bluuebunny/crossref_metadata_2025 huggingface dataset:
BIFURCATIONS AND INSTABILITIES
Authors: Ghoniem Nasr M. , Walgraef Daniel D.
Published: May 2008

This chapter focuses on the mathematical structures underlying the notions of stability, bifurcation, and instabilities in complex nonlinear dynamical systems described by sets of ordinary or partial differential equations. It begins by presenting the basic ideas of stability analysis in systems described by ordinary differential equations, introducing Lyapunov functions and their utilization in stability analysis. The stability of systems described by partial differential equations is discussed, emphasizing some of the basic ideas that allow quantitative descriptions of patterns. Specific models illustrating the concepts behind Hopf and Turing instabilities are also discussed.
AMPLITUDE EQUATIONS AND PATTERN FORMATION
Authors: Ghoniem Nasr M. , Walgraef Daniel D.
Published: May 2008

This chapter begins with a discussion of reduced dynamics and amplitude equations. It then discusses the generic aspects of pattern selection and stability, the effect of external fields; group velocity, convective, and absolute instabilities; and pattern formation and front propagation.
PHASE INSTABILITIES AND PATTERNS
Authors: Ghoniem Nasr M. , Walgraef Daniel D.
Published: May 2008

This chapter begins with a discussion of phase transformations and the design of materials. It then presents a case study on the art of steel-making. This is followed by a discussion of precipitate evolution and structure, phase instabilities, stress effects on spinodal decomposition, and martensitic phase transformations.
MECHANICAL INSTABILITIES
Authors: Ghoniem Nasr M. , Walgraef Daniel D.
Published: May 2008

This chapter is focused on mechanical instabilities, which give rise to microstructure pattern formation and eventual failure of stressed solids. Plastic instabilities are described in detail because of their importance in understanding the mechanical behaviour of materials, and because of the strong link between mechanical instabilities and failure. The problem of fracture and damage is also discussed within the present framework. Finally, some aspects of the mechanics of granular materials and associated instabilities are considered.
CONCLUSIONS
Authors: Ghoniem Nasr M. , Walgraef Daniel D.
Published: May 2008

This concluding chapter begins with a discussion of universality of self-organization. It then considers the connections between patterns, defects and instabilities; and the dilemma of modeling and the multi-scale approach. It addresses the question of whether self-organization will ever be practical.
SYCAMORE—a

sy

stems biology

c

omputational

a

nalysis and

mo

deling

r

esearch

e

nvironment
Authors: Weidemann Andreas , Richter Stefan , Stein Matthias , Sahle Sven , Gauges Ralph , Gabdoulline Razif , Surovtsova Irina , Semmelrock Nils , Besson Bruno , Rojas Isabel , Wade Rebecca , Kummer Ursula
Published: May 2008

Summary: SYCAMORE is a browser-based application that facilitates construction, simulation and analysis of kinetic models in systems biology. Thus, it allows e.g. database supported modelling, basic model checking and the estimation of unknown kinetic parameters based on protein structures. In addition, it offers some guidance in order to allow non-expert users to perform basic computational modelling tasks.

Availability: SYCAMORE is freely available for academic use at http://sycamore.eml.org. Commercial users may acquire a license.

Contact:  ursula.kummer@bioquant.uni-heidelberg.de
Immunostimulation‐Mediated Anti‐Tumor Activity of Bamboo (Sasa senanensis) Leaf Extracts Obtained under ‘Vigorous’ Condition
Authors: Seki Takahiro , Kida Kenji , Maeda Hiroshi
Published: May 2008

Traditional Japanese medicine uses the leaves of Kumaizasa bamboo extracted in hot water at 100°C. For this study, we developed a new, ‘vigorous’ extraction method involving steps at 100, 121 and 196°C. This procedure not only yielded greater amounts of extract but also with significant increase in immunostimulating activity, which induces activation of human natural killer (NK) cells, macrophages and potent induction of IL‐2, IL‐12 and IFN‐γ in tumor bearing mice. The efficacy of the extract to facilitate phagocytosis and nitric oxide production by mouse peritoneal macrophages was determined and compared with that of 1,3‐β‐glucan. Anti‐tumor activity was evaluated in vivo in several mouse tumor models (S‐180, C38 and Meth‐A). Oral administration of the extracts was carried out when tumor reached size of approximately 6 mm at concentrations of 0.05% or higher. The extracts significantly suppressed tumor growth in S‐180 and C38 tumor models. Overall survival was significantly prolonged in the treatment group than that of control. Activation of macrophages and NK cells by the extracts suggests that the anti‐tumor efficacy of the extract is mediated by immunopotentiation. The extracts resolved into three major fractions (F‐I, F‐II and F‐III) in Sephadex gel chromatography. Fraction F‐I consists of 1,3‐β‐glucan and stimulated both macrophages and NK cells suggesting that it may be the primary immunopotentiating factor in suppressing cancer. Fraction F‐III has potent free radical scavenging effects and may play an important role in cancer prevention. These results warrant further translation and clinical investigations.
Two Sides of the Same Coin? Employing Granger Causality Tests in a Time Series Cross-Section Framework
Authors: Hood M. V. , Kidd Quentin , Morris Irwin L.
Published: May 2008

In this paper, we introduce a recently developed methodology for assessing the assumption of causal homogeneity in a time series cross-section Granger framework. Following a description of the procedure and the analytical contexts for which it is appropriate, we implement this new approach to examine the transformation of the post-World War II party system in the South. Specifically, we analyze the causal relationship between black mobilization and GOP growth in the region. We find that black mobilization Granger caused Republican growth throughout the South, whereas Republican growth Granger caused black mobilization only in the deep South. We discuss the substantive significance of our results and conclude with guidelines for the appropriate use of this procedure and suggestions for future extensions of the method.
Twenty Years of Transgenic Plants Resistant toCucumber mosaic virus
Authors: Morroni Marco , Thompson Jeremy R. , Tepfer Mark
Published: May 2008

Plant genetic engineering has promised researchers improved speed and flexibility with regard to the introduction of new traits into cultivated crops. A variety of approaches have been applied to produce virus-resistant transgenic plants, some of which have proven to be remarkably successful. Studies on transgenic resistance to Cucumber mosaic virus probably have been the most intense of any plant virus. Several effective strategies based on pathogen-derived resistance have been identified; namely, resistance mediated by the viral coat protein, the viral replicase, and post-transcriptional gene silencing. Techniques using non-pathogen-derived resistance strategies, some of which could offer broader resistance, generally have proven to be much less effective. Not only do the results obtained so far provide a useful guide to help focus on future strategies, but they also suggest that there are a number of possible mechanisms involved in conferring these resistances. Further detailed studies on the interplay between viral transgene-derived molecules and their host are needed in order to elucidate the mechanisms of resistance and pathogenicity.
Expression of Medicago truncatula Genes Responsive to Nitric Oxide in Pathogenic and Symbiotic Conditions
Authors: Ferrarini Alberto , De Stefano Matteo , Baudouin Emmanuel , Pucciariello Chiara , Polverari Annalisa , Puppo Alain , Delledonne Massimo
Published: May 2008

Nitric oxide (NO) is involved in diverse physiological processes in plants, including growth, development, response to pathogens, and interactions with beneficial microorganisms. In this work, a dedicated microarray representing the widest database available of NO-related transcripts in plants has been produced with 999 genes identified by a cDNA amplified fragment length polymorphism analysis as modulated in Medicago truncatula roots treated with two NO donors. The microarray then was used to monitor the expression of NO-responsive genes in M. truncatula during the incompatible interaction with the foliar pathogen Colletotrichum trifolii race 1 and during the symbiotic interaction with Sinorhizobium meliloti 1021. A wide modulation of NO-related genes has been detected during the hypersensitive reaction or during nodule formation and is discussed with special emphasis on the physiological relevance of these genes in the context of the two biotic interactions. This work clearly shows that NO-responsive genes behave differently depending on the plant organ and on the type of interaction, strengthening the need to consider regulatory networks, including different signaling molecules.
The Root-Colonizing Endophyte Pirifomospora indica Confers Drought Tolerance in Arabidopsis by Stimulating the Expression of Drought Stress–Related Genes in Leaves
Authors: Sherameti Irena , Tripathi Swati , Varma Ajit , Oelmüller Ralf
Published: May 2008

Piriformospora indica is an endophytic fungus that colonizes the roots of many plant species, including Arabidopsis. We exposed 18-day-old Arabidopsis seedlings, which were either cocultivated with the fungus or mock-treated for the last 9 days, to mild drought stress for 84 h. During the first 36 to 48 h, seedlings cocultivated with the fungus continued to grow, while the uncolonized controls did not. This results in a threefold difference in the fresh weight and a more than twofold difference in the chlorophyll content. The photosynthetic efficiency was only slightly reduced in the colonized (F variable/F maximum [Fv/Fm] at t0h = 0.82 and t36h = 0.79) and was severely impaired in the uncolonized (Fv/Fm at t0h = 0.81 and t36h = 0.49) seedlings, which also showed symptoms of withering. When seedlings exposed to drought stress for 72 or 84 h were transferred to soil, 10% (72 h) and none (84 h) of uncolonized seedlings reached the flowering stage and produced seeds, while 59% (72 h) and 47% (84 h) of the colonized seedlings flowered and produced seeds. After exposure to drought stress for 3 h, the message levels for RESPONSE TO DEHYDRATION 29A, EARLY RESPONSE TO DEHYDRATION1, ANAC072, DEHYDRATION-RESPONSE ELEMENT BINDING PROTEIN2A, SALT-, AND DROUGHT-INDUCED RING FINGER1, phospholipase Dδ, CALCINEURIN B-LIKE PROTEIN (CBL)1, CBL-INTERACTING PROTEIN KINASE3, and the histone acetyltransferase (HAT) were upregulated in the leaves of P. indica–colonized seedlings. Uncolonized seedlings responded 3 to 6 h later, and the message levels increased much less. We identified an Arabidopsis ethylmethane-sulfonate mutant that is less resistant to drought stress and in which the stress-related genes were not upregulated in the presence of P. indica. Thus, P. indica confers drought-stress tolerance to Arabidopsis, and this is associated with the priming of the expression of a quite diverse set of stress-related genes in the leaves. Transfer to soil was again associated with a faster and stronger upregulation of the message levels for phospholipase Dδ, CBL1, and HAT in P. indica–colonized seedlings, indicating that this response might also contribute to better survival on soil.
Salamander-like development in a seymouriamorph revealed by palaeohistology
Authors: Sanchez Sophie , Klembara Jozef , Castanet Jacques , Steyer J. Sébastien
Published: May 2008

The amniotes generally lay eggs on land and are thereby differentiated from lissamphibians (salamanders, frogs and caecilians) by their developmental pattern. Although a number of 330–300-Myr old fossils are regarded as early tetrapods placed close to amniotes on the basis of anatomical data, we still do not know whether their developmental pattern was more similar to those of lissamphibians or amniotes. Here we report palaeohistological and skeletochronological evidence supporting a salamander-like development in the seymouriamorph
Discosauriscus
. Its long-bone growth pattern, slow diaphyseal growth rate and delayed sexual maturity (at more than 10 years old) are more comparable with growth features of extant salamanders rather than extant amniotes, even though they are mostly hypothesized to be phylogenetically closer to living amniotes than salamanders.
Numerical removal of water vapour effects from terahertz time-domain spectroscopy measurements
Authors: Withayachumnankul Withawat , Fischer Bernd M , Abbott Derek
Published: May 2008

The use of T-rays, or terahertz radiation, to identify substances by their spectroscopic fingerprints is a rapidly moving field. The dominant approach is presently terahertz time-domain spectroscopy. However, a key problem is that ambient water vapour is ubiquitous and the consequent water absorption distorts the T-ray pulses. Water molecules in the gas phase selectively absorb incident T-rays at discrete frequencies corresponding to their molecular rotational transitions. When T-rays propagate through an atmosphere, this results in prominent resonances spread over the T-ray spectrum; furthermore, in the time domain, fluctuations after the main pulse are observed in the T-ray signal. These effects are generally undesired, since they may mask critical spectroscopic data. So, ambient water vapour is commonly removed from the T-ray path by using a closed chamber during the measurement. Yet, in some applications, a closed chamber is not always feasible. This situation, therefore, motivates the need for an optional alternative method for reducing these unwanted artefacts. This paper represents a study on a computational means that is a step towards addressing the problem arising from water vapour absorption over a moderate propagation distance. Initially, the complex frequency response of water vapour is modelled from a spectroscopic catalogue. Using a deconvolution technique, together with fine tuning of the strength of each resonance, parts of the water vapour response are removed from a measured T-ray signal, with minimal signal distortion, thus providing experimental validation of the technique.
Scaling laws for delay-sensitive traffic in Rayleigh fading networks
Authors: Karamchandani Nikhil , Franceschetti Massimo
Published: May 2008

The throughput of delay-sensitive traffic in a Rayleigh fading network is studied by adopting a scaling limit approach. The case of the study is that of a pair of nodes establishing a data stream that has routing priority over all the remaining traffic in the network. For every delay constraint, upper and lower bounds on the achievable information rate between the two endpoints of the stream are obtained as the network size grows. The analysis concerns
decentralized schemes
, in the sense that all nodes make next-hop decisions based only on
local
information, namely their channel strength to other nodes in the network and the position of the destination node. This is particularly important in a fading scenario, where the channel strength varies with time and hence pre-computing routes can be of little help. Natural applications are remote surveillance using sensor networks and communication in emergency scenarios.
Multi-level trophic cascades in a heavily exploited open marine ecosystem
Authors: Casini Michele , Lövgren Johan , Hjelm Joakim , Cardinale Massimiliano , Molinero Juan-Carlos , Kornilovs Georgs
Published: May 2008

Anthropogenic disturbances intertwined with climatic changes can have a large impact on the upper trophic levels of marine ecosystems, which may cascade down the food web. So far it has been difficult to demonstrate multi-level trophic cascades in pelagic marine environments. Using field data collected during a 33-year period, we show for the first time a four-level community-wide trophic cascade in the open Baltic Sea. The dramatic reduction of the cod (
Gadus morhua
) population directly affected its main prey, the zooplanktivorous sprat (
Sprattus sprattus
), and indirectly the summer biomass of zooplankton and phytoplankton (top-down processes). Bottom-up processes and climate–hydrological forces had a weaker influence on sprat and zooplankton, whereas phytoplankton variation was explained solely by top-down mechanisms. Our results suggest that in order to dampen the occasionally harmful algal blooms of the Baltic, effort should be addressed not only to control anthropogenic nutrient inputs but also to preserve structure and functioning of higher trophic levels.
Rethinking convective quasi-equilibrium: observational constraints for stochastic convective schemes in climate models
Authors: Neelin J. David , Peters Ole , Lin Johnny W.-B , Hales Katrina , Holloway Christopher E
Published: May 2008

Convective quasi-equilibrium (QE) has for several decades stood as a key postulate for parametrization of the impacts of moist convection at small scales upon the large-scale flow. Departures from QE have motivated stochastic convective parametrization, which in its early stages may be viewed as a sensitivity study. Introducing plausible stochastic terms to modify the existing convective parametrizations can have substantial impact, but, as for so many aspects of convective parametrization, the results are sensitive to details of the assumed processes. We present observational results aimed at helping to constrain convection schemes, with implications for each of conventional, stochastic or ‘superparametrization’ schemes. The original vision of QE due to Arakawa fares well as a leading approximation, but with a number of updates. Some, like the imperfect connection between the boundary layer and the free troposphere, and the importance of free-tropospheric moisture to buoyancy, are quantitatively important but lie within the framework of ensemble-average convection slaved to the large scale. Observations of critical phenomena associated with a continuous phase transition for precipitation as a function of water vapour and temperature suggest a more substantial revision. While the system's attraction to the critical point is predicted by QE, several fundamental properties of the transition, including high precipitation variance in the critical region, need to be added to the theory. Long-range correlations imply that this variance does not reduce quickly under spatial averaging; scaling associated with this spatial averaging has potential implications for superparametrization. Long tails of the distribution of water vapour create relatively frequent excursions above criticality with associated strong precipitation events.
Bird-like sex chromosomes of platypus imply recent origin of mammal sex chromosomes
Authors: Veyrunes Frédéric , Waters Paul D. , Miethke Pat , Rens Willem , McMillan Daniel , Alsop Amber E. , Grützner Frank , Deakin Janine E. , Whittington Camilla M. , Schatzkamer Kyriena , Kremitzki Colin L. , Graves Tina , Ferguson-Smith Malcolm A. , Warren Wes , Marshall Graves Jennifer A.
Published: May 2008

In therian mammals (placentals and marsupials), sex is determined by an XX female: XY male system, in which a gene (SRY) on the Y affects male determination. There is no equivalent in other amniotes, although some taxa (notably birds and snakes) have differentiated sex chromosomes. Birds have a ZW female: ZZ male system with no homology with mammal sex chromosomes, in which dosage of a Z-borne gene (possibly DMRT1) affects male determination. As the most basal mammal group, the egg-laying monotremes are ideal for determining how the therian XY system evolved. The platypus has an extraordinary sex chromosome complex, in which five X and five Y chromosomes pair in a translocation chain of alternating X and Y chromosomes. We used physical mapping to identify genes on the pairing regions between adjacent X and Y chromosomes. Most significantly, comparative mapping shows that, contrary to earlier reports, there is no homology between the platypus and therian X chromosomes. Orthologs of genes in the conserved region of the human X (including SOX3, the gene from which SRY evolved) all map to platypus chromosome 6, which therefore represents the ancestral autosome from which the therian X and Y pair derived. Rather, the platypus X chromosomes have substantial homology with the bird Z chromosome (including DMRT1) and to segments syntenic with this region in the human genome. Thus, platypus sex chromosomes have strong homology with bird, but not to therian sex chromosomes, implying that the therian X and Y chromosomes (and the SRY gene) evolved from an autosomal pair after the divergence of monotremes only 166 million years ago. Therefore, the therian X and Y are more than 145 million years younger than previously thought.
The roles of the medial prefrontal cortex and hippocampus in a spatial paired-association task
Authors: Lee Inah , Solivan Frances
Published: May 2008

Although the roles of both the hippocampus and the medial prefrontal cortex (mPFC) have been suggested in a spatial paired-associate memory task, both areas were investigated separately in prior studies. The current study investigated the relative contributions of the hippocampus and mPFC to spatial paired-associate learning within a single behavioral paradigm. In a novel behavioral task, a pair of different objects appeared repeatedly across trials, but in different arms in a radial maze, and different rules were associated with those arms for reward. Specifically, in an “object-in-place” arm, the rat was required to choose a particular object associated with the arm. In a “location-in-place” arm, the animal was required to choose a certain within-arm location (ignoring the object occupying the location). Compared to normal animals, rats with ibotenic acid-based lesions in the hippocampus showed an irrecoverable impairment in performance in both object-in-place and location-in-place arms. When the mPFC was inactivated by muscimol (GABAA receptor agonist) in the normal animals with intact hippocampi, they showed the same severe impairment as seen in the hippocampal lesioned rats only in object-in-place arms. The results confirm that the hippocampus is necessary for a biconditional paired-associate task when space is a critical component. The mPFC, however, is more selectively involved in the object–place paired-associate task than in the location-place paired-associate task. The current task powerfully demonstrates an experimental situation in which both the hippocampus and mPFC are required and may serve as a useful paradigm for investigating the neural mechanisms of object–place association.
The basolateral amygdala is necessary for learning but not relearning extinction of context conditioned fear
Authors: Laurent Vincent , Marchand Alain R. , Westbrook R. Frederick
Published: May 2008

Extinction of conditioned fear involves new learning that inhibits but does not eliminate the original fear memory. This inhibitory learning is thought to require activation of NMDA receptors (NMDAr) within the basolateral amygdala (BLA). However, once extinction has been learned, the role played by the BLA during subsequent extinction procedures remains unknown. The present study examined the role of neuronal activity and NMDAr activation in rats receiving their first or second extinction of context fear. We found that BLA infusion of DL-APV, a competitive antagonist of NMDAr, depressed fear responses at both the first and second extinction. It impaired learning extinction but spared and even facilitated relearning extinction. BLA infusion of muscimol, a GABAA agonist, produced a similar outcome, suggesting that DL-APV not only blocked NMDAr-dependent plasticity but also disrupted neuronal activity. In contrast, infusion of ifenprodil, a more selective antagonist of NMDAr containing the NR2B subunit, did not depress fear responses but impaired short- and long-term inhibition of fear at both the first and second extinction. Therefore, we suggest that relearning extinction normally requires NMDAr containing the NR2B subunit in the BLA. However, simultaneous blockade of these receptors and neuronal activity in the BLA results in compensatory learning that is able to promote long-term re-extinction. These data are consistent with a current model that attributes fear extinction to interactions between several neural substrates, including the amygdala and the medial prefrontal cortex.
Growth–mortality relationships as indicators of life‐history strategies: a comparison of nine tree species in unmanaged European forests
Authors: Wunder Jan , Brzeziecki Bogdan , Żybura Henryk , Reineking Björn , Bigler Christof , Bugmann Harald
Published: May 2008

Forest succession depends strongly on the life history strategies of individual trees. An important strategic element is the ability to survive unfavourable environmental conditions that result in strongly reduced tree growth. In this study, we investigated whether the relationship between growth and mortality differs among tree species and site conditions. We analysed 10 329 trees of nine tree species (Picea abies, Taxus baccata, Fagus sylvatica, Tilia cordata, Carpinus betulus, Fraxinus excelsior, Quercus robur, Betula spp. and Alnus glutinosa) from unmanaged forests of Europe: the continental Białowieża forest (Poland) and several oceanically influenced Swiss forest reserves. For each species, we calculated a set of flexible logistic regression models with the explanatory variables growth (as measured by relative basal area increment), tree size and site. We selected the species‐specific model with the highest goodness‐of‐fit and calculated its discriminatory power (area under the receiver operating characteristic curve, AUC) and calibration measures. Most models achieved at least a good discriminatory power (AUC>0.7) and the AUC ranged from 0.62 to 0.87; calibration curves did not indicate any overfitting. Almost all growth–mortality relationships differed among species and sites, i.e. there is no universal growth–mortality relationship. Some species such as F. excelsior showed reduced survival probabilities for both unfavourable and very good growth conditions. We conclude that the growth–mortality relationships presented here can contribute to the life‐history classification of trees and that they should also help to improve projections of forest succession models.
Postglacial dispersal limitation of widespread forest plant species in nemoral Europe
Authors: Svenning Jens‐Christian , Normand Signe , Skov Flemming
Published: May 2008

Climate is often singled out as the primary range limiting factor at large scales, while other environmental factors, notably soil, are thought to predominate at smaller scales. However, the postglacial migrational lag hypothesis controversially suggests that many species are strongly dispersal‐limited and still expanding from their ice age refugia. We investigated the importance of postglacial migrational lag, climate, and soil as range determinants for 47 widespread forest plant species across nemoral Europe (47.0–60.0°N, west of 24.0°E) using regression modeling, information‐theoretic model selection, multi‐model inference, and variation partitioning. Migrational lag was represented by a measure of accessibility to recolonization from ice age refugia.

Twelve species were largely ubiquitous and not analyzed further. For the remaining species, there was strong support for climate, soil, and accessibility to postglacial recolonization. Accessibility accounted for a small to moderate amount of variation, but its model‐averaged regression coefficient was stronger than those for climate or soil for 11 species and the second or third strongest coefficient for an additional 10 species. The resulting odds ratios were greater than one for 33 out of 35 species, i.e. adjusted for climate and soil, prevalence for the far majority of the 35 non‐ubiquitous species increased with increasing accessibility. There were no differences among growth forms in the importance of accessibility. In contrast, compared to non‐boreal species, accessibility had little importance for species with wide boreal distributions, as expected from their more widespread, northern glacial distributions.

In conclusion, even the ranges of many widespread forest plant species are probably still moderately to strongly limited by postglacial migrational lag. Therefore, although species ranges are also strongly influenced by climate, we cannot expect most forest plant species to closely track the expected 21st century climatic changes.
Nest survival for two species of manakins (Pipridae) in lowland Ecuador
Authors: Ryder Thomas B. , Durães Renata , Tori Wendy P. , Hidalgo José R. , Loiselle Bette A. , Blake John G.
Published: May 2008

Estimates of reproductive success are essential to understand life‐history strategies, yet tropical species remain under‐studied relative to their temperate counterparts. Here, we report nest survival probabilities for two manakin species (Pipridae). We monitored 61 wire‐tailed manakinPipra filicaudaand 45 blue‐crowned manakinLepidothrix coronatanests during three breeding seasons. Both species suffered high nest failure (84%). We modeled the effects of year, nest height, nest age (forP. filicaudaonly), as well as nest manipulation on daily survival rates (DSR) using program MARK. DSR decreased with nest age inP. filicaudawhereas a constant survival model was best fitted forL. coronata. Average DSR was 89% forP. filicaudaand 85% forL. coronata.This study reports some of the lowest nest survival rates among tropical passerines and poses important questions about population maintenance.
Migration across the sinusoidal endothelium regulates neutrophil mobilization in response to ELR + CXC chemokines
Authors: Burdon Peter C. E. , Martin Coralie , Rankin Sara M.
Published: May 2008

An increase in circulating neutrophils is a characteristic feature of many inflammatory reactions and is a result of the rapid mobilization of neutrophils from the bone marrow, driven by inflammatory mediators, including the ELR + CXC chemokines. In this paper, using a combination of light and electron microscopy and anin situperfusion system of the rat femoral bone marrow, we examined this mobilization process in detail. We show that mobilization of neutrophils stimulated by the CXC chemokine, rat MIP‐2, involves neutrophil migration from the haematopoietic compartment of the bone marrow across the bone marrow sinusoidal endothelium via a transcellular route. The critical role of the bone marrow sinusoidal endothelium in regulating neutrophil mobilization was demonstrated by artificially disrupting the bone marrow endothelial barrier by treatment with cytochalasin D, which results in the non‐selective release of leucocytes from the bone marrow. In contrast, inhibiting the activity of p38 mitogen‐activated protein kinase, inhibited both MIP‐2 stimulated chemotaxis of bone marrow neutrophilsin vitroand neutrophil mobilizationin situwhile, a broad spectrum matrix metalloproteinase inhibitor, BB94, had no effect on neutrophil mobilization. These results support the hypothesis that neutrophil migration drives their mobilization and highlights the function of the sinusoidal endothelium in regulating this process.
Haploinsufficiency of RPS14 in 5q− syndrome is associated with deregulation of ribosomal‐ and translation‐related genes
Authors: Pellagatti Andrea , Hellström‐Lindberg Eva , Giagounidis Aristoteles , Perry Janet , Malcovati Luca , Della Porta Matteo G. , Jädersten Martin , Killick Sally , Fidler Carrie , Cazzola Mario , Wainscoat James S. , Boultwood Jacqueline
Published: May 2008

We have previously demonstrated haploinsufficiency of the ribosomal gene RPS14, which is required for the maturation of 40S ribosomal subunits and maps to the commonly deleted region, in the 5q− syndrome. Patients with Diamond‐Blackfan anaemia (DBA) show haploinsufficiency of the closely related ribosomal protein RPS19, and show a consequent downregulation of multiple ribosomal‐ and translation‐related genes. By analogy with DBA, we have investigated the expression profiles of a large group of ribosomal‐ and translation‐related genes in the CD34+ cells of 15 myelodysplastic syndrome (MDS) patients with 5q− syndrome, 18 MDS patients with refractory anaemia (RA) and a normal karyotype, and 17 healthy controls. In this three‐way comparison, 55 of 579 ribosomal‐ and translation‐related probe sets were found to be significantly differentially expressed, with approximately 90% of these showing lower expression levels in the 5q− syndrome patient group. Using hierarchical clustering, patients with the 5q− syndrome could be separated both from other patients with RA and healthy controls solely on the basis of the deregulated expression of ribosomal‐ and translation‐related genes. Patients with the 5q− syndrome have a defect in the expression of genes involved in ribosome biogenesis and in the control of translation, suggesting that the 5q− syndrome represents a disorder of aberrant ribosome biogenesis.
Transient anomalies in genital appearance in some extremely preterm female infants may be the result of foetal programming causing a surge in LH and the over activation of the pituitary–gonadal axis
Authors: Greaves Ronda , Hunt Rodney W. , Zacharin Margaret
Published: May 2008

Aim  Animal studies have linked foetal programming with the development of the polycystic ovarian syndrome, and metabolic syndrome, in adulthood. The objective is to describe the investigation of four extreme‐premature female infants born between 25 and 29 weeks’ gestation with apparent genital abnormalities in association with unusually high androgens and gonadotrophins, to postulate a cause and to raise awareness of pitfalls in assessment of these infants.

Methods  Clinical examination and biochemical evaluation of four infants referred for apparent congenital ambiguity.

Results  Female gender was assigned at birth. Chromosome analysis confirmed 46XX, urine steroid profiles demonstrated no evidence of congenital adrenal hyperplasia and only the expected levels of foetal adrenal steroids.

Elevated LH (up to 162 IU/l), testosterone (up to 2·6 nmol/l), Δ4 androstenedione (up to > 35 nmol/l) and dehydro‐epiandrosterone sulphate (DHEAS) (up to 26·6 µmol/l) were seen in all four infants. These decreased over time but were significantly different from a control population of premature infants of similar gestational age.

Conclusions  We postulate that the clinical pattern of apparent clitoral enlargement in some extremely premature infants may reflect true temporary virilization due to an unusually high (or excessive) LH surge, in turn causing high foetal androgens. Foetal programming of gonadotrophin excess is probably the primary cause of androgen increase, in turn causing virilization, in some extreme‐premature infants. These may potentially be a group at future risk of polycystic ovary or metabolic syndrome, however, further work needs to be conducted to substantiate this hypothesis.
Increase in the fracture toughness and bond energy of clay by a root exudate
Authors: Zhang B. , Hallett P. D. , Zhang G.
Published: May 2008

Root exudates help drive the formation of the rhizosphere by binding soil particles, but the underlying physical mechanisms have not been quantified. This was addressed by measuring the impact of a major component of root exudates, polygalacturonic acid (PGA), on the interparticle bond energy and fracture toughness of clay. Pure kaolinite was mixed with 0, 1.2, 2.4, 4.9 or 12.2 g PGA kg−1to form test specimens. Half of the specimens were washed repeatedly to remove unbound PGA and evaluate the persistence of the effects, similar to weathering in natural soils. Fracture toughness,KIC, increased exponentially with added PGA, with washing increasing this trend. In unwashed specimensKICranged from 54.3 ± 2.5 kPa m−1/2for 0 g PGA kg−1to 86.9 ± 4.7 kPa m−1/2for 12.2 g PGA kg−1. Washing increasedKICto 61.3 ± 1.2 kPa m−1/2for 0 g PGA kg−1and 132.1 ± 4.9 kPa m−1/2for 12.2 g PGA kg−1. The apparent bond energy, γ, of the fracture surface increased from 5.9 ± 0.6 J m−2for 0 g kg−1to 12.0 ± 1.1 J m−2for 12.2 g kg−1PGA in the unwashed specimens. The washed specimens had γ of 13.0 ± 1.9 J m−2for 0 g kg−1and 21.3 ± 2.6 J m−2for 12.2 g PGA kg−1. Thus PGA, a major component of root exudates, has a large impact on the fracture toughness and bond energy of clay, and is likely to be a major determinant in the formation of the rhizosphere. This quantification of the thermodynamics of fracture will be useful for modelling rhizosphere formation and stability.
Impacts of long‐term waste‐water irrigation on the development of sandy Luvisols: consequences for metal pollutant distributions
Authors: VanOort F , Jongmans A. G. , Lamy I. , Baize D. , Chevallier P.
Published: May 2008

Studies relating macro‐ and microscopic aspects of impacts of long‐term contaminative practices on soils are scarce. We performed such an approach by assessing the fate of metal pollutants in an area close to Paris, where sandy Luvisols were irrigated for 100 years with urban waste water. As a result, these soils display strong accumulation of organic matter, dissolved salts and metal pollutants in surface horizons, but also migration of metals to depth. We examined soil development and metal distribution patterns in two irrigated soils, in comparison with a non‐irrigated reference soil. Soil macromorphological characteristics were studied in the field. Soil micromorphology and micro‐scale metal distributions were both studied in situ in thin sections, the latter by synchrotron X‐ray mapping. Microscopic study focussed on characteristic parts of the Ap and Bt horizons, mainly involved in metal retention. For Ap horizons, both large and diffuse metal concentrations were revealed, mainly associated with organic matter and dissolved components added by irrigation water. For Bt horizons, zinc accumulation was detected on clay‐iron coatings. Our results suggest that with time, a double metal‐filtering capacity has developed in these sandy Luvisols: in the Ap horizon, an anthropogenic filter resulted from input of metal pollutants together with highly reactive organic matter, carbonates and phosphates, thus favouring metal immobilization and limiting migration to depth. In the Bt horizon, the evidence is of a second, natural filter. However, this filtering capacity is endangered by clay destruction due to ferrolysis, as revealed by micromorphology. Ferrolysis, here initiated by intensive irrigation practices, leads to a reduction of the natural filtering potential and an increasing risk of metal transfer towards the groundwater.
The cellular prion protein is preferentially expressed by CD4+ CD25+ Foxp3+ regulatory T cells
Authors: Isaacs Jeremy D. , Garden Oliver A. , Kaur Gurman , Collinge John , Jackson Graham S. , Altmann Daniel M.
Published: May 2008

Post‐translational modification of the cellular prion protein (PrPC) is intimately associated with the pathogenesis of prion disease, yet the normal function of the protein remains unclear. PrPC is expressed in lymphoid cells and is known to be a T‐cell activation antigen. Further, transcription profiling studies of regulatory T cells have shown preferential overexpression of PrPC, suggesting a possible role in regulatory function. We report that both the expression of PrP message and cell surface PrPC levels are increased in murine CD4+ CD25+ regulatory T cells compared with CD4+ CD25− cells. However, PrP0/0 mice do not show altered regulatory T‐cell numbers or forkhead box P3 (Foxp3) expression levels, or impaired regulatory T‐cell function in vitro. Nevertheless, the preferential expression of surface PrPC by regulatory T cells raises the possibility that therapeutic ligation of PrPC might alter immune regulation.
A review of instruments measuring two aspects of meaning: search for meaning and meaning in illness
Authors: Fjelland Joyce E. , Barron Cecilia R. , Foxall Martha
Published: May 2008

Title.  A review of instruments measuring two aspects of meaning: search for meaning and meaning in illness.

Aim.  This paper is a report of narrative review of psychosocial instruments measuring two aspects of meaning: the search for meaning and meaning in illness.

Background.  Studies have shown that meaning has significance for well‐being, particularly for those experiencing illness/negative events. Understanding a person’s ascription of meaning to a stressful event can facilitate planning of supportive nursing interventions.

Method.  A literature search was conducted using Medline, PsycInfo, PsycArticles, CINAHL, ProQuest, Ebsco and MasterFile Premier for the period 1956–2006. The search terms were: meaning instruments, search for meaning, meaning in illness, significance of meaning and positive meaning. Only studies that employed measurement of one of these two aspects of meaning were included.

Findings.  Twelve instruments were retrieved from the search. Five were measures of search for meaning and seven were measures of meaning in illness. With a few exceptions these instruments were conceptually and operationally congruent and had acceptable psychometric properties. Limiting factors were the infrequent use of some of the instruments clinically or in research, and lack of evidence that cultural or age‐specific factors had been considered in the development of the instruments.

Conclusion.  Progress with research into meaning and clinical use of meaning instruments may be augmented by refinement of instruments in the areas of conceptual clarity, operational congruence, psychometric properties and cultural and age‐specific considerations. Good quantitative assessment will facilitate analysis of the relationship between ascriptions of meaning and psychosocial functioning, and lead to improved nursing interventions.
Elucidating empowerment in El Proyecto Bienestar (the Well‐Being Project)
Authors: Postma Julie
Published: May 2008

Title. Elucidating empowerment in El Proyecto Bienestar (the Well‐Being Project).

Aim. This paper describes differences in how socioculturally diverse participants in one community‐based participatory research project negotiated ‘empowerment’, and the implications of those differences for nurses involved in farmworker health and safety efforts.

Background. Internationally, empowerment and community participation are increasingly being used as strategies to reduce health disparities. Theories of empowerment vary in the academic literature and their connotations vary across cultures.

Method. Study participants were part of El Proyecto Bienestar, a community‐based participatory research (CBPR) project whose aim was to identify and respond to occupational and environmental health threats in one Mexican‐American farmworker community in the United States of America. Participant observation was used to audiorecord 18 participants in the third year (2006) of this 4‐year project discussing future project activities. Discourse analysis was used to analyse the transcripts.

Results. While participants agreed that ‘empowerment’ was central to the project, they had different perspectives on what the term meant and the role that the project should play in empowering the farmworker community. Empowerment discourses positioned the project in three ways: (1) as an instrument used to strengthen farmworkers’ collective political voice, (2) as an instrument used to represent multiple community interests and (3) as an instrument used to advocate on behalf of farmworkers. Individuals used multiple discourses signifying the complexity in participants’ roles and obligations.

Conclusions. Balancing power and developing knowledge collaboratively requires understanding multiple approaches to empowerment. Community empowerment as an outcome should not come at the expense of individual empowerment as part of the CBPR process.
Italian oncology nurses’ knowledge of complementary and alternative therapies: national survey
Authors: Zanini Antonietta , Quattrin Rosanna , Goi Debora , Frassinelli Barbara , Panariti Mateo , Carpanelli Ivana , Brusaferro Silvio
Published: May 2008

Title.  Italian oncology nurses’ knowledge of complementary and alternative therapies: national survey.

Aim.  This paper is a report of a study to investigate the knowledge of Italian oncology nurses in relation to complementary and alternative therapies.

Background.  In the last decade, the use of complementary and alternative therapies by the general public has increased dramatically. As primary care providers who play a key role in healthcare delivery, it is likely that nurses will be asked about these therapies by their patients. Only if they have an adequate knowledge base, however, can nurses give useful information and counsel patients effectively to allow them to make informed healthcare decisions.

Method.  A survey was carried out in 2007 with, 270 nurses registered with the Italian Association of Oncology Nursing. A self‐administered questionnaire was used and the response rate was of 57·4% (155/270).

Findings.  Ninety‐four (60·6%) nurses claimed to have knowledge about complementary and alternative therapies. Over two‐thirds (60·6%, 57/94) reported that books were a primary source of their knowledge. Other common sources included other healthcare workers (50%, 47/94), the Internet (48·9%, 46/94), workshops and seminars (29·8%, 28/94), and formal nursing education (17·0%, 16/94). Only 5·3% (5/94) reported that professional journals were a source of knowledge. During their professional activities, 71·6% (111/155) of the nurses encountered patients using complementary and alternative therapies, while 47·1% (73/155) treated patients asking for information about these techniques.

Conclusion.  The fact that nurses are responding to demands for these therapies without a solid knowledge base makes it imperative that the nursing curriculum be expanded to include these topics.
ORIGINAL ARTICLE: Coalescent analyses support multiple mainland‐to‐island dispersals in the evolution of Malagasy Triaenops bats (Chiroptera: Hipposideridae)
Authors: Russell Amy L. , Goodman Steven M. , Cox Murray P.
Published: May 2008

Aim  We investigate the directionality of mainland‐to‐island dispersals, focusing on a case study of an African‐Malagasy bat genus, Triaenops (Hipposideridae). Taxa include T. persicus from east Africa and three Triaenops species from Madagascar (T. auritus, T. furculus, and T. rufus). The evolution of this bat family considerably post‐dated the tectonic division of Madagascar from Africa, excluding vicariance as a viable hypothesis. Therefore, we consider three biogeographical scenarios to explain these species' current ranges: (A) a single dispersal from Africa to Madagascar with subsequent speciation of the Malagasy species; (B) multiple, unidirectional dispersals from Africa to Madagascar resulting in multiple, independent Malagasy lineages; or (C) early dispersal of a proto‐species from Africa to Madagascar, with later back‐dispersal of a descendant Malagasy taxon to Africa.

Location  East Africa, Madagascar, and the Mozambique Channel.

Methods  We compare the utility of phylogenetic and coalescent methodologies to address the question of directionality in a mainland‐to‐island dispersal event for recently diverged taxa. We also emphasize the application of biologically explicit demographic systems, such as the non‐equilibrium isolation‐with‐migration model. Here, these methods are applied to a four‐species haploid genetic data set, with simulation analyses being applied to validate this approach.

Results  Coalescent simulations favour scenario B: multiple, unidirectional dispersals from Africa to Madagascar resulting in multiple, independent Malagasy bat lineages. From coalescent dating, we estimate that the genus Triaenops was still a single taxon approximately 2.25 Ma. The most recent Africa to Madagascar dispersal occurred much more recently (c. 660 ka), and led to the formation of the extant Malagasy species, T. rufus.

Main conclusions  Haploid genetic data from four species of Triaenops are statistically most consistent with multiple, unidirectional dispersals from mainland Africa to Madagascar during the late Pleistocene.