bluuebunny/crossref_metadata_2025 huggingface dataset:
Validation of an Alt locus for aluminium tolerance scored with eriochrome cyanine R staining method in barley cultivar Honen (Hordeum vulgare L.)
Authors: Wang Junping , Raman Harsh , Read Barbara , Zhou Meixue , Mendham Neville , Venkatanagappa Shoba
Published: January 2006

Aluminium (Al) phytotoxicity is one of the major constraints for barley (Hordeum vulgare L.) production on acid soils. Genetic variation for Al tolerance is present in barley germplasm. Previous studies have shown that Al tolerance in cv. Dayton and WB229 is controlled by a single locus on 4H. The present study was conducted to investigate the genetic control of Al tolerance in Japanese barley cv. Honen, and validate the linkage relationship between the Al tolerance locus and the molecular markers established previously. An F3 progeny representing 94 F2s from the cross of F6ant28B48-16 (Al sensitive) × Honen (Al tolerant) was evaluated for Al tolerance by staining roots with eriochrome cyanine R. A single Al tolerance locus Alt was validated on the long arm of chromosome 4H in Honen. Single sequence repeat (SSR) markers Bmag353 and HVM68 flanked the Alt locus at a distance of 1.6 ± 0.9 and 5.1 ± 1.7 cM, respectively. Our results have shown that the linkage between SSR markers and the Al tolerance locus can be used to characterise the ‘unknown source’ for Al tolerance.
Variation among Australian accessions of the wild mungbean (Vigna radiata ssp. sublobata) for traits of agronomic, adaptive, or taxonomic interest
Authors: Lawn R. J. , Rebetzke G. J.
Published: January 2006

The wild mungbean, Vigna radiata ssp. sublobata, is an ‘old world’ tropical species indigenous throughout the better watered areas of northern Australia. Variation among 115 accessions, mainly from Australia, West Timor, and Papua New Guinea, was evaluated for several diverse traits. The plants were cultivated in the field at 2 sowing dates, at both a tropical and a subtropical location, with 6 accessions from India and a mungbean cultivar for comparison. Substantial variation was identified for traits of potential agronomic, adaptive, or taxonomic interest. For some traits, like phenology, the variation appeared to be systematic, with plausible underlying physiological and/or adaptive explanation. Among accessions, wild type traits, like prostrate habit, more gracile morphology, twining form, and small hard seeds, tended to be associated. There was a general geographic trend for lines collected from locations more remote from where mungbean has historically been cultivated to show greater expression of wild type traits, with few ‘traits of domestication’ evident in the Australian accessions. Some of the identified variation, e.g. higher seed protein content, hardseededness, and putative disease resistance, may be of value in mungbean variety improvement. A more targetted evaluation of the collection would likely reveal other adaptations, especially tolerance to environmental stresses. As such, the wild accessions are a potentially valuable if under-utilised germplasm resource.
Capturing expert knowledge with argumentation: a case study in bioinformatics
Authors: Jefferys Benjamin R. , Kelley Lawrence A. , Sergot Marek J. , Fox John , Sternberg Michael J. E.
Published: January 2006

Motivation: The output of a bioinformatic tool such as BLAST must usually be interpreted by an expert before reliable conclusions can be drawn. This may be based upon the expert’s experience, additional data and statistical analysis. Often the process is laborious, goes unrecorded and may be biased. Argumentation is an established technique for reasoning about situations where absolute truth or precise probability is impossible to determine.

Results: We demonstrate the application of argumentation to 3D-PSSM, a protein structure prediction tool. The expert’s interpretation of results is represented as an argumentation framework. Given a 3D-PSSM result, an automated procedure constructs arguments for and against the conclusion that the result is a good predictor of protein structure. In addition to capturing the unique expertise of the author of 3D-PSSM for distribution to users, an improvement in recall of 5–10 percentage points is achieved. This technique can be applied to a wide range of bioinformatic tools.

Availability: Example public server and benchmarking data are available at . Source code available on request.

Contact:  m.sternberg@imperial.ac.uk
AMiGA: the arthropodan mitochondrial genomes accessible database
Authors: Feijão Pedro Cipriano , Neiva Lissiene Silva , Azeredo-Espin Ana Maria Lima de , Lessinger Ana Cláudia
Published: January 2006

Summary: The Arthropodan Mitochondrial Genomes Accessible database (AMiGA) is a relational database developed to help in managing access to the increasing amount of data arising from developments in arthropodan mitochondrial genomics (136 mitochondrial genomes as of September 2005). The strengths of AMiGA include (1) a more accessible and up-to-date database containing a more comprehensive set of mitochondrial genomes for this phylum, (2) the provision of flexible search options for retrieving detailed information such as bibliographical data, genomic graphics, FASTA sequences and taxonomical status, (3) the possibility of enhanced comparative analyses by multiple alignment of single or concatenated sets of genes, (4) more accurate and updated information resulting from a specific curation process called AMiGA Notes and (5) the possibility of including unpublished sequences in a password-restricted area for comparative analysis with the other sequences stored in the database.

Availability:  

Contact:  lessinger@amiga.cbmeg.unicamp.br

Supplementary information: Detailed information, including an illustrated tutorial, is available from the above URL.
Eigenvalue of a semi-infinite elastic strip
Authors: Zernov V. , Pichugin A.V. , Kaplunov J.
Published: January 2006

A semi-infinite elastic strip, subjected to traction free boundary conditions, is studied in the context of in-plane stationary vibrations. By using normal (Rayleigh–Lamb) mode expansion the problem of existence of the strip eigenmode is reformulated in terms of the linear dependence within infinite system of normal modes. The concept of Gram's determinant is used to introduce a generalized criterion of linear dependence, which is valid for infinite systems of modes and complex frequencies. Using this criterion, it is demonstrated numerically that in addition to the edge resonance for the Poisson ratio
ν
=0, there exists another value of
ν
≈0.22475 associated with an undamped resonance. This resonance is best explained physically by the orthogonality between the edge mode and the first Lamé mode. A semi-analytical proof for the existence of the edge resonance is then presented for both described cases with the help of the augmented scattering matrix formalism.
Real-time dynamic substructuring in a coupled oscillator–pendulum system
Authors: Kyrychko Y.N , Blyuss K.B , Gonzalez-Buelga A , Hogan S.J , Wagg D.J
Published: January 2006

Real-time dynamic substructuring is a powerful testing method, which brings together analytical, numerical and experimental tools for the study of complex structures. It consists of replacing one part of the structure with a numerical model, which is connected to the remainder of the physical structure (the substructure) by a transfer system. In order to provide reliable results, this hybrid system must remain stable during the whole test. A primary mechanism for destabilization of these type of systems is the delays which are naturally present in the transfer system. In this paper, we apply the dynamic substructuring technique to a nonlinear system consisting of a pendulum attached to a mechanical oscillator. The oscillator is modelled numerically and the transfer system is an actuator. The system dynamics is governed by two coupled second-order neutral delay differential equations. We carry out local and global stability analyses of the system and identify the delay dependent stability boundaries for this type of system. We then perform a series of hybrid experimental tests for a pendulum–oscillator system. The results give excellent qualitative and quantitative agreement when compared to the analytical stability results.
Field study on the interception efficiency of lightning protection systems and comparison with models
Authors: D'Alessandro F , Petrov N.I
Published: January 2006

We present and analyse the collective statistical results of a long-term field study quantifying the number of lightning strikes to buildings equipped with lightning protection systems. The observations were made over the period 1990–2003 in a region with one of the highest lightning activities in the world. The data sample comprised 86 structures with a mean height and exposure time of 57 metres and 6.9 yr, respectively. These structures were subjected to 384 flashes over the total observation time of 592 yr. The positioning of the protective air terminals on these structures was carried out with an improved electrogeometric model of lightning attachment.

The collective observational data have been compared with the expected number of incident flashes using a variety of analytical relations and statistical tests. The expected strike frequency was determined with three different, contemporary models of lightning attachment to structures. The protection level or interception efficiency estimated from the models is compared with the actual value derived from the long-term field observations involving measurements of captured strikes and evidence of lightning by-pass events.

The results show that the observational data used in this study are well-described by a Poisson distribution. There is a highly significant positive correlation between the observational data and the number of strikes expected from the application of the theoretical models. Finally, the observed and expected values for the mean interception efficiency of the lightning protection systems in the study are shown to be in good agreement.
Calculating the lift on a finite stack of cylindrical aerofoils
Authors: Crowdy Darren
Published: January 2006

The classic exact solution due to Lagally (Lagally, M. 1929 Die reibungslose strömung im aussengebiet zweier kreise.Z. Angew. Math. Mech.9, 299–305.) for streaming flow past two cylindrical aerofoils (or obstacles) is generalized to the case of an arbitrary finite number of cylindrical aerofoils. Given the geometry of the aerofoils, the speed and direction of the oncoming uniform flow and the individual round-aerofoil circulations, the complex potential associated with the flow is found in analytical form in a parametric pre-image region that can be conformally mapped to the fluid region. A complete determination of the flow then follows from knowledge of the conformal mapping between the two regions. In the special case where the aerofoils are all circular, the conformal mapping from the parametric pre-image region to the fluid domain is a Möbius mapping. The solution for the complex potential in such a case can then be used, in combination with the Blasius theorem, to compute the distribution of hydrodynamic forces on the multi-aerofoil configuration.
Are subspecies useful in evolutionary and conservation biology?
Authors: Phillimore Albert B , Owens Ian P.F
Published: January 2006

The taxonomic rank of subspecies remains highly contentious, largely because traditional subspecies boundaries have sometimes been contradicted by molecular phylogenetic data. The most complete meta-analysis to date, for instance, found that only 3% of traditional avian subspecies represented distinct phylogenetic lineages. However, the global generality of this phenomenon remains unclear due to this previous study's narrow geographic focus on continental Nearctic and Palearctic subspecies. Here, we present a new global analysis of avian subspecies and show that 36% of avian subspecies are, in fact, phylogenetically distinct. Among biogeographic realms we find significant differences in the proportion of subspecies that are phylogenetically distinct, with Nearctic/Palearctic subspecies showing significantly reduced levels of differentiation. Additionally, there are differences between island and continental subspecies, with continental subspecies significantly less likely to be genetically distinct. These results indicate that the overall level of congruence between taxonomic subspecies and molecular phylogenetic data is greater than previously thought. We suggest that the widespread impression that avian subspecies are not real arises from a predominance of studies focusing on continental subspecies in North America and Eurasia, regions which show unusually low levels of genetic differentiation. The broader picture is that avian subspecies often provide an effective short-cut for estimating patterns of intraspecific genetic diversity, thereby providing a useful tool for the study of evolutionary divergence and conservation.
How much evolutionary history in a 10×10 m plot?
Authors: Procheş Şerban , Wilson John R.U , Cowling Richard M
Published: January 2006

We use a fully dated phylogenetic tree of the angiosperm families to calculate phylogenetic diversity (PD) in four South African vegetation types with distinct evolutionary histories. Since the branch length values are in this case represented by the ages of plant lineages, PD becomes the cumulative evolutionary age (CEA) of assemblages. Unsurprisingly, total CEA increases with family and with species diversity and observed values are the same as expected from random sampling of family lists. However, when random sampling is done from species lists, observed CEAs are generally lower than expected. In vegetation types which have undergone recent diversification—grassland, fynbos and Nama-karoo—co-occurring species are more closely related than expected, but in subtropical thicket the observed CEAs are well described by random sampling. The use of CEA has great potential for assessing the age of biotic assemblages, particularly as the dating of genus and species-level phylogenies become more accurate.
Attentional modulation of perceptual stabilization
Authors: Kanai Ryota , Verstraten Frans A.J
Published: January 2006

Perceptual priming is generally regarded as a passive and automatic process, as it is obtained even without awareness of the prime. Recent studies have introduced a more active form of perceptual priming in which priming for a subsequent ambiguous stimulus is triggered by the subjective percept, that is, interpretation of a previous ambiguous stimulus. This phenomenon known as stabilization does not require a conscious effort to actively maintain one perceptual interpretation. In this study, we show that distraction of attention, during and even after the prime presentation, interferes with the build-up of perceptual memory for stabilization. This implies that despite the apparent automaticity, stabilization involves an active attentional process for encoding and retention. The disruption during the encoding can be attributed to the reduction in sensory signals for the prime. However, the disruption during the retention suggests that the implicit memory trace of the prime necessitates the attentional resource to fully develop. The active nature of the build-up of perceptual memory for stabilization is consistent with the idea that perceptual memory increases its strength gradually over a few seconds. These findings suggest that seemingly automatic and effortless cognitive processes can compete with online perceptual processing for common attentional resources.
The status and evolution of plasma wakefield particle accelerators
Authors: Joshi C , Mori W.B
Published: January 2006

The status and evolution of the electron beam-driven Plasma Wakefield Acceleration scheme is described. In particular, the effects of the radial electric field of the wake on the drive beam such as multiple envelope oscillations, hosing instability and emission of betatron radiation are described. Using ultra-short electron bunches, high-density plasmas can be produced by field ionization by the electric field of the bunch itself. Wakes excited in such plasmas have accelerated electrons in the back of the drive beam to greater that 4 GeV in just 10 cm in experiments carried out at the Stanford Linear Accelerator Centre.
Laser–plasma accelerator: status and perspectives
Authors: Malka V , Faure J , Glinec Y , Lifschitz A.F
Published: January 2006

Laser–plasma accelerators deliver high-charge quasi-monoenergetic electron beams with properties of interest for many applications. Their angular divergence, limited to a few mrad, permits one to generate a small
γ
ray source for dense matter radiography, whereas their duration (few tens of fs) permits studies of major importance in the context of fast chemistry for example. In addition, injecting these electron beams into a longer plasma wave structure will extend their energy to the GeV range. A GeV laser-based accelerator scheme is presented; it consists of the acceleration of this electron beam into relativistic plasma waves driven by a laser. This compact approach (centimetres scale for the plasma, and tens of meters for the whole facility) will allow a miniaturization and cost reduction of future accelerators and derived X-ray free electron laser (XFEL) sources.
Clustered gases as a medium for efficient plasma waveguide generation
Authors: Milchberg H.M , Kim K.Y , Kumarappan V , Layer B.D , Sheng H
Published: January 2006

Clustered gas jets are shown to be an efficient means for plasma waveguide generation, for both femtosecond and picosecond generation pulses. These waveguides enable significantly lower on-axis plasma density (less than 10
18
 cm
−3
) than in conventional hydrodynamic plasma waveguides generated in unclustered gases. Using femtosecond pump pulses, self-guided propagation and strong absorption (more than 70%) are used to produce long centimetre scale channels in an argon cluster jet, and a subsequent intense pulse is coupled into the guide with 50% efficiency and guided at above 10
17
 W cm
−2
intensity over 40 Rayleigh lengths. We also demonstrate efficient generation of waveguides using 100 ps axicon-generated Bessel-beam pump pulses. Despite the expected sub-picosecond cluster disassembly time, we observe long pulse absorption efficiencies up to a maximum of 35%. Simulations show that in the far leading edge of the long laser pulse, the volume of heated clusters evolves to a locally uniform and cool plasma already near ionization saturation, which is then efficiently heated by the remainder of the pulse.
Laser wakefield acceleration: the injection issue. Overview and latest results
Authors: van der Wiel M.J , Luiten O.J , Brussaard G.J.H , van der Geer S.B , Urbanus W.H , van Dijk W , van Oudheusden Th
Published: January 2006

External injection of electron bunches into laser-driven plasma waves so far has not resulted in ‘controlled’ acceleration, i.e. production of bunches with well-defined energy spread. Recent simulations, however, predict that narrow distributions can be achieved, provided the conditions for properly trapping the injected electrons are met. Under these conditions, injected bunch lengths of one to several plasma wavelengths are acceptable. This paper first describes current efforts to demonstrate this experimentally, using state-of-the-art radio frequency technology. The expected charge accelerated, however, is still low for most applications. In the second part, the paper addresses a number of novel concepts for significant enhancement of photo-injector brightness. Simulations predict that, once these concepts are realized, external injection into a wakefield accelerator will lead to accelerated bunch specs comparable to those of recent ‘laser-into-gasjet’ experiments, without the present irreproducibility of charge and final energy of the latter.
Novel techniques of laser acceleration: from structures to plasmas
Authors: Kalmykov S , Polomarov O , Korobkin D , Otwinowski J , Power J , Shvets G
Published: January 2006

Compact accelerators of the future will require enormous accelerating gradients that can only be generated using high power laser beams. Two novel techniques of laser particle acceleration are discussed. The first scheme is based on a solid-state accelerating structure powered by a short pulse CO
2
laser. The planar structure consists of two SiC films, separated by a vacuum gap, grown on Si wafers. Particle acceleration takes place inside the gap by a surface electromagnetic wave excited at the vacuum/SiC interface. Laser coupling is accomplished through the properly designed Si grating. This structure can be inexpensively manufactured using standard microfabrication techniques and can support accelerating fields well in excess of 1 GeV m
−1
without breakdown. The second scheme utilizes a laser beatwave to excite a high-amplitude plasma wave, which accelerates relativistic particles. The novel aspect of this technique is that it takes advantage of the nonlinear bi-stability of the relativistic plasma wave to drive it close to the wavebreaking.
Early life history of Syngnathus abaster
Authors: Silva K. , Monteiro N. M. , Almada V. C. , Vieira M. N.
Published: January 2006

The embryonic and larval development of the pipefish Syngnathus abaster is described, based on ex situ observations. The full development sequence lasted 24–32 days (at 18–19° C), which was shortened to 21 days at higher temperatures (21–22° C). Newborn juveniles, with a uniform dark brown colouration, immediately assumed a benthic spatial distribution. This vertical distribution pattern remained unchanged at least during the first 4 weeks, after the release from the marsupium. The apparent absence of a pelagic life phase might have important repercussions in terms of population connectivity given increasing fragmentation and degradation of the eelgrass habitat in the species’ range.
Nest site characteristics and nesting success of the five‐spotted wrasse Symphodus roissali in the north‐western Mediterranean Sea
Authors: Raventos N.
Published: January 2006

The effects of site characteristics on the distribution of nests and nesting success were examined in the five‐spotted wrasse Symphodus roissali in the north‐western Mediterranean Sea. Nesting males selected nest sites mainly on flat substrata and close to a margin in the rocky littoral strip; however, substratum slope and degree of shelter from wave action were the determinants for a greater success.
Reproductive behaviour of a temperate serranid fish,Paralabrax clathratus(Girard), from Santa Catalina Island, California, U.S.A.
Authors: Erisman B. E. , Allen L. G.
Published: January 2006

The reproductive behaviour of the kelp bassParalabrax clathratuswas studied on Santa Catalina Island, California, U.S.A. from April 2000 to September 2002. Adults formed aggregations of three to > 200 individuals, and spawning occurred within subgroups of three to 23 individuals that contained a single female. The gonado‐somatic index (IG) of collected ripe males (mean = 5·8%, range = 0·5–13·1%) indicated a large investment in sperm production that is common in group‐spawning fishes characterized by intense sperm competition. Spawning occurred 32 min before sunset to 120 min after sunset, and both males and females were capable of spawning multiple times during a single evening. Behavioural observations of adults and estimates of spawning periodicity from the collection of females with hydrated oocytes suggested that spawning occurred continuously throughout the summer months and showed no significant relationship with the lunar cycle. In general, the spawning behaviour of kelp bass was similar to other functionally gonochoric, group‐spawning serranids. The dynamics ofP. clathratusspawning aggregations, however, were inconsistent with that of tropical reef fish spawning aggregations, including the transient spawning aggregations of some tropical serranids. Aggregation spawning appeared to be an important component of the annual reproduction of this species.
Determinants of male mating success in a natural population of a stream goby of the genus Rhinogobius
Authors: Ito S. , Yanagisawa Y.
Published: January 2006

The mating success of individually identified males of a stream goby, Rhinogobius sp. CB (cross‐band type), was recorded over one breeding season. One to 3 year‐old males were active in mating, but 3 year‐old males, which accounted for 36% of the population, amounted to c. 70% of the total males guarding eggs in the nest. Three quarters of the breeding males had only one brooding cycle, but the others had two or three. All the latter males changed their nest sites between cycles within a riffle. In 1 and 2 year‐old males, the number of brooding cycles contributed more to the mating success than egg mass size in one brooding cycle. For mating success of 3 year‐old males, the egg mass size in one brooding cycle, which can be enhanced by spawning with a large female or multiple females, was as important as the number of brooding cycles. These male reproductive tactics could be attributed to the age‐related ability of nest construction and mate acquisition.
Statistical model of variable allometric growth: otolith growth in Micropogonias furnieri(Actinopterygii, Sciaenidae)
Authors: Bervian G. , Fontoura N. F. , Haimovici M.
Published: January 2006

The main objective of this study was to develop a statistical model for accurate estimates of relative growth. The method was based on identifying patterns of the residuals obtained from the Huxley's allometric equation. Three different approaches were applied: (1) growth with variable proportionality and constant allometry coefficient, (2) growth with constant proportionality and variable allometry coefficient and (3) distinct growth phases in which proportionality and allometry coefficients remained constant. The proposed statistical models were applied to the relationship of the otolith size and fish size of whitemouth croaker Micropogonias furnieri. The best fit was obtained when using approach (3). A change in the growth parameters was associated with the attainment of sexual maturity.
Distribution of an asymmetrical copepod, Hatschekia plectropomi, on the gills of Plectropomus leopardus
Authors: Scott–Holland T. B. , Bennett S. M. , Bennett M. B.
Published: January 2006

Hatschekia plectropomi, an ectoparasitic copepod found on the gills, infected Plectropomus leopardus from Heron Island Reef with 100% prevalence (n = 32) and a mean ± s.e. infection intensity of 131·9 ± 22·1. The distribution of 4222 adult female parasites across 32 individual host fish was investigated at several organizational levels ranging from the level of holobranch pairs to that of individual filaments. Parasites demonstrated a site preference for the two central holobranchs (2 and 3). Along the lengths of hemibranchs, filaments near the dorsal and ventral ends and those in the proximity of the bend region were rarely occupied. The probability of coming into contact with a suitable attachment site and the ability to withstand ventilation forces at that site were proposed as the major factors affecting distribution. Two H. plectropomi morphotypes were identified based on the direction of body curvature. Regardless of morphotype, 99·9% of individuals were attached such that the convex side of the body was oriented towards the oncoming ventilating water currents. Further, 93·3% of individuals attached to the posterior faces of filaments, leading to a predictable pattern of attachment for this species. It is suggested that the direction of body curvature develops in response to the direction of the ventilating water currents.
Nuclear import and export of plant virus proteins and genomes
Authors: KRICHEVSKY ALEXANDER , KOZLOVSKY STANISLAV V. , GAFNI YEDIDYA , CITOVSKY VITALY
Published: January 2006

Nuclear import and export are crucial processes for any eukaryotic cell, as they govern substrate exchange between the nucleus and the cytoplasm. Proteins involved in the nuclear transport network are generally conserved among eukaryotes, from yeast and fungi to animals and plants. Various pathogens, including some plant viruses, need to enter the host nucleus to gain access to its replication machinery or to integrate their DNA into the host genome; the newly replicated viral genomes then need to exit the nucleus to spread between host cells. To gain the ability to enter and exit the nucleus, these pathogens encode proteins that recognize cellular nuclear transport receptors and utilize the host's nuclear import and export pathways. Here, we review and discuss our current knowledge about the molecular mechanisms by which plant viruses find their way into and out of the host cell nucleus.
Magnaporthe oryzae isolates causing gray leaf spot of perennial ryegrass possess a functional copy of the AVR1‐CO39 avirulence gene
Authors: PEYYALA REBECCA , FARMAN MARK L.
Published: January 2006

Gray leaf spot of perennial ryegrass (Lolium perenne) is a severe foliar disease caused by the ascomycete fungus Magnaporthe oryzae (formerly known as Magnaporthe grisea). Control of gray leaf spot is completely dependent on the use of fungicides because currently available perennial ryegrass cultivars lack genetic resistance to this disease. M. oryzae isolates from perennial ryegrass (prg) were unable to cause disease on rice cultivars CO39 and 51583, and instead triggered a hypersensitive response. Southern hybridization analysis of DNA from over 50 gray leaf spot isolates revealed that all of them contain sequences corresponding to AVR1‐CO39, a host specificity gene that confers avirulence to rice cultivar CO39, which carries the corresponding resistance gene Pi‐CO39(t). There was also an almost complete lack of restriction site polymorphism at the avirulence locus. Cloning and sequencing of the AVR1‐CO39 gene (AVR1‐CO39Lp) from 16 different gray leaf spot isolates revealed just two point mutations, both of which were located upstream of the predicted open reading frame. When an AVR1‐CO39Lp gene copy was transferred into ML33, a rice pathogenic isolate that is highly virulent to rice cultivar CO39, the transformants were unable to cause disease on CO39 but retained their virulence to 51583, a rice cultivar that lacks Pi‐CO39(t). These data demonstrate that the AVR1‐CO39 gene in the gray leaf spot pathogens is functional, and suggest that interaction of AVR1‐CO39Lp and Pi‐CO39(t) is responsible, at least in part, for the host specificity expressed on CO39. This indicates that it may be possible to use the Pi‐CO39(t) resistance gene as part of a transgenic strategy to complement the current deficiency of gray leaf spot resistance in prg. Furthermore, our data indicate that, if Pi‐CO39(t) can function in prg, the resistance provided should be broadly effective against a large proportion of the gray leaf spot pathogen population.
The UGA3‐GLT1 intergenic region constitutes a promoter whose bidirectional nature is determined by chromatin organization in Saccharomyces cerevisiae
Authors: Ishida Cecilia , Aranda Cristina , Valenzuela Lourdes , Riego Lina , DeLuna Alexander , Recillas‐Targa Félix , Filetici Patrizia , López‐Revilla Rubén , González Alicia
Published: January 2006

Transcription of an important number of divergent genes of Saccharomyces cerevisiae is controlled by intergenic regions, which constitute factual bidirectional promoters. However, few of such promoters have been characterized in detail. The analysis of the UGA3‐GLT1 intergenic region has provided an interesting model to study the joint action of two global transcriptional activators that had been considered to act independently. Our results show that Gln3p and Gcn4p exert their effect upon cis‐acting elements, which are shared in a bidirectional promoter. Accordingly, when yeast is grown on a low‐quality nitrogen source, or under amino acid deprivation, the expression of both UGA3 and GLT1 is induced through the action of both these global transcriptional modulators that bind to a region of the bidirectional promoter. In addition, we demonstrate that chromatin organization plays a major role in the bidirectional properties of the UGA3‐GLT1 promoter, through the action of an upstream Abf1p‐binding consensus sequence and a polydAdTtract. Mutations in these cis‐elements differentially affect transcription of UGA3 and GLT1, and thus alter the overall relative expression. This is the first example of an intergenic region constituting a promoter whose bidirectional character is determined by chromatin organization.
The integration host factor (IHF) integrates stationary‐phase and virulence gene expression in Salmonella enterica serovar Typhimurium
Authors: Mangan Michael W. , Lucchini Sacha , Danino Vittoria , Cróinín Tadhg Ó , Hinton Jay C. D. , Dorman Charles J.
Published: January 2006

The integration host factor (IHF) is a DNA‐binding and ‐bending protein with roles in local DNA structural organization and transcriptional regulation in Gram‐negative bacteria. This heterodimeric protein is composed of the two highly homologous subunits IHFα and IHFβ. DNA microarray analysis was used to define the regulon of genes subject to IHF control in Salmonella enterica serovar Typhimurium (S. Typhimurium). The transcription profile of the wild type was compared with those of mutants deficient in IHFα, IHFβ, or both IHFα and IHFβ. Our data reveal a new connection between IHF and the expression of genes required by the bacterium to undergo the physiological changes associated with the transition from exponential growth to stationary phase. When a mutant lacking IHF entered stationary phase, it displayed downregulated expression of classic stationary‐phase genes in the absence of any concomitant change in expression of the RpoS sigma factor. Purified IHF was found to bind to the regulatory regions of stationary‐phase genes indicating an auxiliary and direct role for IHF in RpoS‐dependent gene activation. Loss of IHF also had a profound influence on expression of the major virulence genes and epithelial cell invasion, indicating a role in co‐ordinating regulation of the pathogenic traits with adaptation to stationary phase. Although the three mutants showed considerable overlaps in the genes affected by the ihf lesions, the observed patterns were not identical, showing that S. Typhimurium has not one but three overlapping IHF regulons.
Eosinophil interactions with Haemonchus contortus larvae in the ovine gastrointestinal tract
Authors: BALIC A. , CUNNINGHAM C. P. , MEEUSEN E. N. T.
Published: January 2006

Sheep were immunized by weekly oral infections with Haemonchus contortus for 9 weeks followed by anthelmintic treatment. They were challenged either 9 or 22 weeks later with PBS (sham controls) or one million exsheathed L3 surgically injected in the abomasum, and killed 24 h or 48 h later. Sheep challenged 9 weeks after immunization displayed varying degrees of tissue eosinophilia that showed a significant inverse relationship with the number of intra‐epithelial mast cells (globule leucocytes). Close association of eosinophils with tissue larvae was observed mainly in the gastric pits (24 h) or on the mucosal surface (48 h). All L3‐challenged sheep in this group had detectable globule leucocytes and tissue IL‐4 mRNA, as measured by Southern blot RT‐PCR. In contrast, sheep challenged 22 weeks after immunization had no detectable globule leucocytes or IL‐4 mRNA and although they exhibited consistent tissue eosinophilia, eosinophils were not closely associated with tissue larvae. Scanning and transmission electron microscopy of sheep sensitized and rested for 9 weeks before challenge showed that L3 surrounded by eosinophils were at varying stages of damage and structural collapse. These studies strongly indicate that eosinophils can damage and probably kill gastrointestinal nematode larvae in vivo. In addition, they also suggest that effective killing by tissue eosinophils may depend on other microenvironmental factors such as intra‐epithelial mast cells and IL‐4.
Carbonates calibrated against oceanographic parameters along a latitudinal transect in the Gulf of California, Mexico
Authors: HALFAR J. , GODINEZ‐Orta L. , MUTTI M. , VALDEZ‐HOLGUIN J. E. , BORGES J. M.
Published: January 2006

Trophic resources are an important control governing carbonate production. Though this importance has long been recognized, no calibration exists to quantitatively compare biogenic assemblages within trophic resource fields. This study presents a field calibration of carbonate producers in a range of settings against high‐resolution in situ measurements of nutrients, temperature and salinity. With its latitudinal extent from 30° to 23° N, the Gulf of California, Mexico, spans the warm‐temperate realm and encompasses nutrient regimes from oligo‐mesotrophic in the south to eutrophic in the north. Accordingly, from south to north carbonates are characterized by: (i) coral‐dominated shallow carbonate factories (5–20 m water depth) with average sea‐surface temperatures of 25 °C (min. 18 °C, max. 31 °C), average salinities of 35·06‰ and average chlorophyll a levels, which are a proxy for nutrients, of 0·25 mg Chl a m−3 (max. 0·48, min. 0·1). (ii) Red algal‐dominated subtidal to inner‐shelf carbonate formation (10–25 m) in the central Gulf of California exhibiting average temperatures of 23 °C (min. 18 °C, max. 30 °C), average salinities of 35·25‰, and average Chl a levels of 0·71 Chl a m−3 (max. 5·62, min. 0). (iii) Molluskan bryozoan‐rich inner to outer shelf factories in the northern Gulf of California (20–50 m) with average sea surface temperatures of only 20 °C (min. 13 °C, max 29 °C), average salinities of 35·01‰, and average contents of 2·2 mg Chl a m−3 (max. 8·38, min. 0). By calibrating sedimentological data with in situ measured oceanographic information in different environments, the response of carbonate producers to environmental parameters was established and extrapolated to carbonates on a global scale. The results demonstrate the importance of recognizing and quantifying trophic resources as a dominant control determining the biogenic composition and facies character of both modern and fossil carbonates.
Multiple pathways of maternal effects in black-headed gull eggs: constraint and adaptive compensatory adjustment
Authors: Groothuis T. G. G. , Eising C. M. , Blount J. D. , Surai P. , Apanius V. , Dijkstra C. , Müller W.
Published: January 2006

We investigated in the black-headed gull whether female deposition of antioxidants and immunoglobulins (enhancing early immune function), and testosterone (suppressing immune function and increasing early competitive skills) correlate suggesting that evolution has favoured the mutual adjustment of different pathways for maternal effects. We also took egg mass, the position of the egg in the laying sequence and offspring sex into account, as these affect offspring survival. Yolk antioxidant and immunoglobulin concentrations decreased across the laying order, while yolk testosterone concentrations increased. This may substantially handicap the immune defence of last-hatched chicks. The decrease in antioxidant levels was greater when mothers had a low body mass and when the increase in testosterone concentrations was relatively large. This suggests that female black-headed gulls are constrained in the deposition of antioxidants in last-laid eggs and compensate for this by enhanced testosterone deposition. The latter may be adaptive since it re-allocates the chick's investment from costly immune function to growth and competitive skills, necessary to overcome the consequences of hatching late from an egg of reduced quality.
Primary adenoid squamous cell carcinoma of the oral cavity
Authors: Kusafuka Kimihde , Ebihara Mitsuru , Ishiki Hiroto , Takizawa Yoshinori , Iida Yoshiyuki , Onitsuka Tetsuro , Takakuwa Reiko , Kasami Masako , Ito Ichiro , Kameya Toru
Published: January 2006

Adenoid squamous cell carcinoma (ASCC) is an uncommon but well‐recognized variant of squamous cell carcinoma that was first described by Lever in 1947. ASCC has been reported to originate in the sun‐exposed skin of the head and neck and in other sites. An additional case of ASCC is reported here. The patient was a 64‐year‐old Japanese woman who requested examination of a reddish lesion on the left floor of the mouth. The biopsy material was diagnosed as squamous cell carcinoma. Clinical examination showed a well‐circumscribed, 20 × 10 mm‐sized lesion, which was categorized as cT2cN0cm 0. Tumor resection was therefore performed. Histologically, most parts of the lesion were conventional squamous cell carcinoma in situ, but the invasive part consisted of ASCC with gland‐like or reticular appearance. The latter part was negative for mucin staining. Immunohistochemically, this lesion was positive for pancytokeratin, high‐molecular‐weight keratin, cytokeratin (CK) 7/8, CK19, E‐cadherin and p53, but negative for vimentin, CK20, and S‐100 protein. The Ki‐67 labeling index was 50.3% in the ASCC part and 34.5% in the carcinoma in situ part. These findings and a review of the literature indicate that a gland‐like feature of ASCC is associated with the loss of cell adhesion in the center of the cancer nests, and it can be confirmed simply by mucin staining to be neither an adenosquamous carcinoma nor ductal involvement of conventional squamous cell carcinoma.
Myxoid variant of adrenocortical carcinoma: Report of a unique case
Authors: Karim Rooshdiya Z. , Wills Edward J. , McCarthy Stanley W. , Scolyer Richard A.
Published: January 2006

Myxoid variant of adrenocortical carcinomas (ACC) are rare, there being only 11 cases in the literature to date. Reported herein are the findings of a case, which in contrast to all previously reported myxoid ACC, was devoid of typical non‐myxoid areas. The patient was a 61‐year‐old man in whom a left adrenal mass was detected during investigation of Cushing's syndrome. The adrenal was replaced by malignant cells and expanses of myxoid material. The cells were positive for melan‐A, synaptophysin, vimentin and α‐inhibin. The ultrastructural features of the cells were typical of adrenal cortical differentiation. The differential diagnosis of myxoid ACC includes extraskeletal myxoid chondrosarcoma, chordoma, myxoid adenocarcinoma, myxoma, lipomatous tumors, nerve sheath tumors, smooth muscle tumors, gastrointestinal stromal tumor and other sarcomas. The presence of myxoid material in a retroperitoneal lesion raises a broad differential diagnosis in which myxoid adrenocortical neoplasms should be included. Clinicoradiological correlation may be helpful, but special stains, immunohistochemistry and ultrastructural examination may be necessary to establish the diagnosis.
Linear‐representation Based Estimation of Stochastic Volatility Models
Authors: FRANCQ CHRISTIAN , ZAKOÏAN JEAN‐MICHEL
Published: January 2006

Abstract.  A new way of estimating stochastic volatility models is developed. The method is based on the existence of autoregressive moving average (ARMA) representations for powers of the log‐squared observations. These representations allow to build a criterion obtained by weighting the sums of squared innovations corresponding to the different ARMA models. The estimator obtained by minimizing the criterion with respect to the parameters of interest is shown to be consistent and asymptotically normal. Monte‐Carlo experiments illustrate the finite sample properties of the estimator. The method has potential applications to other non‐linear time‐series models.
Making up is hard to do, especially for mothers with high levels of depressive symptoms and their infant sons
Authors: Katherine Weinberg M. , Olson Karen L. , Beeghly Marjorie , Tronick Edward Z.
Published: January 2006

Background:  The goal of this study was to evaluate the interactions of mothers with normative or high levels of depressive symptomatology on the Center for Epidemiologic Studies‐Depression Scale (CES‐D) and their 3‐month‐old infants. Although successful mutual regulation of affect is critical to children's socio‐emotional development, little is known about the factors that influence dyadic processes such as synchrony, matching, mismatching, and bi‐directionality during early infancy. Therefore, this study evaluated the effects of maternal depressive symptom status, infant gender, and interactional context on mother–infant affective expressiveness and the dyadic features of their interactions.

Methods:  Participants were 133 mothers and their healthy full‐term infants. Mothers were classified into three groups on the basis of their total score on the CES‐D at 2 months of infant age: a high symptom group (CES‐D score ≥ 16), a mid symptom control group (CES‐D score = 2–12), and a low symptom group (CES‐D score = 0–1). Mothers and infants were then videotaped in the Face‐to‐Face Still‐Face paradigm at 3 months of infant age. The mothers’ and infants’ affect during the interactions prior to (first play) and following the still‐face (reunion play) were coded microanalytically using Izard's AFFEX system.

Results:  Results indicated that male as compared to female infants were more vulnerable to high levels of maternal depressive symptoms and that high symptom mothers and their sons had more difficult interactions in the challenging reunion episode.

Conclusions:  The findings suggest that a cycle of mutual regulatory problems may become established between high symptom mothers and their sons, particularly in challenging social contexts. The long‐term consequences of this early social interactive vulnerability in terms of later development need to be further investigated.
Test–retest reliability and criterion validity of the Chinese version of CBCL, TRF, and YSR
Authors: Leung Patrick W.L. , Kwong S.L. , Tang C.P. , Ho T.P. , Hung S.F. , Lee C.C. , Hong S.L. , Chiu C.M. , Liu W.S.
Published: January 2006

Background: Psychometric properties of the Chinese version of CBCL, TRF, and YSR were understudied. This study aimed at examining their test–retest reliability and criterion validity.

Methods: Three Chinese community and clinic samples were recruited in Hong Kong. The parents, teachers, and youths respectively completed the CBCL, TRF, and YSR.

Results: The Chinese CBCL, TRF, and YSR were test–retest reliable and valid. However, there was score/case attenuation at retest. CBCL and TRF appeared to screen externalizing and ADHD problems better, while YSR screened internalizing problems better.

Conclusions: Clinicians should be cautious about score/case attenuation at retest while using CBCL, TRF, and YSR to chart patients’ progress. They should also recognize their different strengths in screening various disorders.
The prevalence of autistic spectrum disorders in adolescents with a history of specific language impairment (SLI)
Authors: Conti‐Ramsden Gina , Simkin Zoë , Botting Nicola
Published: January 2006

Background:  Traditionally, autism and specific language impairment (SLI) have been regarded as distinct disorders but, more recently, evidence has been put forward for a closer link between them: a common set of language problems, in particular receptive language difficulties and the existence of intermediate cases including pragmatic language impairment. The present study aimed to examine the prevalence of autism spectrum disorders in a large sample of adolescents with a history of SLI.

Method:  The presence of autism spectrum disorders was examined in seventy‐six 14‐year‐olds with a confirmed history of SLI. A variety of instruments were employed, including the Autism Diagnostic Interview‐Revised (ADI‐R), the Autism Diagnostic Observation Schedule (ADOS) and the Family History Interview (FHI).

Results:  The prevalence of autism spectrum disorders in young people with SLI was found to be 3.9%, about 10 times what would be expected from the general population. In addition, a much larger number of young people with a history of SLI showed only some autism spectrum symptoms or showed them in a mild form.

Conclusions:  Young people with SLI have an increased risk of autism. The magnitude of this risk is considerable. In addition, a larger proportion (a quarter of individuals) present with a number of behaviours consistent with autism spectrum disorders.