Ma Haiting , Sun Ying , Xing Laijun
Published: December 2003

A cDNA sequence putatively encoding a Δ6‐fatty acid desaturase was isolated from Rhizopus arrhizus using reverse transcription polymerase chain reaction and rapid amplification of cDNA ends methods. Sequence analysis indicated that this cDNA sequence had an open reading frame of 1377 bp encoding 458 amino acids of 52 kDa. The deduced amino acid sequence showed high similarity to those of fungal Δ6‐fatty acid desaturases which comprised the characteristics of membrane‐bound desaturases, including three conserved histidine‐rich motifs and hydropathy profile. A cytochrome b
5‐like domain was observed at the N‐terminus. To elucidate the function of this novel putative desaturase, the coding sequence was expressed heterologously in Saccharomyces cerevisiae strain INVScl. The result demonstrated that the coding product of the sequence exhibited Δ6‐fatty acid desaturase activity by the accumulation of γ‐linolenic acid.
AtPNP‐A is a systemically mobile natriuretic peptide immunoanalogue with a role in Arabidopsis thaliana cell volume regulation
Authors: Morse Monique , Pironcheva Ganka , Gehring Chris
Published: December 2003

Cellular and physiological evidence suggests the presence of a novel class of systemically mobile plant molecules that are recognized by antibodies against vertebrate atrial natriuretic peptides (ANPs). In order to characterize the function of these immunoanalogues we have expressed the full‐length recombinant (AtPNP‐A[1–126]) and demonstrate that this molecule induces osmoticum‐dependent H2O uptake into protoplasts at nanomolar concentrations and thus affects cell volume. A similar response is also seen with a recombinant that does not contain the signal peptide (AtPNP‐A[26–126]) as well as a short domain (AtPNP‐A[33–66]) that shows homology to the vertebrate peptide. Taken together, these findings suggest that AtPNP‐A has an important and systemic role in plant growth and homeostasis.
The V‐PLC3 gene encodes a putative plasma membrane‐localized phosphoinositide‐specific phospholipase C whose expression is induced by abiotic stress in mung bean (Vigna radiata L.)1
Authors: Kim Yun Ju , Kim Jee Eun , Lee Jae-Hoon , Lee Myoung Hui , Jung Ho Won , Bahk Young Yil , Hwang Byung Kook , Hwang Inhwan , Kim Woo Taek
Published: December 2003

Phosphoinositide‐specific phospholipase C (PI‐PLC) catalyzes the hydrolysis of phosphatidylinositol 4,5‐bisphosphate to generate inositol 1,4,5‐trisphosphate and diacylglycerol, both of which act as secondary messengers in animal cells. In this report, we identified in Vigna radiata L. (mung bean) three distinct partial cDNAs (pVr‐PLC1, pVr‐PLC2, and pVr‐PLC3), which encode forms of putative PI‐PLC. All three Vr‐PLC genes were transcriptionally active and displayed unique patterns of expression. The Vr‐PLC1 and Vr‐PLC2 transcripts were constitutively expressed to varying degrees in every tissue of mung bean plants examined. In contrast, the Vr‐PLC3 mRNA level was very low under normal growth conditions and was rapidly induced in an abscisic acid‐independent manner under environmental stress conditions (drought and high salinity). An isolated genomic clone, about 8.2 kb in length, showed that Vr‐PLC1 and Vr‐PLC3 are in tandem array in the mung bean genome. The predicted primary sequence of Vr‐PLC3 (M
r=67.4 kDa) is reminiscent of the δ‐isoform of animal enzymes which contain core sequences found in typical PI‐PLCs, such as the catalytic domain comprising X and Y motifs, a lipid‐binding C2 domain, and the less conserved EF‐hand domain. Results of in vivo targeting experiment using a green fluorescent protein (GFP) showed that the GFP‐Vr‐PLC3 fusion protein was localized primarily to the plasma membrane of the Arabidopsis protoplast. The C2 domain was essential for Vr‐PLC3 to be targeted to the plasma membrane. The possible biological functions of stress‐responsive Vr‐PLC3 in mung bean plants are discussed.
Structural implications for heavy metal‐induced reversible assembly and aggregation of a protein: the case of Pyrococcus horikoshii CutA1
Authors: Tanaka Yoshikazu , Tsumoto Kouhei , Nakanishi Takeshi , Yasutake Yoshiaki , Sakai Naoki , Yao Min , Tanaka Isao , Kumagai Izumi
Published: December 2003

CutA is a small protein that appears to be involved in the mechanism of divalent metal cation tolerance in microorganisms. Here we report the crystal structure of Pyrococcus horikoshii CutA (PhoCutA), with and without Cu2+, and its metal‐binding properties. Crystallographic analyses revealed that PhoCutA forms a stable trimeric structure with intertwined antiparallel β‐strands. The crystal structure of the Cu2+–PhoCutA complex shows that the Cu2+ is located at a trimer–trimer interface and is recognized by the side chains of one Asp48 from each trimer. In an in vitro experiment, PhoCutA bound to several heavy metals, most of which led to reversible aggregation of the protein; i.e. the aggregates could be completely solubilized by addition of ethylenediamine tetraacetic acid (EDTA) or dialysis against metal free buffer. Substitution of Asp48 with Ala led to a decrease in the amount of aggregates, suggesting the significant contribution of Asp48 to the reversible aggregation. To the best of our knowledge, this is the first report which provides the structural evidence for heavy metal‐induced multimerization of a protein.
Delivery of antisense peptide nucleic acids (PNAs) to the cytosol by disulphide conjugation to a lipophilic cation
Authors: Filipovska Aleksandra , Eccles Michael R , Smith Robin A.J , Murphy Michael P
Published: December 2003

Peptide nucleic acids (PNAs) are effective antisense reagents that bind specific mRNAs preventing their translation. However, PNAs cannot cross cell membranes, hampering delivery to cells. To overcome this problem we made PNAs membrane‐permeant by conjugation to the lipophilic triphenylphosphonium (TPP) cation through a disulphide bond. The TPP cation led to efficient PNA uptake into the cytoplasm where the disulphide bond was reduced, releasing the antisense PNA to block expression of its target gene. This method of directing PNAs into cells is a significant improvement on current procedures and will facilitate in vitro and pharmacological applications of PNAs.
Construction of a plasminogen activator inhibitor‐1 variant without measurable affinity to vitronectin but otherwise normal
Authors: Jensen Jan K , Durand Michelle K.V , Skeldal Sune , Dupont Daniel M , Bødker Julie S , Wind Troels , Andreasen Peter A
Published: December 2003

Vitronectin (VN) and plasminogen activator inhibitor‐1 (PAI‐1) have important functional interactions: VN stabilises the protease inhibitory activity of PAI‐1 and PAI‐1 inhibits binding of adhesion receptors to VN. Having previously mapped the PAI‐1 binding area for VN, we have now constructed a PAI‐1 variant, R103A‐M112A‐Q125A, without measurable affinity to VN, but with full protease inhibitory activity and endocytosis receptor binding. As a tool for evaluating the physiological and pathophysiological functions of the PAI‐1–VN interaction, our new variant is far superior to the previously widely used PAI‐1 variant Q125K, which we have found possesses an only about 10‐fold reduced affinity to VN.
Efficient and cost‐effective experimental determination of kinetic constants and data: the success of a Bayesian systematic approach to drug transport, receptor binding, continuous culture and cell transport kinetics
Authors: Murphy Emma F. , Gilmour Steven G. , Crabbe M.James C.
Published: December 2003

Details about the parameters of kinetic systems are crucial for progress in both medical and industrial research, including drug development, clinical diagnosis and biotechnology applications. Such details must be collected by a series of kinetic experiments and investigations. The correct design of the experiment is essential to collecting data suitable for analysis, modelling and deriving the correct information. We have developed a systematic and iterative Bayesian method and sets of rules for the design of enzyme kinetic experiments. Our method selects the optimum design to collect data suitable for accurate modelling and analysis and minimises the error in the parameters estimated. The rules select features of the design such as the substrate range and the number of measurements. We show here that this method can be directly applied to the study of other important kinetic systems, including drug transport, receptor binding, microbial culture and cell transport kinetics. It is possible to reduce the errors in the estimated parameters and, most importantly, increase the efficiency and cost‐effectiveness by reducing the necessary amount of experiments and data points measured.
Middle Permian plume‐related magmatism of the Hawasina Nappes and the Arabian Platform: Implications on the evolution of the Neotethyan margin in Oman
Authors: Maury René C. , Béchennec François , Cotten Joseph , Caroff Martial , Cordey Fabrice , Marcoux Jean
Published: December 2003

Permian pillow basalts are commonly found in Oman either at the base of the Hawasina Nappes or within the Arabian Platform successions exposed in the Saih Hatat tectonic window. There is an ongoing debate on whether these lavas include normal mid‐oceanic ridge basalts (NMORB) witnessing the Permian opening of the Neotethys or if they are plume‐related magmas that are emplaced either on the Arabian Platform or on its thinned continental margin. We sampled these lavas from several paleontologically dated middle Permian sites. Four of them (Buday'ah, Rustaq, Al Ajal, and Wadi Wasit) are located within the Hawasina Nappes and are exposed as thrust slices overlain by the Samail Nappe, and one (Wadi Aday) is within the Arabian Platform units and is exposed in the Saih Hatat window. These lavas are associated with marine sediments deposited in environments ranging from proximal (Saih Hatat, Wadi Wasit, and base of the thrust pile of Al Ajal) to distal (Buday'ah, Rustaq, and top of the Al Ajal pile) with respect to the Arabian Platform. Major and trace element features of the basalts allow two groups to be recognized. Enriched high‐Ti basalts similar to alkali basalts from intracontinental traps, rifted continental zones, and oceanic islands are exposed in Wadi Aday, Wadi Wasit, and at the structural base of the Al Ajal pile. Moderately enriched to slightly depleted low‐Ti tholeiitic basalt magmas resembling the low‐Ti flood basalts and those from seaward dipping reflector sequences are represented in Wadi Al Hulw in Saih Hatat, Buday'ah, Rustaq, and at the top of the Al Ajal thrust pile. Both groups show distinct plume‐related trace element signatures, and they do not include typical NMORB. Although emplaced in shallow to deep submarine environments, these basalts provide no direct evidence for a Neotethyan seafloor‐spreading event in the Hawasina Basin. Instead, they were likely erupted through the crust of the already rifted and drowned Arabian continental margin. Thus, despite their characteristic plume‐related geochemical signatures, the middle Permian basalts from Oman were not likely emplaced during the evolution of a typical volcanic rifted margin. We suggest that they originated from a mantle plume which ascended beneath the Arabian passive margin well after the initiation of seafloor spreading of the Neotethys.
Architecture of the Focşani Depression: A 13 km deep basin in the Carpathians bend zone (Romania)
Authors: Tărăpoancă M. , Bertotti G. , Maţenco L. , Dinu C. , Cloetingh S. A. P. L.
Published: December 2003

In front of the SE Carpathians Bend a very deep basin (Focşani Depression) developed in Miocene to Recent times. An important part of its subsidence occurred after the main stages of thrusting in the Carpathians. Apparently, the basin lies in the “wrong” place and evolved in the “wrong” time. In this study, we constrain its architecture and evolution by analyzing a large database consisting of more than 1000 km two‐dimensional seismic lines and more than 60 wells. Around 13 km thick, Badenian‐to‐Quaternary (<16.5 Myr) sediments were deposited in the central part of the Focşani Depression. During the Badenian (16.5–13 Myr), the foreland (south of Trotuş fault) underwent NE‐SW directed extension and NW trending basins opened in the eastern Moesian platform. A NW‐SE oriented area of subsidence stretched from the Transylvania basin through the Focşani Depression to the SE of the Moesian platform while thrusting was going on in the East European/Scythian platform, East Carpathians, and Getic Depression. Starting with the Sarmatian (13–10 Myr), the Focşani Depression depocenter moved out of the Carpathian belt coeval with the exhumation of the south and the East Carpathians north of the Trotuş fault. The basin became wider and was tilted toward the belt. Tilting was accompanied by dextral shearing mainly along the Intramoesian and Peceneaga‐Camena faults. After Sarmatian times, subsidence occurred practically only SSE of Trotuş fault. During Meotian‐Pontian (10–5 Myr), subsidence slowed down. Stronger, Pliocene‐Quaternary subsidence is coeval with normal faulting and shearing in Moesian platform. The western margin of the Focşani Depression was then tilted eastward, coeval with the exhumation of the bend zone and opening of the intramontane basins in the inner part of the belt.
SAGE III observations of Arctic polar stratospheric clouds – December 2002
Authors: Poole Lamont R. , Trepte Charles R. , Harvey V. Lynn , Toon Geoffrey C. , VanValkenburg Randal L.
Published: December 2003

Stratospheric Aerosol and Gas Experiment (SAGE) III aerosol extinction data from the Arctic in December 2002 are presented and used to illustrate the instrument's capability for polar stratospheric cloud (PSC) observations. Numerous PSCs were observed during the month at potential temperatures from about 450–700 K, and Types 1a and 1b PSCs could be discriminated in plots of 1022‐nm extinction versus color ratio (the ratio of 1022‐nm and 449‐nm extinctions). Type 1a (1b) PSCs were observed primarily above (below) a threshold temperature of 4 K below the nitric acid trihydrate (NAT) equilibrium temperature. Mie calculations show that some of the Type 1a PSC observations are consistent with a mixture of background aerosol and very few large NAT particles. This suggests that SAGE III offers the potential for systematic observations of these clouds, which would greatly improve our understanding of how they form and lead to stratospheric denitrification.
Sub‐daily sea ice motion and deformation from RADARSAT observations
Authors: Kwok Ron , Cunningham Glenn F. , Hibler William D.
Published: December 2003

We find a persistent level of oscillatory sea ice motion and deformation, superimposed on the large‐scale wind‐driven field, in May 2002 (spring) and February 2003 (mid‐winter), in the high Arctic over a region centered at ∼(85°N, 135°W). At this latitude, the RADARSAT wide‐swath SAR coverage provides 4–5 sequential observations every day, for ice motion retrieval, with a sampling interval at the orbital period of ∼101 minutes. Periodic correlations in ice motion and deformation can be seen in length scales from 10 km and above, and suggest a 12‐hr oscillation that is more likely associated with inertial rather than tidal frequencies. Divergence/convergence of ∼0.1–0.2% peak‐to‐peak or rates of ∼10−7/s is seen in both datasets, with the mid‐winter dataset having smaller values. These observations are remarkable in that short‐period ice motion is previously believed to be inhibited by the strength of the ice pack in the high Arctic during winter. New ice production due to the recurrent openings and closings at these temporal scales, if ubiquitous, could be significant within the winter pack.