bluuebunny/crossref_metadata_2025 huggingface dataset:
The effect of temperature on photoperiodically regulated gonadal maturation, regression and moult in starlings – potential consequences of climate change
Authors: DAWSON A.
Published: December 2005

Birds use increasing photoperiod during spring as the major cue to time gonadal maturation and breeding so that nestlings are growing during peak food (normally invertebrate) abundance. Climate warming will advance invertebrate abundance, so birds relying entirely on photoperiod will breed too late. Can temperature modulate responses to photoperiod?

Common Starlings, Sturnus vulgaris, were kept in two indoor aviaries, in which photoperiod tracked natural changes, but temperature was held at either 20 °C or 5 °C (year 1), or at 18 °C or 8 °C (year 2).

Despite the large differences in temperature (15 °C and 10 °C), this had no effect on the rate or timing of testicular maturation.

However, unexpectedly, testicular regression occurred significantly earlier at the higher temperatures. Post‐nuptial moult also started significantly earlier in both males and females.

Therefore, the degree to which birds can advance the timing of egg‐laying in response to increasing spring temperature may be constrained. At the same time, increasing spring temperature will advance the end of the breeding season (fewer breeding attempts). The reported advances in median egg‐laying dates may, in part, be a consequence of this rather than an indication of successful adaptation. Adaptation to climate change may require evolutionary changes in the physiological responses to photoperiod.
Effect of pretreatments and freezing rate on the firmness of potato tissue after a freeze–thaw cycle
Authors: Carbonell Sergio , Oliveira Jorge C. , Kelly Alan L.
Published: December 2005

The texture of potato tissue after a freeze–thaw process using different freezing rates and different pretreatments was analysed, in order to select the best strategy for optimum preservation of the textural characteristics of pre‐frozen potato. Ten blanching conditions were tested and a two‐step blanching process with calcium chloride (0.07 g mL−1) proved the most effective in protecting the tissue after a freeze–thaw process (maximum load force around 10–55% of the raw tissue, depending on potato batch, for air‐blast freezing and 20–60% for immersion freezing). Vacuum impregnation at 100 and 400 mbar, even when followed by different pre‐drying treatments to remove excess water, was very detrimental to resistance to a freeze–thaw process (maximum load force below 10% of the raw tissue for air‐blast freezing and below 20% for immersion freezing). Microstructure analysis confirmed better tissue integrity retention with ethyleneglycol immersion freezing instead of air‐freezing. Differences were found between batches with a 6‐month difference in storage time, indicating that the fresher batch was more suitable for freezing.
Climate and spatio‐temporal variation in the population dynamics of a long distance migrant, the white stork
Authors: SÆTHER BERNT‐ERIK , GRØTAN VIDAR , TRYJANOWSKI PIOTR , BARBRAUD CHRISTOPHE , ENGEN STEINAR , FULIN MIROSLAV
Published: December 2005

A central question in ecology is to separate the relative contribution of density dependence and stochastic influences to annual fluctuations in population size. Here we estimate the deterministic and stochastic components of the dynamics of different European populations of white storkCiconia ciconia. We then examined whether annual changes in population size was related to the climate during the breeding period (the ‘tap hypothesis’sensuSæther, Sutherland & Engen (2004,Advances in Ecological Research,35, 185–209) or during the nonbreeding period, especially in the winter areas in Africa (the ‘tube hypothesis’).

A general characteristic of the population dynamics of this long‐distance migrant is small environmental stochasticity and strong density regulation around the carrying capacity with short return times to equilibrium.

Annual changes in the size of the eastern European populations were correlated by rainfall in the wintering areas in Africa as well as local weather in the breeding areas just before arrival and in the later part of the breeding season and regional climate variation (North Atlantic Oscillation). This indicates that weather influences the population fluctuations of white storks through losses of sexually mature individuals as well as through an effect on the number of individuals that manages to establish themselves in the breeding population. Thus, both the tap and tube hypothesis explains climate influences on white stork population dynamics.

The spatial scale of environmental noise after accounting for the local dynamics was 67 km, suggesting that the strong density dependence reduces the synchronizing effects of climate variation on the population dynamics of white stork.

Several climate variables reduced the synchrony of the residual variation in population size after accounting for density dependence and demographic stochasticity, indicating that these climate variables had a synchronizing effect on the population fluctuations. In contrast, other climatic variables acted as desynchronizing agents.

Our results illustrate that evaluating the effects of common environmental variables on the spatio‐temporal variation in population dynamics require estimates and modelling of their influence on the local dynamics.
Effects of neighbourhood structure and tussock dynamics on genet demography of Festuca rubra in a mountain meadow
Authors: SUZUKI JUN‐ICHIROU , HERBEN TOMÁŠ , KRAHULEC FRANTIŠEK , ŠTORCHOVÁ HELENA , HARA TOSHIHIKO
Published: December 2005

We examined whether genet demography in the clonal grass Festuca rubra in a mountain grassland in the Krkonoše Mountains (Czech Republic) changes in response to local environment. The data were also used to compare genet recruitment with estimates of genet mortality.

We sampled F. rubra from four permanent plots in which ramet densities of all species have been recorded at a fine scale for a decade. Identities of 224 ramets were assessed by means of RAPD, yielding 145 different genets, of which most (68%) were found only once. The genet with the highest number of sampled ramets was recorded nine times.

By assuming that the probability that two ramets are genetically identical is a function of distance between ramets, we estimated that successful seedling recruitment rates were between 0.15 and 16 genets m−2 yr−1 depending on the plot. Genet mortality was estimated from ramet mortality using the assumption that ramet mortality was uncorrelated over space. In three of the four plots, genet mortalities fell into the same range as the genet recruitment rates.

The total number of genets per unit area must be known to enable determination of per capita recruitment and mortality rates. We developed an estimation technique involving simulation of the sampling process, which yielded values of 231–968 genets m−2. Genet turnover was therefore low (0.1–1% annually) and the high genet diversity is maintained by a very low recruitment.

Spatial analysis showed that two ramets were more likely to be genetically identical when they came from a microhabitat where Festuca ramet density had recently increased; patches in which Festuca ramet density had decreased were more likely to contain ramets from several genets. Expanding tussocks are thus more likely to be composed of ramets of one genet only. Density and biomass of other species in the neighbourhood showed little correlation with the genet structure of Festuca rubra.

Although ramets of Festuca rubra intermingle with other species at a fine scale, the population biology of its genets is driven mainly by the dynamics of its own ramets. Interactions with other species and response to local environments have little effect on genet structure.
Beta diversity and the scale‐dependence of the productivity‐diversity relationship: a test in the Californian serpentine flora
Authors: HARRISON SUSAN , DAVIES KENDI F. , SAFFORD HUGH D. , VIERS JOSHUA H.
Published: December 2005

The relationship of productivity to species diversity is usually positive at regional scales, but is often neutral, unimodal or negative at local spatial scales. Recent studies have pointed out that beta diversity, or among‐locality and within‐region variation in species composition, must therefore tend to increase with productivity.

We tested for a positive relationship of productivity to beta diversity in herbaceous plants at 105 widely distributed sites on serpentine soil in California. We also asked whether any such pattern could be explained, as previously proposed, by increased environmental heterogeneity at higher levels of productivity.

We found that one measure of beta diversity (the species dissimilarity between paired 500 m2 plots on adjacent north and south slopes) was positively related to productivity (as measured by the normalized difference vegetation index, a remotely sensed index). However, this effect was not strong enough to transform the neutral relationship of productivity with alpha (1 m2) diversity to a positive relationship of productivity with gamma (1000 m2) diversity.

The positive effect of productivity on beta diversity was not related to increasing heterogeneity in coarse measures of vegetation structure (percentage cover of shade, litter, rocks, moss, bare soil, animal disturbance). We speculate that the effect may instead have a ‘top‐down’ explanation: higher beta diversity may be caused by the positive influence of productivity on the size of the regional species pool.

Our study illustrates the principle of a ‘scale transition’, in which an ecological pattern is qualitatively different at different spatial scales. Careful attention to scale‐dependence may help narrow the search for mechanisms for such long‐studied ecological puzzles as the latitudinal diversity gradient.
Predictors of asphyxiation risk in adults with intellectual disabilities and dysphagia
Authors: Samuels R. , Chadwick D. D.
Published: December 2005

Background Adults with learning disabilities referred for assessment of their eating and drinking are frequently reported to cough and choke when eating and drinking. The research literature investigating dysphagia has often overlooked asphyxiation risk, highlighting coughing and choking as indicators of aspiration only. This is a notable oversight due to the prevalence of asphyxia as a cause of mortality in this population.

Aim This study aims to identify the physiological and environmental factors that predict asphyxiation risk in adults with intellectual disabilities and dysphagia.

Method Data were collected from dysphagia‐trained speech and language therapists (SLTs) working with the participant adults with intellectual disabilities and dysphagia. The SLTs used case notes, clinical assessment and videofluoroscopic assessment reports to gather the data.

Results Speed of eating, cramming food and premature loss of the bolus into the pharynx were identified as significant predictors of asphyxiation risk in this population.

Conclusions The findings highlight the importance of maladaptive eating strategies in exacerbating the risk of asphyxiation and choking. These factors should be considered in the assessment of asphyxiation and choking risk and management. Finally, the need for joint assessment and management with other members of the multidisciplinary team is advocated.
Practical modelling of porous media from second‐order statistics: the phase‐retrieval problem and the interpretation of the covariance
Authors: ANGUY YANNICK , LE TRONG EMMANUEL , EHRLICH ROBERT
Published: December 2005

In many disciplines, binary numerical porous media are commonly generated as realizations of a random process characterized by a limited set of morphological measurements, e.g. the conditioning and truncated Gaussian random field (GRF) model or the Monte Carlo simulated annealing (SA) reconstruction. Whether the output microstructures of a model are quantitative or qualitative depends largely on the information carried by the constraints that are implemented. We focus on the standard two‐point correlation function, also referred to as the covariance. The isotropic situation has been previously extensively studied. Here, we concentrate on a vector distance‐dependent covariance. Relying on practical solutions to the phase‐retrieval problem (retrieving an object from its Fourier modulus) encountered in general imaging, we show empirically that a finite binary two‐ or three‐dimensional actual sample can be recovered systematically to within a pixel from its correlation integral (the volume average covariance to within a scale factor). In random modelling, this characteristic, describing uniquely a single sample of finite size, must be simplified, i.e. reduced to its statistical content, prior to be fitted in a random model (GRF, SA) as the characteristic of a series of realizations of a porous medium. We consider a common simplification, i.e. truncation, in which that part of the covariance relating to the small‐scale features of the observed sample is preserved only. This arbitrary simplification is empirically supported by numerous published numerical experiments showing that the small‐scale content of a volume‐averaged covariance can be fairly well reproduced in realizations of various random models: its statistical nature is thus illustrated with the GRF model. The unique solution to the phase‐retrieval problem confers an important sense to this numerical agreement: the correlation integral being the most complete descriptor, the actual sample and the model outputs are considered as true analogues over scales smaller or equal to the cutoff length attached to the truncation. Thus, awareness of the phase‐retrieval problem supports on an empirical basis the generation of synthetic binary objects from a direct measurement on an available sample.
Studies on depth‐of‐field effects in microscopy supported by numerical simulations
Authors: OVERBY DARRYL R. , JOHNSON MARK
Published: December 2005

Micrographs are two‐dimensional (2D) representations of three‐dimensional (3D) objects. When the depth‐of‐field of a micrograph is comparable with or larger than the characteristic dimension of objects within the micrograph, measured 2D parameters (e.g. particle number density, surface area of particles, fraction of open space) require stereological correction to determine the correct 3D values. Here, we develop a stereological theory using a differential approach to relate the 3D volume fraction and specific surface area to the 2D projected area and perimeter fractions, accounting for the influence of depth‐of‐field. The stereological theory is appropriate for random isotropic arrangements of non‐interpenetrating particles and is valid for convex geometries (e.g. spheres, spheroids, cylinders). These geometrical assumptions allow the stereological formulae to be expressed as a set of algebraic equations incorporating a single parameter to describe particle shape that is tightly bounded between 1.5π and 2π. The stereological theory may also be applied to arrangements of interpenetrating convex particles, and for this case, the resulting stereological formulae become identical to the formulae previously presented by Miles. To test the accuracy of the stereological theory, random computational arrangements of non‐interpenetrating and interpenetrating spheres or cylinders are analysed, and the projected area and perimeter fractions are numerically determined as a function of depth‐of‐field. The computational results show very good agreement with the theoretical predictions over a broad range of depth‐of‐field, volume fraction and particle geometry for both non‐interpenetrating and interpenetrating particles, demonstrating the overall accuracy of the stereological theory. Applications of the stereological theory towards analysis of biological tissues and extracellular matrix are discussed.
Tracking quasi‐stationary flow of weak fluorescent signals by adaptive multi‐frame correlation
Authors: JI L. , DANUSER G.
Published: December 2005

We have developed a novel cross‐correlation technique to probe quasi‐stationary flow of fluorescent signals in live cells at a spatial resolution that is close to single particle tracking. By correlating image blocks between pairs of consecutive frames and integrating their correlation scores over multiple frame pairs, uncertainty in identifying a globally significant maximum in the correlation score function has been greatly reduced as compared with conventional correlation‐based tracking using the signal of only two consecutive frames. This approach proves robust and very effective in analysing images with a weak, noise‐perturbed signal contrast where texture characteristics cannot be matched between only a pair of frames. It can also be applied to images that lack prominent features that could be utilized for particle tracking or feature‐based template matching. Furthermore, owing to the integration of correlation scores over multiple frames, the method can handle signals with substantial frame‐to‐frame intensity variation where conventional correlation‐based tracking fails. We tested the performance of the method by tracking polymer flow in actin and microtubule cytoskeleton structures labelled at various fluorophore densities providing imagery with a broad range of signal modulation and noise. In applications to fluorescent speckle microscopy (FSM), where the fluorophore density is sufficiently low to reveal patterns of discrete fluorescent marks referred to as speckles, we combined the multi‐frame correlation approach proposed above with particle tracking. This hybrid approach allowed us to follow single speckles robustly in areas of high speckle density and fast flow, where previously published FSM analysis methods were unsuccessful. Thus, we can now probe cytoskeleton polymer dynamics in living cells at an entirely new level of complexity and with unprecedented detail.
Dissociation of basal dislocations in hexagonal barium titanate
Authors: WU Y. C. , HO N. J. , LU H. Y.
Published: December 2005

Dislocation substructure in hot‐pressed hexagonal BaTiO3 ceramics was analysed by transmission electron microscopy. Two dislocation networks each consisting of dissociated half‐partials were determined for the Burgers vectors (b) using the g · b = 0 effective invisibility criteria, and the true directions (u) by trace analysis. Each of the networks contains three partial nodes that are in the form: 1/3[010]+1/3[100]+1/3[100]+1/3[100] = 0, where four partials meet at a point and the Burgers vectors are conserved, as analysed by the weak‐beam dark field technique. Basal dislocation with bb = 1/3<110> is dissociated into two prism plane half‐partials with bhp = 1/3<100> by: 1/3<110> → 1/3<010> + 1/3<100>. Dissociation of basal dislocation by a glide mechanism creates a stacking fault when shear occurs along <100> in the c‐layer of (000l), where l = 1, 3, 4 and 6, of the (chc)1(chc)2 (or (CBC)(ABA)) stacking sequence. The slip system of 1/3<110>(0001) in hexagonal BaTiO3 has been activated at 1300 °C by hot‐pressing under ∼25.8 MPa. Plastic flow contributing to the densification of hexagonal BaTiO3 ceramics occurs through glide of half‐partials in the basal plane by a glide‐controlled dislocation glide mechanism. Dislocation motion governed by the Peierls mechanism, where velocity is determined by both correlated and uncorrelated double‐kink nucleation on two half‐partials, is discussed.
Long‐term evolution of serum and liver viral markers in patients treated for chronic hepatitis C and sustained response
Authors: Moreno M. , Pérez‐Alvarez R. , Rodrigo L. , Pérez‐López R. , Suárez‐Leiva P.
Published: December 2005

Summary.  Few studies have analysed the evolution of HCV markers in chronic hepatitis C (CHC)‐treated patients. We have evaluated the presence or absence of serum and liver HCV‐RNA, the core antigen (HCV‐cAg) and the loss of specific antibodies (anti‐HCV), in long‐term sustained responders (SR). One hundred and seventy‐six patients (132 SR and 44 nonresponders (NR) were included in the study. HCV‐RNA was determined in serum and liver by a commercial PCR‐kit. HCV‐Ag was determined by ELISA and specific antibodies against HCV by means of a commercial line immunoblot assay (LIA) technique. Serum HCVcAg was found positive in three (4.2%) SR and in one (4%) NR (NS). Four SR (3.6%) and 44 NR (100%) were also HCV‐RNA (+) in liver tissue. Two patients were HCV‐cAg (+). A good correlation was found between the serum levels of HCV‐cAg and HCV‐RNA (r = 0.847, P < 0.001). Specific antibodies (anti‐HCV) were determined by LIA in 45 patients. A decrease was found in the number of patients who presented reactivity to bands E2 and NS4 when we compared SR with a follow‐up of more than 5 years with NR and SR with a follow‐up <5 years (P < 0.01 and 0.005). A good correlation was found between the HCV‐cAg and HCV‐RNA serum levels in CHC‐treated patients (P < 0.001). Few SR (3.6%) had HCV‐RNA in the liver, and HCV‐cAg (1.8%) in serum. In SR with more than 5 years of follow‐up a clear tendency exists in the trend to clarify the bands E2 and NS4 of anti‐HCV in serum.
Gene lineages and eastern North American palaeodrainage basins: phylogeography and speciation in salamanders of the Eurycea bislineata species complex
Authors: KOZAK KENNETH H. , BLAINE RUSSELL A. , LARSON ALLAN
Published: December 2005

sAbstract

Contemporary North American drainage basins are composites of formerly isolated drainages, suggesting that fragmentation and fusion of palaeodrainage systems may have been an important factor generating current patterns of genetic and species diversity in stream‐associated organisms. Here, we combine traditional molecular‐phylogenetic, multiple‐regression, nested clade, and molecular‐demographic analyses to investigate the relationship between phylogeographic variation and the hydrogeological history of eastern North American drainage basins in semiaquatic plethodontid salamanders of the Eurycea bislineata species complex. Four hundred forty‐two sequences representing 1108 aligned bases from the mitochondrial genome are reported for the five formally recognized species of the E. bislineata complex and three outgroup taxa. Within the ingroup, 270 haplotypes are recovered from 144 sampling locations. Geographic patterns of mtDNA‐haplotype coalescence identify 13 putatively independent population‐level lineages, suggesting that the current taxonomy of the group underestimates species‐level diversity. Spatial and temporal patterns of phylogeographic divergence are strongly associated with historical rather than modern drainage connections, indicating that shifts in major drainage patterns played a pivotal role in the allopatric fragmentation of populations and build‐up of lineage diversity in these stream‐associated salamanders. More generally, our molecular genetic results corroborate geological and faunistic evidence suggesting that palaeodrainage connections altered by glacial advances and headwater erosion occurring between the mid‐Miocene and Pleistocene epochs explain regional patterns of biodiversity in eastern North American streams.
The relative influence of natural selection and geography on gene flow in guppies
Authors: CRISPO ERIKA , BENTZEN PAUL , REZNICK DAVID N. , KINNISON MICHAEL T. , HENDRY ANDREW P.
Published: December 2005

Two general processes may influence gene flow among populations. One involves divergent selection, wherein the maladaptation of immigrants and hybrids impedes gene flow between ecological environments (i.e. ecological speciation). The other involves geographic features that limit dispersal. We determined the relative influence of these two processes in natural populations of Trinidadian guppies (Poecilia reticulata). If selection is important, gene flow should be reduced between different selective environments. If geography is important, gene flow should be impeded by geographic distance and physical barriers. We examined how genetic divergence, long‐term gene flow, and contemporary dispersal within a watershed were influenced by waterfalls, geographic distance, predation, and habitat features. We found that waterfalls and geographic distance increased genetic divergence and reduced dispersal and long‐term gene flow. Differences in predation or habitat features did not influence genetic divergence or gene flow. In contrast, differences in predation did appear to reduce contemporary dispersal. We suggest that the standard predictions of ecological speciation may be heavily nuanced by the mating behaviour and life history strategies of guppies.
Hybrid origin and differentiation of two tetraploidAchilleaspecies in East Asia: molecular, morphological and ecogeographical evidence
Authors: GUO Y.‐P. , VOGL C. , VAN LOO M. , EHRENDORFER F.
Published: December 2005

Achillea(Asteraceae‐Anthemideae) offers classical models for speciation by hybridization and polyploidy. Here, we test the suspected allotetraploid origin of two species,Achillea alpinaandAchillea wilsonianabetween phylogenetically distinct lineages in East Asia. A total of 421 AFLP bands from 169 individuals and 19 populations of five 2x‐ and two 4x‐species were obtained. The data set was analysed with a newly developed model that accounts for polyploidy and assumes lack of recombination between the parental chromosome sets (i.e. disomic inheritance).A.alpinaandA.wilsonianathen appear to be allotetraploids betweenAchillea acuminata‐2x (sect.Ptarmica) andAchillea asiatica‐2x (sect.Achillea). The two 4x‐species share 44% and 48% of their AFLP bands withA.acuminata‐2x, and 39% and 38% withA.asiatica‐2x, respectively. Eight plastid haplotypes (A–H) were detected by polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP) analyses.A.alpina‐4x andA. wilsoniana‐4x share haplotype F only withA. asiatica‐2x. This is consistent with the hybrid origin(s) involving the latter as the maternal ancestor. This result corroborates our previous DNA sequence data, whereA. alpina‐4x andA. wilsoniana‐4x are also placed close toA. asiatica‐2x. Morphology, ecology, and amplified fragment length polymorphism (AFLP) profiles of the two 2x‐species are distinct, whereas the two 4x‐species, grouped asA.alpinaaggregate,form a nearly continuous link between them. Considering all evidence, this 4x‐aggregate is regarded as the product of a hybridization between genetically distant 2x‐ancestors limited to China and adjacent areas: oneA.acuminata‐like, and the otherA. asiatica‐like. The allopolyploidA.alpinaagg. exhibits considerable morphological variation and ecological flexibility, and has expanded throughout eastern Asia and to northern North America, far beyond the ranges of their presumed 2x‐ancestors.
Matching the origin of an invasive weed for selection of a herbivore haplotype for a biological control programme
Authors: GOOLSBY JOHN A. , DE BARRO PAUL J. , MAKINSON JEFFREY R. , PEMBERTON ROBERT W. , HARTLEY DIANA M. , FROHLICH DONALD R.
Published: December 2005

The Florida Everglades have been invaded by an exotic weed fern, Lygodium microphyllum. Across its native distribution in the Old World tropics from Africa to Australasia it was found to have multiple location‐specific haplotypes. Within this distribution, the climbing fern is attacked by a phytophagous mite, Floracarus perrepae, also with multiple haplotypes. The genetic relationship between mite and fern haplotypes was matched by an overarching geographical relationship between the two. Further, mites that occur in the same location as a particular fern haplotype were better able to utilize the fern than mites from more distant locations. From a biological control context, we are able to show that the weed fern in the Everglades most likely originated in northern Queensland, Australia/Papua New Guinea and that the mite from northern Queensland offers the greatest prospect for control.
Beringian origins and cryptic speciation events in the fly agaric (Amanita muscaria)
Authors: GEML J. , LAURSEN G. A. , O'NEILL K. , NUSBAUM H. C. , TAYLOR D. L.
Published: December 2005

Amanita muscaria sensu lato has a wide geographic distribution, occurring in Europe, Asia, Africa, Australia, New Zealand, and North, Central and South America. Previous phylogenetic work by others indicates three geographic clades (i.e. ‘Eurasian’, ‘Eurasian‐alpine’ and ‘North American’ groups) within A. muscaria. However, the historical dispersal patterns of A. muscaria remained unclear. In our project, we collected specimens from arctic, boreal and humid temperate regions in Alaska, and generated DNA sequence data from the protein‐coding beta‐tubulin gene and the internal transcribed spacer (ITS) and large subunit (LSU) regions of the ribosomal DNA repeat. Homologous sequences from additional A. muscaria isolates were downloaded from GenBank. We conducted phylogenetic and nested clade analyses (NCA) to reveal the phylogeographic history of the species complex. Although phylogenetic analyses confirmed the existence of the three above‐mentioned clades, representatives of all three groups were found to occur sympatrically in Alaska, suggesting that they represent cryptic phylogenetic species with partially overlapping geographic distributions rather than being allopatric populations. All phylogenetic species share at least two morphological varieties with other species, suggesting ancestral polymorphism in pileus and wart colour pre‐dating their speciations. The ancestral population of A. muscaria likely evolved in the Siberian–Beringian region and underwent fragmentation as inferred from NCA and the coalescent analyses. The data suggest that these populations later evolved into species, expanded their range in North America and Eurasia. In addition to range expansions, populations of all three species remained in Beringia and adapted to the cooling climate.
Management of patients with chronic abdominal pain in clinical practice
Authors: Camilleri M.
Published: December 2005

Abstract  A practical approach to the management of chronic abdominal pain is needed, given the high prevalence and impact of this problem. This article describes an approach that has evolved based on clinical experience and review of the literature: identifying predominant bloaters and abdominal wall pain; exclusion of organic disease, including consideration of laparoscopy for diagnosis; consideration of chronic functional abdominal pain and the first and second line pharmacotherapies; and seeking specialist care in a pain clinic, psychiatry, or behavioural therapy.
Circumnutation of rice coleoptiles: its relationships with gravitropism and absence in lazy mutants
Authors: YOSHIHARA TAKESHI , IINO MORITOSHI
Published: December 2005

Although circumnutation occurs widely in higher plants, its mechanism is little understood. The idea that circumnutation is based on gravitropism has long been investigated, but the reported results have been controversial. We used dark‐grown coleoptiles of rice (Oryza sativa L.) to re‐investigate this issue. The following results supported the existence of a close relationship between gravitropism and circumnutation: (1) circumnutation disappears on a horizontal clinostat; (2) circumnutation is interrupted by a gravitropic response and re‐initiated at a definable phase after gravitropic curvature; (3) circumnutation can be re‐established by submergence and a brief gravitropic stimulation in the coleoptiles that have stopped nutating in response to red light; and (4) lazy mutants show no circumnutation. In spite of these results, however, there were cases in which gravitropism and circumnutation could be separated. Firstly, the non‐circumnutating lazy coleoptile showed nearly a wild‐type level of gravitropic responsiveness in its upper half, although this part was an active site of both gravitropism and circumnutation in wild‐type coleoptiles. Secondly, coleoptiles could nutate without overshooting the vertical when developing phototropic curvature. It is concluded that gravitropism influences, but it is not directly involved in the process of circumnutation. It is further suggested that a gravity signal, shared with gravitropism, contributes to the maintenance of circumnutation.
Effects of chronic ozone exposure on gene expression in Arabidopsis thaliana ecotypes and in Thellungiella halophila
Authors: LI PINGHUA , MANE SHRINIVASRAO P. , SIOSON ALLAN A. , ROBINET CECILIA VASQUEZ , HEATH LENWOOD S. , BOHNERT HANS J. , GRENE RUTH.
Published: December 2005

Arabidopsis thaliana (At) ecotypes Columbia‐0 (Col‐0), Wassilewskija (WS), Cape Verde Islands (Cvi‐0) and a relative, Thellungiella halophila (Th), were exposed to 20–25% over ambient ozone [O3] in a free air concentration enrichment (FACE) experiment (http://www.soyFACE.uiuc.edu), mirroring increases expected in the near future. Col‐0 and WS accelerated development and developed lesions within 10 d under increased ozone, while Cvi‐0 and Th grew slowly. RNAs were used in microarray hybridizations (Col‐0‐based 26 000 elements, 70‐mer oligonucleotides). A two‐step analysis of variance (anova) model, including comparison with values obtained under [O3], was used for analyses. WS showed the greatest number of changes in gene expression in response to ozone. Th showed the least changes, suggesting that its expression state at [O3] was sufficient for resistance at increased ozone. Patterns observed in ambient air controls for Cvi‐0 and Col‐0 were most similar, while Th showed the greatest number of differences compared with the other controls. Compared with Col‐0, however, Cvi‐0 showed higher levels of expression of chaperones, receptor kinase‐like and photosynthesis‐related genes in ambient air. Cvi‐0 exhibited ozone‐mediated changes in a pathway involving AtSR, a homologue of the mammalian NFκB family of redox‐sensitive transcription factors, changes in chaperones, WRKY and C2H2 proteins and antioxidants. WS displayed ozone‐mediated decreases in the expression of two AtSR/NFκB family members, C2‐domain proteins and genes associated with cell wall growth and changes in the expression of marker genes for programmed cell death (PCD), among them RCD1, a key regulator in this pathway. Microarray data were verified by reverse transcriptase (RT)‐PCR. We relate O3‐response diversity across the four lines to different responses among signaling and transcriptional response networks and differences in gene expression at [O3] levels.
Cysteines 449 and 459 modulate the reduction–oxidation conformational changes of ribulose 1·5‐bisphosphate carboxylase/oxygenase and the translocation of the enzyme to membranes during stress
Authors: MARÍN‐NAVARRO JULIA , MORENO JOAQUÍN
Published: December 2005

The role of cysteines 449 (Cys449) and 459 (Cys459) from the large subunit (LS) of ribulose 1·5‐bisphosphate carboxylase/oxygenase (Rubisco) in the reduction–oxidation (redox) regulation of the enzyme was assessed by site‐directed mutagenesis of these residues and chloroplast transformation of Chlamydomonas reinhardtii. In vitro studies indicated that mutations C449S, C459S or C449S/C459S do not affect the activity and proteolytic susceptibility of the enzyme in the reduced state. However, when oxidized, the mutant enzymes differed from the wild type (WT), showing an increased resistance to inactivation and, in the case of the double mutant (DM), an altered structural conformation as reflected by the kinetics of proteolysis with subtilisin. The response of the DM strain to saline stress revealed that the absence of Cys449 and Cys459 intensifies Rubisco degradation and the covalent disulfide and non‐disulfide polymerization of the enzyme in vivo. Saline stress also induced Rubisco translocation to a membrane (M) fraction that contained only covalently polymerized enzyme. Rubisco mobilization to this M fraction was enhanced also in the DM strain. Altogether, these results indicate that Cys449 and Cys459 participate in the modulation of the conformational changes promoted by oxidative modifications retarding processes related to the catabolism of the enzyme in vivo.
Relationships of disease and leaf area variables with yield in the Alternaria helianthi–sunflower pathosystem
Authors: Leite R. M. V. B. C. , Amorim L. , Bergamin Filho A.
Published: December 2005

Three field experiments were carried out in 1997/1998, 1998/1999 and 1999/2000 to investigate the relationship between severity (S) of alternaria leaf spot, caused by Alternaria helianthi, area under disease progress curve (AUDPC), healthy leaf area index at any given day (HLAI), healthy leaf area duration (HAD), radiation intercepted by healthy leaf area at any given day (HRI), total healthy leaf area absorption (HAA), and yield components of sunflower sown on four dates. AUDPC showed a relationship with yield in two years, following the negative exponential model coefficient of determination (R2 = 0·79 and 0·60). The HAD–yield relationship was linear for each of three trials (0·73 < R2 < 0·83). Among the integral variables analysed, the HAA–yield relationship was the best, fitted by the exponential model (0·77 < R2 < 0·89). Single‐point models using disease severity, HLAI and HRI to estimate yield at various times during the crop season were tested. The slope of the severity–yield relationship was stable from the R1 (inflorescence visible) growth stage. The HLAI–yield relationship was stable between R1 and R6 (anthesis completed) and increased from the R7 (first phase of achene development) stage. The HRI–yield relationship was variable and not stable. The relationship between severity and yield in the R3 (second phase of inflorescence elongation) growth stage proved that plants with disease severity higher than 10% had yield lower than 500 kg ha−1, regardless of the sowing date. This value can be used as a damage threshold for the disease. Disease severity can be used as an independent variable in a sunflower–alternaria leaf spot management system and can be used to produce recommendations at the research level, such as genetic breeding for disease resistance or studies on sowing date.
Biological control of fusarium crown and root rot of tomato with antagonistic bacteria and integrated control when combined with the fungicide carbendazim
Authors: Omar I. , O'Neill T. M. , Rossall S.
Published: December 2005

Two bacterial isolates, Bacillus megaterium (c96) and Burkholderia cepacia (c91), demonstrated to be antagonistic against Fusarium oxysporum f.sp. radicis‐lycopersici, the causal organism of fusarium crown and root rot of tomato, were evaluated as biocontrol agents alone and when integrated with the fungicide carbendazim. In an initial screening, these isolates reduced disease incidence by 75 and 88%, respectively. In vitro, both biocontrol agents were highly tolerant to the fungicide carbendazim, commonly used to control fusarium diseases. Carbendazim reduced disease symptoms by over 50% when used at > 50 µg mL−1, but had little effect at lower concentrations. Combination of the bacterial isolates and carbendazim gave significant (P ≤ 0·05) control of the disease when plants were artificially inoculated with the pathogen. Application of carbendazim at a low concentration (1 µg mL−1) in combination with B. cepacia c91 reduced disease symptoms by 46%, compared with a reduction of 20% obtained with the bacterium alone and no control with the chemical treatment alone. A combination of B. megaterium c96 with an increased application rate of 10 µg mL−1 carbendazim significantly reduced disease symptoms by 84% compared with inoculated controls and by 77% compared with carbendazim treatment alone. In this experiment, the integrated treatment also slightly outperformed application of 100 µg mL−1 carbendazim, and bacteria applied without fungicide also provided good disease control.
Assessing mango anthracnose using a new three‐dimensional image‐analysis technique to quantify lesions on fruit
Authors: Corkidi G. , Balderas‐Ruíz K. A. , Taboada B. , Serrano‐Carreón L. , Galindo E.
Published: December 2005

An accurate image‐analysis method was developed to assess quantitatively the spot‐like lesions on fruits resulting from pathogen attack. The technique was applied to evaluation of the development and severity of anthracnose of mango fruit, caused by the fungus Colletotrichum gloeosporioides. In this method, a stepper motor rotates the mango fruit along its longitudinal axis while acquiring a sequence of 360 images of its total surface (one image for each degree). This set of images is used to create a pseudocylindrical ‘equal‐area’ projection of the fruit in a two‐dimensional map containing complete morphometrical and photometrical information of its surface. The lesion area can easily be evaluated from this map with image‐analysis procedures. Quantitative data (percentage of area affected) can be used to establish an assessment scale for the disease based on lesion spots measured, as well as for detailed laboratory studies of mango anthracnose development. The average error of the method is −0·1%, standard deviation 0·44 (r2 = 0·99), and it may be adapted for use with most commercial image analysers and for other diseases with spot‐like symptoms.
Trapping of sustained turbidity currents by intraslope minibasins
Authors: LAMB MICHAEL P. , TONIOLO HORACIO , PARKER GARY
Published: December 2005

Depositional turbidity currents have filled many intraslope minibasins with sediment creating targets for petroleum exploration. The dynamics of sustained turbidity currents and their depositional characteristics are investigated in a scaled physical model of a minibasin. Each turbidity current deposited a downstream thinning wedge of sediment near the inlet. Farther downstream the turbidity current was ponded by a barrier. The ponded part of the turbidity current was separated from the sediment‐free water above by a relatively sharp, horizontal settling interface indicating highly Froude‐subcritical flow. The very slow moving flow within the ponded zone created conditions for the passive rainout of suspended sediment onto the bed. In the lower part of the ponded zone, the concentration and mean grain‐size of the sediment in suspension tended to be relatively uniform in both the vertical and streamwise directions. As a result, the deposit emplaced in the ponded zone showed only a weak tendency toward downstream fining and was passively draped over the bed in such a way that irregularities in the inerodible bed were accurately reflected. The discharge of suspended sediment overflowing the downstream end of the minibasin was significantly less than the inflow discharge, resulting in basin sediment trapping efficiencies >95%. A simple model is developed to predict the trapping of sediment within the basin based on the relative magnitudes of the input discharge of turbid water and the detrainment discharge of water across the settling interface. This model shows a limiting case in which an intraslope basin captures 100% of the sediment from a ponded turbidity current, even through a succession of sustained flow events, until sediment deposition raises the settling interface above the downstream lip of the minibasin. This same process defines one of the mechanisms for minibasin filling in nature, and, when this mechanism is operative, the trap efficiency of sediment can be expected to be high until the minibasin is substantially filled with sediment.
Formation of subglacial till under transient bed conditions: deposition, deformation, and basal decoupling under a Weichselian ice sheet lobe, central Poland
Authors: PIOTROWSKI J. A. , LARSEN N. K. , MENZIES J. , WYSOTA W.
Published: December 2005

A multi‐proxy approach involving a study of sediment architecture, grain size, grain roundness and crushing index, petrographic and clay mineral composition, till fabric and till micromorphology was applied to infer processes of till formation and deformation under a Weichselian ice sheet at Kurzetnik, Poland. The succession consists of three superposed till units overlying outwash sediments deformed at the top. The textural characteristics of tills vary little throughout the till thickness, whereas structural appearance is diversified including massive and bedded regions. Indicators of intergranular bed deformation include overturned, attenuated folds, boudinage structures, a sediment‐mixing zone, grain crushing, microstructural lineations, grain stacking and high fabric strength. Lodgement proxies are grooved intra‐till surfaces, ploughing marks and consistently striated clast surfaces. Basal decoupling by pressurized meltwater is indicated by undisturbed sand stringers, sand‐filled meltwater scours under pebbles and partly armoured till pellets. It is suggested that the till experienced multiple transitions between lodgement, deformation and basal decoupling. Cumulative strain was high, but the depth of (time‐transgressive) deformation much lower (centimetre range) than the entire till thickness (ca 2 m) at any point in time, consistent with the deforming bed mosaic model. Throughout most of ice overriding, porewater pressure was high, in the vicinity of glacier floatation pressure indicating that the substratum, consisting of 11 m thick sand, was unable to drain subglacial meltwater sufficiently.
An evaluation of a GARP model as an approach to predicting the spatial distribution of non‐vagile invertebrate species
Authors: Stockman Amy K. , Beamer David A. , Bond Jason E.
Published: December 2005

One of the primary goals of any systematic, taxonomic or biodiversity study is the characterization of species distributions. While museum collection data are important for ascertaining distributional ranges, they are often biased or incomplete. The Genetic Algorithm for Rule‐set Prediction (GARP) is an ecological niche modelling method based on a genetic algorithm that has been argued to provide an accurate assessment of the spatial distribution of organisms that have dispersal capabilities. The primary objective of this study is to evaluate the accuracy of a GARP model to predict the spatial distribution of a non‐invasive, non‐vagile invertebrate whose full distributional range was unknown. A GARP predictive model based on seven environmental parameters and 42 locations known from historical museum records for species of the trapdoor spider genus Promyrmekiaphila was produced and subsequently used as a guide for ground truthing the model. The GARP model was neither a significant nor an accurate predictor of spider localities and was outperformed by more simplistic BIOCLIM and GLM models. The isolated nature of Promyrmekiaphila populations mandates that environmental layers and their respective resolutions are carefully chosen for model production. Our results strongly indicate that, for modelling the spatial distribution of low vagility organisms, one should employ a modelling method whose results are more conducive to interpretation than models produced by a ‘black box’ algorithm such as GARP.