bluuebunny/crossref_metadata_2025 huggingface dataset:
Sequence survey of receptor tyrosine kinases reveals mutations in glioblastomas
Authors: Rand Vikki , Huang Jiaqi , Stockwell Tim , Ferriera Steve , Buzko Oleksandr , Levy Samuel , Busam Dana , Li Kelvin , Edwards Jennifer B. , Eberhart Charles , Murphy Kathleen M. , Tsiamouri Alexia , Beeson Karen , Simpson Andrew J. G. , Venter J. Craig , Riggins Gregory J. , Strausberg Robert L.
Published: September 2005

It is now clear that tyrosine kinases represent attractive targets for therapeutic intervention in cancer. Recent advances in DNA sequencing technology now provide the opportunity to survey mutational changes in cancer in a high-throughput and comprehensive manner. Here we report on the sequence analysis of members of the receptor tyrosine kinase (RTK) gene family in the genomes of glioblastoma brain tumors. Previous studies have identified a number of molecular alterations in glioblastoma, including amplification of the RTK epidermal growth factor receptor. We have identified mutations in two other RTKs: (i) fibroblast growth receptor 1, including the first mutations in the kinase domain in this gene observed in any cancer, and (ii) a frameshift mutation in the platelet-derived growth factor receptor-α gene. Fibroblast growth receptor 1, platelet-derived growth factor receptor-α, and epidermal growth factor receptor are all potential entry points to the phosphatidylinositol 3-kinase and mitogen-activated protein kinase intracellular signaling pathways already known to be important for neoplasia. Our results demonstrate the utility of applying DNA sequencing technology to systematically assess the coding sequence of genes within cancer genomes.
Neurotransmitter release regulated by a MALS–liprin-α presynaptic complex
Authors: Olsen Olav , Moore Kimberly A. , Fukata Masaki , Kazuta Toshinari , Trinidad Jonathan C. , Kauer Fred W. , Streuli Michel , Misawa Hidemi , Burlingame Alma L. , Nicoll Roger A. , Bredt David S.
Published: September 2005

Synapses are highly specialized intercellular junctions organized by adhesive and scaffolding molecules that align presynaptic vesicular release with postsynaptic neurotransmitter receptors. The MALS/Veli–CASK–Mint-1 complex of PDZ proteins occurs on both sides of the synapse and has the potential to link transsynaptic adhesion molecules to the cytoskeleton. In this study, we purified the MALS protein complex from brain and found liprin-α as a major component. Liprin proteins organize the presynaptic active zone and regulate neurotransmitter release. Fittingly, mutant mice lacking all three MALS isoforms died perinatally with difficulty breathing and impaired excitatory synaptic transmission. Excitatory postsynaptic currents were dramatically reduced in autaptic cultures from MALS triple knockout mice due to a presynaptic deficit in vesicle cycling. These findings are consistent with a model whereby the MALS–CASK–liprin-α complex recruits components of the synaptic release machinery to adhesive proteins of the active zone.
Aurora A activates D-TACC–Msps complexes exclusively at centrosomes to stabilize centrosomal microtubules
Authors: Barros Teresa P. , Kinoshita Kazuhisa , Hyman Anthony A. , Raff Jordan W.
Published: September 2005

Centrosomes are the dominant sites of microtubule (MT) assembly during mitosis in animal cells, but it is unclear how this is achieved. Transforming acidic coiled coil (TACC) proteins stabilize MTs during mitosis by recruiting Minispindles (Msps)/XMAP215 proteins to centrosomes. TACC proteins can be phosphorylated in vitro by Aurora A kinases, but the significance of this remains unclear. We show that Drosophila melanogaster TACC (D-TACC) is phosphorylated on Ser863 exclusively at centrosomes during mitosis in an Aurora A–dependent manner. In embryos expressing only a mutant form of D-TACC that cannot be phosphorylated on Ser863 (GFP-S863L), spindle MTs are partially destabilized, whereas astral MTs are dramatically destabilized. GFP-S863L is concentrated at centrosomes and recruits Msps there but cannot associate with the minus ends of MTs. We propose that the centrosomal phosphorylation of D-TACC on Ser863 allows D-TACC–Msps complexes to stabilize the minus ends of centrosome-associated MTs. This may explain why centrosomes are such dominant sites of MT assembly during mitosis.
Vα14 NK T cell–triggered IFN-γ production by Gr-1+CD11b+ cells mediates early graft loss of syngeneic transplanted islets
Authors: Yasunami Yohichi , Kojo Satoshi , Kitamura Hiroshi , Toyofuku Atsushi , Satoh Masayuki , Nakano Masahiko , Nabeyama Kentaroh , Nakamura Yoshiichiroh , Matsuoka Nobuhide , Ikeda Seiyo , Tanaka Masao , Ono Junko , Nagata Naoki , Ohara Osamu , Taniguchi Masaru
Published: September 2005

Pancreatic islet transplantation is a highly promising approach for the treatment of insulin-dependent diabetes mellitus. However, the procedure remains experimental for several reasons, including its low efficiency caused by the early graft loss of transplanted islets. We demonstrate that Gr-1+CD11b+ cells generated by transplantation and their IFN-γ production triggered by Vα14 NKT cells are an essential component and a major cause of early graft loss of pancreatic islet transplants. Gr-1+CD11b+ cells from Vα14 NKT cell–deficient (Jα281−/−) mice failed to produce IFN-γ, resulting in efficient islet graft acceptance. Early graft loss was successfully prevented through the repeated administration of α-galactosylceramide, a specific ligand for Vα14 NKT cells, resulting in dramatically reduced IFN-γ production by Gr-1+CD11b+ cells, as well as Vα14 NKT cells. Our study elucidates, for the first time, the crucial role of Gr-1+CD11b+ cells and the IFN-γ they produce in islet graft rejection and suggests a novel approach to improving transplantation efficiency through the modulation of Vα14 NKT cell function.
FASL –844C polymorphism is associated with increased activation-induced T cell death and risk of cervical cancer
Authors: Sun Tong , Zhou Yifeng , Li Hua , Han Xiaohong , Shi Yuankai , Wang Li , Miao Xiaoping , Tan Wen , Zhao Dan , Zhang Xuemei , Guo Yongli , Lin Dongxin
Published: September 2005

The FAS receptor–ligand system plays a key role in regulating apoptotic cell death, and corruption of this signaling pathway has been shown to participate in tumor-immune escape and carcinogenesis. We have recently demonstrated (Sun, T., X. Miao, X. Zhang, W. Tan, P. Xiong, and D. Lin. 2004. J. Natl. Cancer Inst. 96:1030–1036; Zhang, X., X. Miao, T. Sun, W. Tan, S. Qu, P. Xiong, Y. Zhou, and D. Lin. 2005. J. Med. Genet. 42:479–484) that functional polymorphisms in FAS and FAS ligand (FASL) are associated with susceptibility to lung cancer and esophageal cancer; however, the mechanisms underlying this association have not been elucidated. We show that the FAS –1377G, FAS –670A, and FASL –844T variants are expressed more highly on ex vivo–stimulated T cells than the FAS –1377A, FAS –670G, and FASL –844C variants. Moreover, activation-induced cell death (AICD) of T cells carrying the FASL –844C allele was increased. We also found a threefold increased risk of cervical cancer among subjects with the FASL –844CC genotype compared with those with the –844TT genotype in a case-control study in Chinese women. Together, these observations suggest that genetic polymorphisms in the FAS–FASL pathway confer host susceptibility to cervical cancers, which might be caused by immune escape of tumor cells because of enhanced AICD of tumor-specific T cells.
Concerted vs. Sequential. Two Activation Patterns of Vast Arrays of Intracellular Ca2+ Channels in Muscle
Authors: Zhou Jinsong , Brum Gustavo , González Adom , Launikonis Bradley S. , Stern Michael D. , Ríos Eduardo
Published: September 2005

To signal cell responses, Ca2+ is released from storage through intracellular Ca2+ channels. Unlike most plasmalemmal channels, these are clustered in quasi-crystalline arrays, which should endow them with unique properties. Two distinct patterns of local activation of Ca2+ release were revealed in images of Ca2+ sparks in permeabilized cells of amphibian muscle. In the presence of sulfate, an anion that enters the SR and precipitates Ca2+, sparks became wider than in the conventional, glutamate-based solution. Some of these were “protoplatykurtic” (had a flat top from early on), suggesting an extensive array of channels that activate simultaneously. Under these conditions the rate of production of signal mass was roughly constant during the rise time of the spark and could be as high as 5 μm3 ms−1, consistent with a release current >50 pA since the beginning of the event. This pattern, called “concerted activation,” was observed also in rat muscle fibers. When sulfate was combined with a reduced cytosolic [Ca2+] (50 nM) these sparks coexisted (and interfered) with a sequential progression of channel opening, probably mediated by Ca2+-induced Ca2+ release (CICR). Sequential propagation, observed only in frogs, may require parajunctional channels, of RyR isoform β, which are absent in the rat. Concerted opening instead appears to be a property of RyR α in the amphibian and the homologous isoform 1 in the mammal.
Defending against parasites: fungus-growing ants combine specialized behaviours and microbial symbionts to protect their fungus gardens
Authors: Little Ainslie E.F , Murakami Takahiro , Mueller Ulrich G , Currie Cameron R
Published: September 2005

Parasites influence host biology and population structure, and thus shape the evolution of their hosts. Parasites often accelerate the evolution of host defences, including direct defences such as evasion and sanitation and indirect defences such as the management of beneficial microbes that aid in the suppression or removal of pathogens. Fungus-growing ants are doubly burdened by parasites, needing to protect their crops as well as themselves from infection. We show that parasite removal from fungus gardens is more complex than previously realized. In response to infection of their fungal gardens by a specialized virulent parasite, ants gather and compress parasitic spores and hyphae in their infrabuccal pockets, then deposit the resulting pellet in piles near their gardens. We reveal that the ants' infrabuccal pocket functions as a specialized sterilization device, killing spores of the garden parasiteEscovopsis. This is apparently achieved through a symbiotic association with actinomycetous bacteria in the infrabuccal pocket that produce antibiotics which inhibitEscovopsis. The use of the infrabuccal pocket as a receptacle to sequesterEscovopsis, and as a location for antibiotic administration by the ants' bacterial mutualist, illustrates how the combination of behaviour and microbial symbionts can be a successful defence strategy for hosts.
Antiphonal four-part synchronized chorusing in a Neotropical wren
Authors: Mann Nigel I , Dingess Kimberly A , Slater P.J.B
Published: September 2005

Plain-tailed wrens (
Thryothorus euophrys
) live in groups that sing synchronized choruses, the contributions of females and males alternating with each other in cycles, within which each sex sings two of the four parts, the whole achieving near perfect synchrony. As each bird has a repertoire of
ca
20 phrases of each type, the synchrony also requires them to choose the same type at the same time as others of their sex. Songs can last up to 2 min, during which individuals join in and drop out. This must be one of the most complex singing performances yet described in a non-human animal.
Loss of muscle fibres in a landlocked dwarf Atlantic salmon population
Authors: Johnston Ian A , Abercromby Marguerite , Andersen Øivind
Published: September 2005

Growth of fast myotomal muscle in teleosts involves the continuous production of muscle fibres until some genetically pre-determined length. The dwarf landlocked (Bleke) population of Atlantic salmon (Salmo salarL.) from Byglands-fjord, Southern Norway mature at about 25 cm fork length and reach a maximum size of only 30 cm in the wild. The maximum diameter (Dmax) of fast muscle fibres in 4-year-old Bleke salmon (25–28 cm fork length) was 118 μm and not significantly different from that found in immature migratory salmon of a similar size. In contrast no evidence for active fibre recruitment was found in the Bleke salmon, such that the maximum fibre number, FNmax, was only 21–30% of that reported in typical farmed and wild migratory populations, respectively. We hypothesise that, once established, the physiological consequences of the dwarf condition led to rapid selection for reduced fibre number, possibly to reduce the maintenance costs associated with ionic homeostasis.
The scaling and temperature dependence of vertebrate metabolism
Authors: White Craig R , Phillips Nicole F , Seymour Roger S
Published: September 2005

Body size and temperature are primary determinants of metabolic rate, and the standard metabolic rate (SMR) of animals ranging in size from unicells to mammals has been thought to be proportional to body mass (
M
) raised to the power of three-quarters for over 40 years. However, recent evidence from rigorously selected datasets suggests that this is not the case for birds and mammals. To determine whether the influence of body mass on the metabolic rate of vertebrates is indeed universal, we compiled SMR measurements for 938 species spanning six orders of magnitude variation in mass. When normalized to a common temperature of 38 °C, the SMR scaling exponents of fish, amphibians, reptiles, birds and mammals are significantly heterogeneous. This suggests both that there is no universal metabolic allometry and that models that attempt to explain only quarter-power scaling of metabolic rate are unlikely to succeed.
Plant–plant interactions vary with different mycorrhizal fungus species
Authors: Hoeksema Jason D
Published: September 2005

Because different species of mycorrhizal fungi have different effects on the growth of particular plant species, variation in mycorrhizal fungus species composition could cause changes in the strength of plant–plant interactions. Results are presented from a growth chamber experiment that compared the strength of interactions among seedlings of ponderosa pine (
Pinus ponderosa
) when the pines were colonized by two different groups of ectomycorrhizal fungi in the genus
Rhizopogon
. Plant density effects differed between the two groups of mycorrhizal fungi: plant growth was low regardless of density when plants were colonized with pine-specific
Rhizopogon
species, while plant growth declined with plant density when plants were colonized by
Rhizopogon
species having a broader host range. This result parallels results from previous studies showing that plant interactions are more antagonistic with mycorrhizal fungi than without, implying that plant responsiveness to beneficial mycorrhizal fungi declines with increasing plant density. If such effects are prevalent in plant communities, then variation in mycorrhizal fungus community composition is predicted to have a density-dependent effect on plants.
A review of attenuation correction techniques for tissue fluorescence
Authors: Bradley Robert S , Thorniley Maureen S
Published: September 2005

Fluorescence intensity measurements have the potential to facilitate the diagnoses of many pathological conditions. However, accurate interpretation of the measurements is complicated by the distorting effects of tissue scattering and absorption. Consequently, different techniques have been developed to attempt to compensate for these effects. This paper reviews currently available correction techniques with emphasis on clinical application and consideration given to the intrinsic accuracy and limitations of each technique.
Complex networks and simple models in biology
Authors: de Silva Eric , Stumpf Michael P.H
Published: September 2005

The analysis of molecular networks, such as transcriptional, metabolic and protein interaction networks, has progressed substantially because of the power of models from statistical physics. Increasingly, the data are becoming so detailed—though not always complete or correct—that the simple models are reaching the limits of their usefulness. Here, we will discuss how network information can be described and to some extent quantified. In particular statistics offers a range of tools, such as model selection, which have not yet been widely applied in the analysis of biological networks. We will also outline a number of present challenges posed by biological network data in systems biology, and the extent to which these can be addressed by new developments in statistics, physics and applied mathematics.
Exaggeration and suppression of iridescence: the evolution of two-dimensional butterfly structural colours
Authors: Wickham Shelley , Large Maryanne C.J , Poladian Leon , Jermiin Lars S
Published: September 2005

Many butterfly species possess ‘structural’ colour, where colour is due to optical microstructures found in the wing scales. A number of such structures have been identified in butterfly scales, including three variations on a simple multi-layer structure. In this study, we optically characterize examples of all three types of multi-layer structure, as found in 10 species. The optical mechanism of the suppression and exaggeration of the angle-dependent optical properties (iridescence) of these structures is described. In addition, we consider the phylogeny of the butterflies, and are thus able to relate the optical properties of the structures to their evolutionary development. By applying two different types of analysis, the mechanism of adaptation is addressed. A simple parsimony analysis, in which all evolutionary changes are given an equal weighting, suggests convergent evolution of one structure. A Dollo parsimony analysis, in which the evolutionary ‘cost’ of losing a structure is less than that of gaining it, implies that ‘latent’ structures can be reused.
Noise, cost and speed-accuracy trade-offs: decision-making in a decentralized system
Authors: Marshall James A.R , Dornhaus Anna , Franks Nigel R , Kovacs Tim
Published: September 2005

Many natural and artificial decision-making systems face decision problems where there is an inherent compromise between two or more objectives. One such common compromise is between the speed and accuracy of a decision. The ability to exploit the characteristics of a decision problem in order to vary between the extremes of making maximally rapid, or maximally accurate decisions, is a useful property of such systems. Colonies of the ant
Temnothorax albipennis
(formerly
Leptothorax albipennis
) are a paradigmatic decentralized decision-making system, and have been shown flexibly to compromise accuracy for speed when making decisions during house-hunting. During emigration, a colony must typically evaluate and choose between several possible alternative new nest sites of differing quality. In this paper, we examine this speed-accuracy trade-off through modelling, and conclude that noise and time-cost of assessing alternative choices are likely to be significant for
T. albipennis
. Noise and cost of such assessments are likely to mean that
T. albipennis
' decision-making mechanism is Pareto-optimal in one crucial regard; increasing the willingness of individuals to change their decisions cannot improve collective accuracy overall without impairing speed. We propose that a decentralized control algorithm based on this emigration behaviour may be derived for applications in engineering domains and specify the characteristics of the problems to which it should be suited, based on our new results.
Elucidating the digital control mechanism for DNA damage repair with the p53–Mdm2 system: single cell data analysis and ensemble modelling
Authors: Ogunnaike Babatunde A
Published: September 2005

Recent experimental evidence about DNA damage response using the p53–Mdm2 system has raised some fundamental questions about the control mechanism employed. In response to DNA damage, an ensemble of cells shows a damped oscillation in p53 expression whose amplitude increases with increased DNA damage—consistent with ‘analogue’ control. Recent experimental results, however, show that the single cell response is a series of discrete pulses in p53; and with increase in DNA damage, neither the height nor the duration of the pulses change, but the mean number of pulses increase—consistent with ‘digital’ control. Here we present a system engineering model that uses published data to elucidate this mechanism and resolve the dilemma of how digital behaviour at the single cell level can manifest as analogue ensemble behaviour. First, we develop a dynamic model of the p53–Mdm2 system that produces non-oscillatory responses to a stress signal. Second, we develop a probability model of the distribution of pulses in a cell population, and combine the two with the simplest digital control algorithm to show how oscillatory responses whose amplitudes grow with DNA damage can arise from single cell behaviour in which each single pulse response is independent of the extent of DNA damage. A stochastic simulation of the hypothesized control mechanism reproduces experimental observations remarkably well.
Analysis of single ion channel data incorporating time-interval omission and sampling
Authors: The Yu-Kai , Timmer Jens
Published: September 2005

Hidden Markov models are widely used to describe single channel currents from patch-clamp experiments. The inevitable anti-aliasing filter limits the time resolution of the measurements and therefore the standard hidden Markov model is not adequate anymore. The notion of time-interval omission has been introduced where brief events are not detected. The developed, exact solutions to this problem do not take into account that the measured intervals are limited by the sampling time. In this case the dead-time that specifies the minimal detectable interval length is not defined unambiguously. We show that a wrong choice of the dead-time leads to considerably biased estimates and present the appropriate equations to describe sampled data.
Infectious disease control using contact tracing in random and scale-free networks
Authors: Kiss Istvan Z , Green Darren M , Kao Rowland R
Published: September 2005

Contact tracing aims to identify and isolate individuals that have been in contact with infectious individuals. The efficacy of contact tracing and the hierarchy of traced nodes—nodes with higher degree traced first—is investigated and compared on random and scale-free (SF) networks with the same number of nodesNand average connectionK. For values of the transmission rate larger than a threshold, the final epidemic size on SF networks is smaller than that on corresponding random networks. While in random networks new infectious and traced nodes from all classes have similar average degrees, in SF networks the average degree of nodes that are in more advanced stages of the disease is higher at any given time. On SF networks tracing removes possible sources of infection with high average degree. However a higher tracing effort is required to control the epidemic than on corresponding random networks due to the high initial velocity of spread towards the highly connected nodes. An increased latency period fails to significantly improve contact tracing efficacy. Contact tracing has a limited effect if the removal rate of susceptible nodes is relatively high, due to the fast local depletion of susceptible nodes.
Ant-inspired sorting by robots: the importance of initial clustering
Authors: Melhuish Chris , Sendova-Franks Ana B , Scholes Sam , Horsfield Ian , Welsby Fred
Published: September 2005

For engineers the prospect of scalable collective robot systems is very appealing. Such systems typically adopt a decentralized approach in their control and coordination mechanism, which employs local sensing and action as well as limited communication. Under these constraints and informed by research on
Temnothorax
ants, two puck sorting algorithms were tested in a combination of simulation and with real robots. Both algorithms employed puck density as a cue. Only the overall local density, irrespective of puck type, was found to be required which offers the prospect for a more simple mechanism than had been previously considered. For one algorithm, this density cue was used both for picking up and dropping items and is, therefore, referred to as the ‘double density’ algorithm (DD). In the second algorithm, density was used as a cue only for picking up. Depositing an item was governed by the distance travelled which was specific to the type of item being carried. This was referred to as the ‘single density’ algorithm (SD). Unlike the DD it was found that, for the SD, the clustering of items is a necessary pre-condition for sorting. Results from ant experiments also showed that sorting is carried out in two phases: a primary clustering episode followed by a spacing phase. This strongly suggests that clustering may also be a precondition for spacing in ants.
Einstein: the classical physicist
Authors: Rowlinson J.S
Published: September 2005

Einstein is remembered for his contributions to the re-ordering of the foundations of physics in the first years of the twentieth century. Much of his achievement was, however, based on the classical physics of the late nineteenth century and it was his work on statistical mechanics that underlay his first contributions to quantum theory. This essay is an account of an aspect of his achievement that is often overlooked.
Diffraction of flexural waves by cracks in orthotropic thin elastic plates. I Formal solution
Authors: Thompson Ian , Abrahams I. David
Published: September 2005

The problem of flexural wave diffraction by a semi-infinite crack in an infinite orthotropic thin plate is considered. Such models have application to the ultrasonic non-destructive inspection of thin components, such as aeroplane wings. For simplicity, the plate is modelled using Kirchhoff theory, and the crack is chosen to be aligned along one of the principal directions of material orthotropy. For incident plane waves, an exact analytical expression for the scattered field is derived by means of the Wiener–Hopf technique. In this model problem, the Wiener–Hopf kernel is scalar and its factorization is expressed in terms of simple, definite, non-singular contour integrals. A detailed numerical evaluation of the solution will be provided in the second part of this work.
Multispecies epitaxial growth on vicinal surfaces with chemical reactions and diffusion
Authors: Cermelli Paolo , Jabbour Michel
Published: September 2005

We derive, in the form of coupled partial differential equations, the evolution equations for the epitaxial growth, via step flow, of a multispecies crystal on a stepped surface. Both adsorption–desorption on the terraces and attachment–detachment along the step edges are accompanied by chemical reactions and adatom diffusion. Moreover, we account for deposition from either a vacuum, e.g., in molecular beam epitaxy, or a gas, e.g., during vapour phase epitaxy (chemical or physical). Our theory (i) endows the steps with athermodynamicstructure whose main ingredients are a free-energy density and species edge chemical potentials, (ii) incorporatesanisotropyinto the terrace species diffusion as well as into the edge free energy, species mobilities, attachment–detachment and reaction-rate coefficients, (iii) allows for large departures from local equilibrium along the steps, and (iv) ensures the consistency of the constitutive relations for the terrace and edge chemical rates with the second law. In particular, a configurational force balance at each step yields a generalization of the classical Gibbs–Thomson relation. Finally, the special case of steady-state growth of abinary compoundis discussed.
Polar linkings, intersections and Weil pairing
Authors: Khesin Boris , Rosly Alexei
Published: September 2005

Polar homology and linkings arise as natural holomorphic analogues in algebraic geometry of the homology groups and links in topology. For complex projective manifolds, the polar
k
-chains are subvarieties of complex dimension
k
with meromorphic forms on them, while the boundary operator is defined by taking the polar divisor and the Poincaré residue on it. We also define the corresponding analogues for the intersection and linking numbers of complex submanifolds, and show that they have properties similar to those of the corresponding topological objects. Finally, we establish the relation between the holomorphic linking and the Weil pairing of functions on a complex curve and its higher-dimensional counterparts.
Asymptotic modelling theorems for the static analysis of linear elastic structures
Authors: Ilanko Sinniah
Published: September 2005

The work presented here justifies the use of restraints with large positive and negative stiffness values to asymptotically model geometric constraints of a structure in linear structural analysis. Replacing constraints by very stiff restraints improves the versatility of variational methods such as the Rayleigh–Ritz method as the limitation on the choice of functions is removed. Based on recently published theorems on the existence of natural frequencies of systems with artificial restraints of positive and negative stiffness and their convergence towards the frequencies of the corresponding constrained systems, a proof is given to show that the displacement of a constrained structure caused by any action along its direction is approached and bracketed by the displacement of systems with artificial restraints of positive and negative stiffness (positive and negative penalty functions) as the magnitude of stiffness is increased. A procedure for the practical use of positive and negative penalty functions in static analysis of linear structures is also proposed.
Asymptotic behaviour of solutions to the generalized Becker–Döring equations for general initial data
Authors: Cañizo Rincón José Alfredo
Published: September 2005

We prove the following asymptotic behaviour for solutions to the generalized Becker–Döring system for general initial data: under a detailed balance assumption and in situations where density is conserved in time, there is a critical density
ρ
s
such that solutions with an initial density
ρ
0
≤
ρ
s
converge strongly to the equilibrium with density
ρ
0
and solutions with initial density
ρ
0
>
ρ
s
converge (in a weak sense) to the equilibrium with density
ρ
s
. This extends the previous knowledge that this behaviour happens under more restrictive conditions on the initial data. The main tool is a new estimate on the tail of solutions with density below the critical density.
Buckling characteristics of embedded multi-walled carbon nanotubes
Authors: Liew K.M , He X.Q , Kitipornchai S
Published: September 2005

An analytical algorithm is proposed to describe the buckling behaviour of multi-walled carbon nanotubes (CNTs) that are embedded in a matrix with consideration of the van der Waals (vdW) interaction. The individual tube is treated as a cylindrical shell, but the tube deflections are coupled with each other due to the vdW interaction. The interaction between the matrix and the outermost tube is modelled as a Pasternak foundation. Based on the proposed model, an accurate expression and a simple approximate expression are derived for the buckling load of double-walled CNTs that are embedded in a matrix. The approximate expression clearly indicates that the vdW force is coupled with the matrix parameters. A numerical simulation is carried out, and the results reveal that the increase in the number of layers leads to a decrease in the critical buckling load for multi-walled CNTs with a fixed innermost radius. In contrast, when the outermost radius is fixed, the critical buckling load increases with the increase in the number of layers for multi-walled CNTs without a matrix. However, for multi-walled CNTs that are embedded in a matrix, the critical buckling load decreases first and then increases with the increase in the number of layers. This implies that there is a given number of layers for a multi-walled CNT at which the critical buckling load is the lowest, and that this number depends on the matrix parameters.
Solitary waves in excitable systems with cross-diffusion
Authors: Biktashev Vadim N , Tsyganov Mikhail A
Published: September 2005

We consider a FitzHugh–Nagumo system of equations where the traditional diffusion terms are replaced with linear cross-diffusion of components. This system describes solitary waves that have unusual form and are capable of quasi-soliton interaction. This is different from the classical FitzHugh–Nagumo system with self-diffusion, but similar to a predator–prey model with taxis of populations on each other's gradient which we considered earlier. We study these waves by numerical simulations and also present an analytical theory, based on the asymptotic behaviour which arises when the local dynamics of the inhibitor field are much slower than those of the activator field.
Stability analysis of three-dimensional breather solitons in a Bose–Einstein condensate
Authors: Matuszewski M , Infeld E , Rowlands G , Trippenbach M
Published: September 2005

We investigated the stability properties of breather soliton trains in a three-dimensional Bose–Einstein condensate (BEC) with Feshbach-resonance management of the scattering length. This is done so as to generate both attractive and repulsive interaction. The condensate is confined only by a one-dimensional optical lattice and we consider strong, moderate and weak confinement. By strong confinement we mean a situation in which a quasi two-dimensional soliton is created. Moderate confinement admits a fully three-dimensional soliton. Weak confinement allows individual solitons to interact. Stability properties are investigated by several theoretical methods such as a variational analysis, treatment of motion in effective potential wells, and collapse dynamics. Armed with all the information forthcoming from these methods, we then undertake a numerical calculation. Our theoretical predictions are fully confirmed, perhaps to a higher degree than expected. We compare regions of stability in parameter space obtained from a fully three-dimensional analysis with those from a quasi two-dimensional treatment, when the dynamics in one direction are frozen. We find that in the three-dimensional case the stability region splits into two parts. However, as we tighten the confinement, one of the islands of stability moves toward higher frequencies and the lower frequency region becomes more and more like that for the quasi two-dimensional case. We demonstrate these solutions in direct numerical simulations and, importantly, suggest a way of creating robust three-dimensional solitons in experiments in a BEC in a one-dimensional lattice.
Laminar flow of a viscoelastic shear-thinning liquid through a plane sudden expansion preceded by a gradual contraction
Authors: Poole R.J , Escudier M.P , Oliveira P.J
Published: September 2005

Experimental observations are reported for the laminar flow of a viscoelastic liquid through a symmetrical plane sudden expansion preceded by a gradual contraction from a square duct. As is well known, for Newtonian fluid flow above a critical Reynolds number the flowfield downstream of an expansion becomes asymmetric. For the viscoelastic liquid investigated here the asymmetry is greatly reduced, with very similar reattachment lengths for the two recirculation regions. More significantly, the flow unexpectedly develops a strongly three-dimensional jet-like structure, with side-to-side symmetry centred on the ‘vertical’ symmetry plane of the contraction/expansion geometry. Especially interesting is the flow within the contraction itself, where the nature of the flow field for the viscoelastic liquid is also fundamentally different to that for a comparable Newtonian fluid flow: large velocity overshoots with very strong gradients occur near to the sidewalls that, due to their appearance, we have termed ‘cat's ears’. The fully developed approach flow in the square duct is unremarkable.
Time-evolution of highly localized positive-energy states of the free Dirac electron
Authors: Bracken A.J , Flohr J.A , Melloy G.F
Published: September 2005

Highly localized positive-energy states of the free Dirac electron are constructed and shown to evolve in a simple way under the action of Dirac's equation. When the initial uncertainty in position is small on the scale of the Compton wavelength, there is an associated uncertainty in the mean energy that is large compared with the rest mass of the electron. However, this does not lead to any breakdown of the one-particle description, associated with the possibility of pair-production, but rather leads to a rapid expansion of the probability density outwards from the point of localization, at speeds close to the speed of light.
Novel dynamical resonances in finite-temperature Bose–Einstein condensates
Authors: Geddes A.J , Morgan S.A , Hutchinson D.A.W
Published: September 2005

We describe a variety of intriguing mode-coupling effects which can occur in a confined Bose–Einstein condensed system at finite temperature. These arise from strong interactions between a condensate fluctuation and resonances of the thermal cloud yielding strongly nonlinear behaviour. We show how these processes can be affected by altering the aspect ratio of the trap, thereby changing the relevant mode-matching conditions. We illustrate how direct driving of the thermal cloud can lead to significant shifts in the excitation spectrum for a number of modes and provide further experimental scenarios in which the dramatic behaviour observed for the
m
=0 mode at JILA can be repeated. Our theoretical description is based on a successful second-order finite-temperature quantum field theory which includes the full coupled dynamics of the condensate and thermal cloud and all relevant finite-size effects.
On the maximal ionization for the atomic Pauli operator
Authors: Melgaard M , Johnson T
Published: September 2005

Within the Born–Oppenheimer approximation Lieb proved that the number of non-relativistic, spin-

particles that can be bound to an atom of nuclear charge
Z
in the presence of an external magnetic field satisfies
N
max
<2
Z
+1, provided the magnetic field tends to zero at infinity and the coupling between the magnetic field and the spin is ignored. Assuming that the magnetic field is generic, we prove an upper bound which holds when the spin-field coupling is included; the set of generic magnetic fields contains an open, dense subset of

.
Quantum computing, postselection, and probabilistic polynomial-time
Authors: Aaronson Scott
Published: September 2005

I study the class of problems efficiently solvable by a quantum computer, given the ability to ‘postselect’ on the outcomes of measurements. I prove that this class coincides with a classical complexity class called PP, or probabilistic polynomial-time. Using this result, I show that several simple changes to the axioms of quantum mechanics would let us solve PP-complete problems efficiently. The result also implies, as an easy corollary, a celebrated theorem of Beigel, Reingold and Spielman that PP is closed under intersection, as well as a generalization of that theorem due to Fortnow and Reingold. This illustrates that quantum computing can yield new and simpler proofs of major results about classical computation.
Brownian excursion with a single mark
Authors: Jansons Kalvis M
Published: September 2005

The joint law of the integral and the maximum of a Brownian excursion
Y
with a single mark of an independent Poisson point process of rate

is determined. We use the identity in law of
Y
and two independent Brownian motions with drift −
u
(
u
>0) joined back-to-back with starting point having an exp(2
u
) distribution and stopped on hitting 0. This characterization of a Brownian excursion is expected to lead to a much easier starting point for calculating many other explicit joint laws associated with Brownian excursions.
From Europe to America: Pliocene to Recent trans-Atlantic expansion of cold-water North Atlantic molluscs
Authors: Vermeij Geerat J
Published: September 2005

Data on the geographical distribution, phylogeny and fossil record of cool-temperate North Atlantic shell-bearing molluscs that live in waters shallower than 100 m depth belong to two biogeographic provinces, one in eastern North America north of Cape Cod, the other in northern Europe. Amphi-Atlantic species, which are found in both provinces, comprise 30.8% of the 402 species in the northeastern Atlantic and 47.3% of the 262 species in the northwestern Atlantic. Some 54.8% of these amphi-Atlantic species have phylogenetic origins in the North Pacific. Comparisons among fossil Atlantic faunas show that amphi-Atlantic distributions became established in the Middle Pliocene (about 3.5 million years ago), and that all represent westward expansions of European taxa to North America. No American taxa spread eastward to Europe without human assistance. These results are in accord with previous phylogeographic studies among populations within several amphi-Atlantic species. Explanations for the unidirectional expansion of species across the Atlantic remain uncertain, but may include smaller size and greater prior extinction of the North American as compared to the European fauna and biased transport mechanisms. Destruction of the European source fauna may jeopardize faunas on both sides of the Atlantic.
Extra-retinal adaptation of cortical motion-processing areas during pursuit eye movements
Authors: Freeman Tom C.A , Sumnall Jane H
Published: September 2005

Repetitive eye movement produces a compelling motion aftereffect (MAE). One mechanism thought to contribute to the illusory movement is an extra-retinal motion signal generated after adaptation. However, extra-retinal signals are also generated during pursuit. They modulate activity within cortical motion-processing area MST, helping transform retinal motion into motion in the world during an eye movement. Given the evidence that MST plays a key role in generating MAE, it may also become indirectly adapted by prolonged pursuit. To differentiate between these two extra-retinal mechanisms we examined storage of the MAE across a period of darkness. In one condition observers were told to stare at a moving pattern, an instruction that induces a more reflexive type of eye movement. In another they were told to deliberately pursue it. We found equally long MAEs when testing immediately after adaptation but not when the test was delayed by 40 s. In the case of the reflexive eye movement the delay almost completely extinguished the MAE, whereas the illusory motion following pursuit remained intact. This suggests pursuit adapts cortical motion-processing areas whereas unintentional eye movement does not. A second experiment showed that cortical mechanisms cannot be the sole determinant of pursuit-induced MAE. Following oblique pursuit, we found MAE direction changes from oblique to vertical. Perceived MAE direction appears to be influenced by a subcortical mechanism as well, one based on the relative recovery rate of horizontal and vertical eye-movement processes recruited during oblique pursuit.
Dissecting the species–energy relationship
Authors: Evans Karl L , Greenwood Jeremy J.D , Gaston Kevin J
Published: September 2005

Environmental energy availability can explain much of the spatial variation in species richness. Such species–energy relationships encompass a diverse range of forms, and there is intense debate concerning which of these predominate, and the factors promoting this diversity. Despite this there has been relatively little investigation of whether the form, and relative strength, of species–energy relationships varies with (i) the currency of energy availability that is used, and (ii) the ecological characteristics of the constituent species. Such investigations can, however, shed light on the causal mechanisms underlying species–energy relationships. We illustrate this using the British breeding avifauna. The strength of the species–energy relationship is dependent on the energy metric used, with species richness being more closely correlated with temperature than the Normalized Difference Vegetation Index, which is a strong correlate of net primary productivity. We find little evidence, however, for the thermoregulatory load hypothesis that high temperatures enable individuals to invest in growth and reproduction, rather than thermoregulation, increasing population sizes that buffer species from extinction. High levels of productive energy may also elevate population size, which is related to extinction risk by a negative decelerating function. Therefore, the rarest species should exhibit the strongest species–energy relationship. We find evidence to the contrary, together with little support for suggestions that high-energy availability elevates species richness by increasing the numbers of specialists or predators.
New insights into butterfly–environment relationships using partitioning methods
Authors: Heikkinen Risto K , Luoto Miska , Kuussaari Mikko , Pöyry Juha
Published: September 2005

Variation partitioning and hierarchical partitioning are novel statistical approaches that provide deeper understanding of the importance of different explanatory variables for biodiversity patterns than traditional regression methods. Using these methods, the variation in occupancy and abundance of the clouded apollo butterfly (Parnassius mnemosyneL.) was decomposed into independent and joint effects of larval and adult food resources, microclimate and habitat quantity. The independent effect of habitat quantity variables (habitat area and connectivity) captured the largest fraction of the variation in the clouded apollo patterns, but habitat connectivity had a major contribution only for occupancy data. The independent effects of resources and microclimate were higher on butterfly abundance than on occupancy. However, a considerable amount of variation in the butterfly patterns was accounted for by the joint effects of predictors and may thus be causally related to two or all three groups of variables. Abundance of the butterfly in the surroundings of the focal grid cell had a significant effect in all analyses, independently of the effects of other predictors. Our results encourage wider applications of partitioning methods in biodiversity studies.