bluuebunny/crossref_metadata_2025 huggingface dataset:
Ethnicity, Religion, and Residential Segregation in London: Evidence from a Computational Typology of Minority Communities
Authors: Brimicombe Allan J
Published: August 2007

Within the context of the growing polarisation and fragmentation of the urban landscape, this paper presents a computational typology applicable to the study of minority communities, both ethnic and religious, which is useful in understanding their spatial distribution and juxtaposition at neighbourhood levels. The typology has been applied to multicultural London with the use of the 2001 Census, in which there were questions on ethnicity and religion. The landscape of religion is found to be more highly segregated in contrast to the landscape of ethnicity. Furthermore, on the basis of a preliminary analysis of indicator variables, minorities seem on aggregate to be in an improved situation given a level of residential segregation, with the exception of residents of segregated Asian-Bangladeshi areas for ethnicity and residents of segregated Muslim areas for religion. This questions the generally held view that segregation in a multicultural society is undesirable per se and suggests that a ‘one size fits all’ government policy towards residential segregation is insufficiently perceptive. The typology introduced here should facilitate a more critically informed approach to multiculturalism and the contemporary city.
Metabolite essentiality elucidates robustness of
Escherichia coli
metabolism
Authors: Kim Pan-Jun , Lee Dong-Yup , Kim Tae Yong , Lee Kwang Ho , Jeong Hawoong , Lee Sang Yup , Park Sunwon
Published: August 2007

Complex biological systems are very robust to genetic and environmental changes at all levels of organization. Many biological functions of
Escherichia coli
metabolism can be sustained against single-gene or even multiple-gene mutations by using redundant or alternative pathways. Thus, only a limited number of genes have been identified to be lethal to the cell. In this regard, the reaction-centric gene deletion study has a limitation in understanding the metabolic robustness. Here, we report the use of flux-sum, which is the summation of all incoming or outgoing fluxes around a particular metabolite under pseudo-steady state conditions, as a good conserved property for elucidating such robustness of
E. coli
from the metabolite point of view. The functional behavior, as well as the structural and evolutionary properties of metabolites essential to the cell survival, was investigated by means of a constraints-based flux analysis under perturbed conditions. The essential metabolites are capable of maintaining a steady flux-sum even against severe perturbation by actively redistributing the relevant fluxes. Disrupting the flux-sum maintenance was found to suppress cell growth. This approach of analyzing metabolite essentiality provides insight into cellular robustness and concomitant fragility, which can be used for several applications, including the development of new drugs for treating pathogens.
Copb1-facilitated axonal transport and translation of κ opioid-receptor mRNA
Authors: Bi Jing , Tsai Nien-Pei , Lu Hsin-Yi , Loh Horace H. , Wei Li-Na
Published: August 2007

mRNA of κ opioid receptor (KOR) can be transported to nerve fibers, including axons of dorsal root ganglia (DRG), and can be locally translated. Yeast three-hybrid screening identifies Copb1 as akormRNA-associated protein that form complexes with endogenouskormRNA, which are colocalized in the soma and axons of DRG neurons. Axonal transport ofkormRNA is demonstrated, directly, by observing mobilization of biotin-labeledkormRNA in Campenot chambers. Efficient transport ofkormRNA into the side chamber requires Copb1 and can be blocked by a drug that disrupts microtubules. The requirement for Copb1 in mobilizingkormRNA is confirmed by using the MS2–GFP mRNA-tagging system. Furthermore, Copb1 also facilitates the translation ofkormRNA in the soma and axons. This study provides evidence for a microtubule-dependent, active axonalkormRNA-transport process that involves Copb1 and can stimulate localized translation and suggests coupling of transport and translation of mRNAs destined to the remote areas such as axons.
Allene formation by gold catalyzed cross-coupling of masked carbenes and vinylidenes
Authors: Lavallo Vincent , Frey Guido D. , Kousar Shazia , Donnadieu Bruno , Bertrand Guy
Published: August 2007

Addition of a sterically demanding cyclic (alkyl)(amino)carbene (CAAC) to AuCl(SMe
2
) followed by treatment with [Et
3
Si(Tol)]
+
[B(C
6
F
5
)
4
]
−
in toluene affords the isolable [(CAAC)Au(η
2
-toluene)]
+
[B(C
6
F
5
)
4
]
−
complex. This cationic Au(I) complex efficiently mediates the catalytic coupling of enamines and terminal alkynes to yield allenes and not propargyl amines as observed with other catalysts. Mono-, di-, and tri-substituted enamines can be used, as well as aryl-, alkyl-, and trimethylsilyl-substituted terminal alkynes. The reaction tolerates sterically hindered substrates and is diastereoselective. This general catalytic protocol directly couples two unsaturated carbon centers to form the three-carbon allenic core. The reaction most probably proceeds through an unprecedented “carbene/vinylidene cross-coupling.”
Structural basis for the acyl chain selectivity and mechanism of UDP-
N
-acetylglucosamine acyltransferase
Authors: Williams Allison H. , Raetz Christian R. H.
Published: August 2007

UDP-
N
-acetylglucosamine (UDP-GlcNAc) acyltransferase (LpxA) catalyzes the first step of lipid A biosynthesis, the reversible transfer of the
R
-3-hydroxyacyl chain from
R
-3-hydroxyacyl acyl carrier protein to the glucosamine 3-OH group of UDP-GlcNAc.
Escherichia coli
LpxA is highly selective for
R
-3-hydroxymyristate. The crystal structure of the
E. coli
LpxA homotrimer, determined previously in the absence of lipid substrates or products, revealed that LpxA contains an unusual, left-handed parallel β-helix fold. We have now solved the crystal structures of
E. coli
LpxA with the bound product UDP-3-
O
-(
R
-3-hydroxymyristoyl)-GlcNAc at a resolution of 1.74 Å and with bound UDP-3-
O
-(
R
-3-hydroxydecanoyl)-GlcNAc at 1.85 Å. The structures of these complexes are consistent with the catalytic mechanism deduced by mutagenesis and with a recent 3.0-Å structure of LpxA with bound UDP-GlcNAc. Our structures show how LpxA selects for 14-carbon
R
-3-hydroxyacyl chains and reveal two modes of UDP binding.
Mechanism of inhibition of bovine F
1
-ATPase by resveratrol and related polyphenols
Authors: Gledhill Jonathan R. , Montgomery Martin G. , Leslie Andrew G. W. , Walker John E.
Published: August 2007

The structures of F
1
-ATPase from bovine heart mitochondria inhibited with the dietary phytopolyphenol, resveratrol, and with the related polyphenols quercetin and piceatannol have been determined at 2.3-, 2.4- and 2.7-Å resolution, respectively. The inhibitors bind to a common site in the inside surface of an annulus made from loops in the three α- and three β-subunits beneath the “crown” of β-strands in their N-terminal domains. This region of F
1
-ATPase forms a bearing to allow the rotation of the tip of the γ-subunit inside the annulus during catalysis. The binding site is a hydrophobic pocket between the C-terminal tip of the γ-subunit and the β
TP
subunit, and the inhibitors are bound via H-bonds mostly to their hydroxyl moieties mediated by bound water molecules and by hydrophobic interactions. There are no equivalent sites between the γ-subunit and either the β
DP
or the β
E
subunit. The inhibitors probably prevent both the synthetic and hydrolytic activities of the enzyme by blocking both senses of rotation of the γ-subunit. The beneficial effects of dietary resveratrol may derive in part by preventing mitochondrial ATP synthesis in tumor cells, thereby inducing apoptosis.
Barriers to Networked Governments: Evidence from Europe
1
Authors: Eynon Rebecca , Dutton William H.
Published: August 2007

Progress towards realizing the full potential of ‘e‐government’—using digital technologies to improve public services and government–citizen engagements—has been slower and less effective than the technologies’ take‐up in spheres such as e‐commerce. Evidence from across Europe reported here, including an online survey and case studies, indicates a significant reason has been an overly narrow focus on substituting electronic for traditional services. Theoretical and empirical perspectives on barriers to e‐government identified (e.g. poor coordination; workplace and organizational inflexibility) suggest greater attention should be given to supporting organization innovations to achieve maximum benefits from networking in the public sector.
The Internationalisation of the Small and Medium‐sized Firm
1
Authors: Rodriguez Jorge
Published: August 2007

In the last few decades, SMEs have become increasingly active in international markets. SMEs do not necessarily follow a pattern of incremental internationalisation as they have a wide range of options and many are opportunistic. A large postal survey was conducted in five countries—the UK, France, Finland, Australia and Mexico. Many similarities in internationalisation strategy were found among these companies.
Fluid skills: drinking games and alcohol consumption among Australian university students
Authors: POLIZZOTTO MARK N. , SAW MELANIE M. , TJHUNG IRENE , CHUA EU HUA , STOCKWELL TIMOTHY R.
Published: August 2007

The objective of this study was to assess participation in drinking games among Australian university students; to determine the range of games played, their context and participant motivations; and to analyse the impact of games on alcohol consumption and its adverse consequences. We used a cross‐sectional survey incorporating structured interviews and a self‐administered questionnaire with students between 18 and 25 years of age at the University of Western Australia. This was a qualitative assessment of drinking game typology and contexts and participant motivation. Quantitative outcomes were rate and frequency of participation in drinking games; amount and rate of alcohol consumption during games; incidence of adverse outcomes following participation. Twenty‐seven interview responses and 256 questionnaire responses were analysed for qualitative and quantitative outcomes, respectively. The qualitative analysis enabled categorisation of drinking games by skill and competitive nature, with varying influence on hazardous drinking. Common reported motivations for play included boredom, social pressure and social unease. The associated heavy drinking and possible hazards were well recognised but did not affect the decision to play. In the quantitative arm, most drinkers (74%) reported having participated in a drinking game. Game players reported playing an average of four drinking games in the previous 6 months. An average of six standard drinks was consumed during the most recent game. Pressure to participate from others was reported by 60% of game participants, while 50% reported that they had placed pressure on others to participate. Half (51%) reported an adverse outcome following participation. Loss of consciousness due to drinking was experienced or witnessed by 89% of game players, of whom 63% reported that the person was put to bed, while 54% reported that the person was watched. Participation in drinking games was common, and plays an important social role in this group. Drinking games were associated commonly with binge drinking and adverse outcomes. Future harm minimisation strategies targeting this group should address the particular risks of these games.
Applied communitarian ethics for harm reduction: promoting a dialogue within the field
Authors: FRY CRAIG , TRELOAR CARLA , MAHER LISA
Published: August 2007

This piece responds to critical points raised in commentaries on our 2005 HRD paper on the topic of harm reduction ethics, and clarifies other aspects of our original arguments that were misinterpreted. In our view, the goal of ethical engagement in harm reduction is not necessarily the production of an agreed moral framework, but instead reflection and awareness raising around the various values and beliefs underlying harm reduction, and consideration of how these influence policy, practice and research decisions and outcomes. This ‘discursive authenticity’ as Hathaway has called it, can help to define a new territory of authority for drug users as participants in harm reduction policy, practice and research.
Application of the paramagnetic dipole field for solution NMR active site structure determination in low‐spin, cyanide‐inhibited ferric hemoproteins
Authors: La Mar Gerd N.
Published: August 2007

The principles for the application of the paramagnetic dipolar field of low‐spin, cyanide‐inhibited ferrihemoproteins for determining active site structure are briefly described. The ubiquitous dipolar shifts for assigned residues, together with crystal coordinates of some appropriate structural homolog, allow determination of the orientation and anisotropies of the paramagnetic dipolar tensor. The orientation of χ uniquely defines the orientation of the Fe‐CN unit, which is tilted variably and sensitively monitors distal steric and H‐bond interactions. The mapped dipolar field, in turn, can be used to determine the orientation of mutated residues. Case studies involving unusual genetic variants and point mutants of myoglobins, human hemoglobins, horseradish peroxidase and its substrate complex of heme oxygenase are presented as examples.
Bach1, a heme‐dependent transcription factor, reveals presence of multiple heme binding sites with distinct coordination structure
Authors: Hira Shusuke , Tomita Takeshi , Matsui Toshitaka , Igarashi Kazuhiko , Ikeda‐Saito Masao
Published: August 2007

The mammalian transcription factor Bach1 functions as a repressor of the enhancers of heme oxygenase‐1 (HO‐1) gene (Hmox‐1) by forming heterodimers with the small Maf proteins such as MafK. The transcription of Hmox‐1 is regulated by the substrate of HO‐1, heme. Heme induces expression of Hmox‐1 in part by inhibiting the binding of Bach1 to the enhancers and inducing the nuclear export of Bach1. A dipeptide motif of cysteine and proline (CP motif) in Bach1 is essential for the heme‐mediated regulation. In this study, we show that five molecules of heme bind to Bach1 by the heme‐titration assay. The Bach1‐heme complex exhibits an absorption spectrum with a major Soret peak at 371 nm and Raman band at 343 cm‐1 in high amounts of heme and a spectrum containing the major Soret peak at 423 nm at low heme concentrations. The spectroscopic characterization indicates that Bach1 has two kinds of heme‐binding sites with different coordination structures. Mutagenesis studies have established that four molecules of heme bind to the cysteine residues of four CP motifs in the C terminus of Bach1. These results raise the possibility that two separated activities of Bach1, DNA‐binding and nuclear export, are regulated by heme binding at the different CP motifs of Bach1 respectively, but not by cooperative heme‐binding.
Multiple strategies for O2 transport: from simplicity to complexity
Authors: Ascenzi Paolo , Bellelli Andrea , Coletta Massimo , Colosimo Alfredo , Falcioni Giancarlo , Giacometti Giorgio M. , Ippoliti Rodolfo , Zolla Lello , Giardina Bruno
Published: August 2007

O2carriers (extracellular and intracellular as well as monomeric and multimeric) have evolved over the last billion of years, displaying iron and copper reactive centers; very different O2carriers may co‐exist in the same organism. Circulating O2carriers, faced to the external environment, are responsible for maintaining an adequate delivery of O2to tissues and organs almost independently of the environmental O2partial pressure. Then, intracellular globins facilitate O2transfer to mitochondria sustaining cellular respiration. Here, molecular aspects of multiple strategies evolved for O2transport and delivery are examined, from the simplest myoglobin to the most complex giant O2carriers and the red blood cell, mostly focusing on the aspects which have been mainly addressed by the so called 'Rome Group'.
Evidence of Intermittency in the Local Field Potentials Recorded from Patients with Parkinson′s Disease: A Wavelet‐Based Approach
Authors: Sen Asok K. , Dostrovsky Jonathan O.
Published: August 2007

Using a continuous wavelet transform we have detected the presence of intermittency in the beta oscillations of the local field potentials (LFPs) that were recorded from the subthalamic nucleus (STN) of patients with Parkinson′s disease. The intermittent behavior was identified by plotting the wavelet power spectrum of the LFP signal on a time–frequency plane. We also computed the temporal variations of scale‐averaged wavelet power and wavelet entropy (WE). An intermittent pattern is characterized by large amounts of power over very short periods of time separated by almost quiescent periods. Time‐localized changes in WE further support the evidence of intermittency. The cause and significance of the intermittent beta activity are presently unclear. It may be due to complex interactions of the cortico‐basal‐ganglia networks converging at the STN level.
Modelling, Analysis and Calculation of Cerebral Hemodynamics
Authors: Daun Silvia , Tjardes Thorsten
Published: August 2007

Mathematical models of cerebral hemodynamics, applicable to humans and rats have been developed and analysed with the purpose of reaching a deeper insight to which degree experimental results on rats can be extrapolated to humans and to clinical management of patients. These models include regulation mechanisms involving the small cerebral arteries and arterioles, flow autoregulation, as well as CO2 and NO reactivity. Bifurcation analysis was conducted on both models.

The human model includes Hopf‐bifurcations, which allow for the existence of periodic solutions with a time scale comparable to Lundberg′s plateau waves in intracranial pressure (Pic). By contrast, the rat model does not manifest Hopf‐bifurcations and thus does not predict the existence of periodic solutions with critical high Pic.

Therefore the model questions the relevance of rodent injury models to predict human physiology following TBI.
Presenilins regulate αβ T cell development by modulating TCR signaling
Authors: Laky Karen , Fowlkes B.J.
Published: August 2007

TCRαβ signaling is crucial for the maturation of CD4 and CD8 T cells, but the role of the Notch signaling pathway in this process is poorly understood. Genes encoding Presenilin (PS) 1/2 were deleted to prevent activation of the multiple Notch receptors expressed by developing thymocytes. PS1/2 knockout thymocyte precursors inefficiently generate CD4 T cells, a phenotype that is most pronounced when thymocytes bear a single major histocompatibility complex (MHC) class II–restricted T cell receptor (TCR). Diminished T cell production correlated with evidence of impaired TCR signaling, and could be rescued by manipulations that enhance MHC recognition. Although Notch appears to directly regulate binary fate decisions in many systems, these findings suggest a model in which PS-dependent Notch signaling influences positive selection and the development of αβ T cells by modifying TCR signal transduction.
Control of Inward Rectifier K Channel Activity by Lipid Tethering of Cytoplasmic Domains
Authors: Enkvetchakul Decha , Jeliazkova Iana , Bhattacharyya Jaya , Nichols Colin G.
Published: August 2007

Interactions between nontransmembrane domains and the lipid membrane are proposed to modulate activity of many ion channels. In Kir channels, the so-called “slide-helix” is proposed to interact with the lipid headgroups and control channel gating. We examined this possibility directly in a cell-free system consisting of KirBac1.1 reconstituted into pure lipid vesicles. Cysteine substitution of positively charged slide-helix residues (R49C and K57C) leads to loss of channel activity that is rescued by in situ restoration of charge following modification by MTSET+ or MTSEA+, but not MTSES− or neutral MMTS. Strikingly, activity is also rescued by modification with long-chain alkyl-MTS reagents. Such reagents are expected to partition into, and hence tether the side chain to, the membrane. Systematic scanning reveals additional slide-helix residues that are activated or inhibited following alkyl-MTS modification. A pattern emerges whereby lipid tethering of the N terminus, or C terminus, of the slide-helix, respectively inhibits, or activates, channel activity. This study establishes a critical role of the slide-helix in Kir channel gating, and directly demonstrates that physical interaction of soluble domains with the membrane can control ion channel activity.
Learning string similarity measures for gene/protein name dictionary look-up using logistic regression
Authors: Tsuruoka Yoshimasa , McNaught John , Tsujii Jun'i;chi , Ananiadou Sophia
Published: August 2007

Motivation: One of the bottlenecks of biomedical data integration is variation of terms. Exact string matching often fails to associate a name with its biological concept, i.e. ID or accession number in the database, due to seemingly small differences of names. Soft string matching potentially enables us to find the relevant ID by considering the similarity between the names. However, the accuracy of soft matching highly depends on the similarity measure employed.

Results: We used logistic regression for learning a string similarity measure from a dictionary. Experiments using several large-scale gene/protein name dictionaries showed that the logistic regression-based similarity measure outperforms existing similarity measures in dictionary look-up tasks.

Availability: A dictionary look-up system using the similarity measures described in this article is available at http://text0.mib.man.ac.uk/software/mldic/

Contact:  yoshimasa.tsuruoka@manchester.ac.uk
Species richness and abundance of forest birds in relation to radiation at Chernobyl
Authors: Møller A.P , Mousseau T.A
Published: August 2007

The effects of low-level radiation on the abundance of animals are poorly known, as are the effects on ecosystems and their functioning. Recent conclusions from the UN Chernobyl forum and reports in the popular media concerning the effects of radiation from Chernobyl on animals have left the impression that the Chernobyl exclusion zone is a thriving ecosystem, filled with an increasing number of rare species. Surprisingly, there are no standardized censuses of common animals in relation to radiation, leaving the question about the ecological effects of radiation unresolved. We conducted standardized point counts of breeding birds at forest sites around Chernobyl differing in level of background radiation by over three orders of magnitude. Species richness, abundance and population density of breeding birds decreased with increasing level of radiation, even after controlling statistically for the effects of potentially confounding factors such as soil type, habitat and height of the vegetation. This effect was differential for birds eating soil invertebrates living in the most contaminated top soil layer. These results imply that the ecological effects of Chernobyl on animals are considerably greater than previously assumed.
Evolution of Pinnipedia lactation strategies: a potential role for α-lactalbumin?
Authors: Reich Coralie M , Arnould John P.Y
Published: August 2007

Despite the considerable variation in milk composition found among mammals, a constituent common across all groups is lactose, the main sugar and osmole in most eutherians milk. Exceptions to this are the families Otariidae (fur seals and sea lions) and Odobenidae (walruses), where lactose has not been detected. We investigated the molecular basis for this by cloning α-lactalbumin, the modifier protein of the lactose synthase complex. A mutation was observed which, in addition to preventing lactose production, may enable otariids to maintain lactation despite the extremely long inter-suckling intervals during the mother's time at sea foraging (more than 23 days in some species).
‘Megapclicks’: acoustic click trains and buzzes produced during night-time foraging of humpback whales (
Megaptera novaeangliae
)
Authors: Stimpert Alison K , Wiley David N , Au Whitlow W.L , Johnson Mark P , Arsenault Roland
Published: August 2007

Humpback whales (
Megaptera novaeangliae
) exhibit a variety of foraging behaviours, but neither they nor any baleen whale are known to produce broadband clicks in association with feeding, as do many odontocetes. We recorded underwater behaviour of humpback whales in a northwest Atlantic feeding area using suction-cup attached, multi-sensor, acoustic tags (DTAGs). Here we describe the first recordings of click production associated with underwater lunges from baleen whales. Recordings of over 34 000 ‘megapclicks’ from two whales indicated relatively low received levels at the tag (between 143 and 154 dB re 1 μPa pp), most energy below 2 kHz, and interclick intervals often decreasing towards the end of click trains to form a buzz. All clicks were recorded during night-time hours. Sharp body rolls also occurred at the end of click bouts containing buzzes, suggesting feeding events. This acoustic behaviour seems to form part of a night-time feeding tactic for humpbacks and also expands the known acoustic repertoire of baleen whales in general.
Things fall apart: biological species form unconnected parsimony networks
Authors: Hart Michael W , Sunday Jennifer
Published: August 2007

The generality of operational species definitions is limited by problematic definitions of between-species divergence. A recent phylogenetic species concept based on a simple objective measure of statistically significant genetic differentiation uses between-species application of statistical parsimony networks that are typically used for population genetic analysis within species. Here we review recent phylogeographic studies and reanalyse several mtDNA barcoding studies using this method. We found that (i) alignments of DNA sequences typically fall apart into a separate subnetwork for each Linnean species (but with a higher rate of true positives for mtDNA data) and (ii) DNA sequences from single species typically stick together in a single haplotype network. Departures from these patterns are usually consistent with hybridization or cryptic species diversity.
Effects of age and gender on success and death of mountaineers on Mount Everest
Authors: Huey Raymond B , Salisbury Richard , Wang Jane-Ling , Mao Meng
Published: August 2007

Increasing numbers of climbers are attempting Mount Everest, the highest mountain on Earth. We compiled interview data and computed the probabilities of summiting and of dying as a function of climber age and gender (2211 climbers, spring season) for the period of 1990–2005. Men and women had similar odds of summiting and of dying. However, climbers older than 40 years have reduced odds of summiting, and those older than 60 years have increased odds of dying, especially when descending from the summit. On Mount Everest, phenotypic selection appears blind to gender but favours young mountaineers.
Interspecific audience effects on the alarm-calling behaviour of a kleptoparasitic bird
Authors: Ridley Amanda R , Child Matthew F , Bell Matthew B.V
Published: August 2007

Audience effects are increasingly recognized as an important aspect of intraspecific communication. Yet despite the common occurrence of interspecific interactions and considerable evidence that individuals respond to the calls of heterospecifics, empirical evidence for interspecific audience effects on signalling behaviour is lacking. Here we present evidence of an interspecific audience effect on the alarm-calling behaviour of the kleptoparasitic fork-tailed drongo (
Dicrurus adsimilis
). When foraging solitarily, drongos regularly alarm at aerial predators, but rarely alarm at terrestrial predators. In contrast, when drongos are following terrestrially foraging pied babblers (
Turdoides bicolor
) for kleptoparasitic opportunities, they consistently give alarm calls to both aerial and terrestrial predators. This change occurs despite no difference in the amount of time that drongos spend foraging terrestrially. Babblers respond to drongo alarm calls by fleeing to cover, providing drongos with opportunities to steal babbler food items by occasionally giving false alarm calls. This provides an example of an interspecific audience effect on alarm-calling behaviour that may be explained by the benefits received from audience response.
Secondary chemicals protect mould from fungivory
Authors: Rohlfs Marko , Albert Martin , Keller Nancy P , Kempken Frank
Published: August 2007

The vast repertoire of toxic fungal secondary metabolites has long been assumed to have an evolved protective role against fungivory. It still remains elusive, however, whether fungi contain these compounds as an anti-predator adaptation. We demonstrate that loss of secondary metabolites in the soil mouldAspergillus nidulanscauses, under the attack of the fungivorous springtailFolsomia candida, a disadvantage to the fungus. Springtails exhibited a distinct preference for feeding on a mutant deleted for LaeA, a global regulator ofAspergillussecondary metabolites. Consumption of the mutant yielded a reproductive advantage to the arthropod but detrimental effects on fungal biomass compared with a wild-type fungus capable of producing the entire arsenal of secondary metabolites. Our results demonstrate that fungal secondary metabolites shape food choice behaviour, can affect population dynamics of fungivores, and suggest that fungivores may provide a selective force favouring secondary metabolites synthesis in fungi.
The thermodynamic driving force for bone growth and remodelling: a hypothesis
Authors: Kirchner Helmut O.K , Lazar Markus
Published: August 2007

The Eshelby stress (static energy momentum) tensor is derived for bone modelled as an inhomogeneous piezoelectric and piezomagnetic Cosserat (micropolar) medium. The divergence of this tensor is the configurational force felt by material gradients and defects in the medium. Just as in inhomogeneous elastic media, this force is identified with the thermodynamic force for phase transformations, in bone it is the thermodynamic cause of structural transformations, i.e. remodelling and growth. The thermodynamic approach shows that some terms of driving force are proportional to the stress, and some acting on material inhomogeneities are quadratic in the stress—the latter outweigh by far the former. Since inertial forces due to acceleration enter the energy–momentum tensor, it follows that the rate of loading matters and that both tension and compression stimulate growth, which is favoured at heterogeneities.
Disease dynamics over very different time-scales: foot-and-mouth disease and scrapie on the network of livestock movements in the UK
Authors: Kao Rowland R , Green Darren M , Johnson Jethro , Kiss Istvan Z
Published: August 2007

We analyse the relationship between the network of livestock movements in the UK and the dynamics of two diseases: foot-and-mouth disease (FMD), which has an incubation period of days, and scrapie, which incubates over years. For FMD, the time-scale of expected epidemics is similar to the time-scale of the evolution of the network. We argue that, under appropriate conditions, a static network analysis can be an appropriate tool for gaining insights into disease dynamics even when the relevant time-scales are similar, as with FMD. We show that a subclass of ‘linkage moves’ maintains the network structure, and so removing these links has a dramatic effect on the number of potentially infected farms, an effect corroborated by simulations. In contrast, because scrapie has a low probability of transmission per contact and a long incubation period, a static network representation is probably appropriate; however, the signature of the network in the pattern of transmission is likely to be faint. Scrapie-notifying farms were more likely to be associated with each other via trading at markets than were control farms; however, network community structure proves to be less representative of prevalence patterns than geographical region. These contradictory indicators emphasize that appropriate observation time frames and good discrimination among types of potentially infectious contacts are vital in order for network analysis to be a valuable epidemiological tool.
Synchrony between fruit maturation and effective dispersers' foraging activity increases seed protection against seed predators
Authors: Boulay Raphaël , Carro Francisco , Soriguer Ramón C , Cerdá Xim
Published: August 2007

The evolution of pollination and seed dispersal mutualisms is conditioned by the spatial and temporal co-occurrence of animals and plants. In the present study we explore the timing of seed release of a myrmecochorous plant (Helleborus foetidus) and ant activity in two populations in southern Spain during 2 consecutive years. The results indicate that fruit dehiscence and seed shedding occur mostly in the morning and correspond to the period of maximum foraging activity of the most effective ant dispersers. By contrast, ant species that do not transport seeds and/or that do not abound near the plants are active either before or afterH. foetidusdiaspores are released. Experimental analysis of diet preference for three kinds of food shows that effective ant dispersers are mostly scavengers that readily feed on insect corpses and sugars. Artificial seed depots suggest that seeds deposited on the ground out of the natural daily time window of diaspore releasing are not removed by ants and suffer strong predation by nocturnal rodentsApodemus sylvaticus. Nevertheless, important inter-annual variations in rodent populations cast doubts on their real importance as selection agents. We argue that traits allowing synchrony between seed presentation and effective partners may constitute a crucial pre-adaptation for the evolution of plant–animal mutualisms involving numerous animal partners.
Do capuchin monkeys (
Cebus apella
) use tokens as symbols?
Authors: Addessi E , Crescimbene L , Visalberghi E
Published: August 2007

In the absence of language, the comprehension of symbols is difficult to demonstrate. Tokens can be considered symbols since they arbitrarily stand for something else without having any iconic relation to their referent. We assessed whether capuchin monkeys (
Cebus apella
) can use tokens as symbols to represent and combine quantities. Our paradigm involved choices between various combinations of tokens A and B, worth one and three rewards, respectively. Pay-off maximization required the assessment of the value of each offer by (i) estimating token numerousness, (ii) representing what each token stands for and (iii) making simple computations. When one token B was presented against one to five tokens A (experiment 1), four out of ten capuchins relied on a flexible strategy that allowed to maximize their pay-off, i.e. they preferred one token B against one and two tokens A, and they preferred four or five tokens A against one token B. Moreover, when two tokens B were presented against three to six tokens A (experiment 2), two out of six capuchins performed summation over representation of quantities. These findings suggest that capuchins can use tokens as symbols to flexibly combine quantities.
New sea spiders from the Jurassic La Voulte-sur-Rhône Lagerstätte
Authors: Charbonnier S , Vannier J , Riou B
Published: August 2007

The diverse and exceptionally well-preserved pycnogonids described herein from the Middle Jurassic La Voulte Lagerstätte fill a 400 Myr gap of knowledge in the evolutionary history of this enigmatic group of marine arthropods. They reveal very close morphological and functional (locomotion, feeding) similarities with present-day pycnogonids and, by contrast, marked differences with all Palaeozoic representatives of the group. This suggests a relatively recent, possibly Mesozoic origin for at least three major extant lineages of pycnogonids (Ammotheidae, Colossendeidae, Endeidae). Combined evidence from depositional environment, faunal associates and recent analogues indicate that the La Voulte pycnogonids probably lived in the upper bathyal zone (
ca
200 m). Our results point to a remarkable morphological and ecological stability of this arthropod group over at least 160 Myr and suggest that the colonization of the deep sea by pycnogonids occurred before the Jurassic.
Fluctuations, correlations and transitions in granular materials: statistical mechanics for a non-conventional system
Authors: Behringer R.P , Daniels Karen E , Majmudar Trushant S , Sperl Matthias
Published: August 2007

In this work, we first review some general properties of dense granular materials. We are particularly concerned with a statistical description of these materials, and it is in this light that we briefly describe results from four representative studies. These are: experiment 1: determining local force statistics, vector forces, force distributions and correlations for static granular systems; experiment 2: characterizing the jamming transition, for a static two-dimensional system; experiment 3: characterizing plastic failure in dense granular materials; and experiment 4: a dynamical transition where the material ‘freezes’ in the presence of apparent heating for a sheared and shaken system.
Fitting ordinary differential equations to short time course data
Authors: Brewer Daniel , Barenco Martino , Callard Robin , Hubank Michael , Stark Jaroslav
Published: August 2007

Ordinary differential equations (ODEs) are widely used to model many systems in physics, chemistry, engineering and biology. Often one wants to compare such equations with observed time course data, and use this to estimate parameters. Surprisingly, practical algorithms for doing this are relatively poorly developed, particularly in comparison with the sophistication of numerical methods for solving both initial and boundary value problems for differential equations, and for locating and analysing bifurcations. A lack of good numerical fitting methods is particularly problematic in the context of systems biology where only a handful of time points may be available. In this paper, we present a survey of existing algorithms and describe the main approaches. We also introduce and evaluate a new efficient technique for estimating ODEs linear in parameters particularly suited to situations where noise levels are high and the number of data points is low. It employs a spline-based collocation scheme and alternates linear least squares minimization steps with repeated estimates of the noise-free values of the variables. This is reminiscent of expectation–maximization methods widely used for problems with nuisance parameters or missing data.
Generating surrogates from recurrences
Authors: Thiel M , Romano M.C , Kurths J , Rolfs M , Kliegl R
Published: August 2007

In this paper, we present an approach to recover the dynamics from recurrences of a system and then generate (multivariate) twin surrogate (TS) trajectories. In contrast to other approaches, such as the linear-like surrogates, this technique produces surrogates which correspond to an independent copy of the underlying system, i.e. they induce a trajectory of the underlying system visiting the attractor in a different way. We show that these surrogates are well suited to test for complex synchronization, which makes it possible to systematically assess the reliability of synchronization analyses. We then apply the TS to study binocular fixational movements and find strong indications that the fixational movements of the left and right eye are phase synchronized. This result indicates that there might be only one centre in the brain that produces the fixational movements in both eyes or a close link between the two centres.
Experimental separation of chaotic signals through synchronization
Authors: Buscarino Arturo , Fortuna Luigi , Frasca Mattia
Published: August 2007

In this paper using a negative feedback scheme we study the problem of synchronizing two systems (each of them made ofnindependent chaotic circuits) through the transmission of a unique signal (i.e. a scalar variable). To find the appropriate values of the feedback gains, an approach based on the design of an asymptotic observer leading to a set of linear matrix inequalities is used for piecewise linear systems, while for systems with continuous nonlinearities a master stability function approach is adopted. Numerical results showing the suitability of the approach are reported. Furthermore, the experiment showing separation and synchronization of two pairs of chaotic circuits is discussed. Despite the presence of parameter mismatches, separation and synchronization of the two systems can be achieved. This is an experimental demonstration of the successful possibility of multiplexing two (or more) chaotic signals in the same channel.
Wind direction modelling using multiple observation points
Authors: Hirata Yoshito , Mandic Danilo P , Suzuki Hideyuki , Aihara Kazuyuki
Published: August 2007

The prediction of wind direction is a prerequisite for the intelligent and efficient operation of wind turbines. This is a complex task, due to the intermittent behaviour of wind, its non-Gaussian and nonlinear nature, and the coupling between the wind speed and direction. To provide improved wind direction forecasting, we propose a nonlinear model with augmented information from an additional measurement point. This is further enhanced by making use of both the speed and direction components of the wind field vector. The analysis and a comprehensive set of simulations demonstrate that the proposed approach achieves improved prediction performance over the standard and persistent model. The potential of the proposed approach is justified by the fact that even relatively small improvements in the forecasts result in large gains in the produced output power.
Piecewise linear approach to an archetypal oscillator for smooth and discontinuous dynamics
Authors: Cao Qingjie , Wiercigroch Marian , Pavlovskaia Ekaterina E , Thompson J. Michael T , Grebogi Celso
Published: August 2007

In a recent paper we examined a model of an arch bridge with viscous damping subjected to a sinusoidally varying central load. We showed how this yields a useful archetypal oscillator which can be used to study the transition from smooth to discontinuous dynamics as a parameter,
α
, tends to zero. Decreasing this smoothness parameter (a non-dimensional measure of the span of the arch) changes the smooth load–deflection curve associated with snap-buckling into a discontinuous sawtooth. The smooth snap-buckling curve is not amenable to closed-form theoretical analysis, so we here introduce a piecewise linearization that correctly fits the sawtooth in the limit at
α
=0. Using a Hamiltonian formulation of this linearization, we derive an analytical expression for the unperturbed homoclinic orbit, and make a Melnikov analysis to detect the homoclinic tangling under the perturbation of damping and driving. Finally, a semi-analytical method is used to examine the full nonlinear dynamics of the perturbed piecewise linear system. A chaotic attractor located at
α
=0.2 compares extremely well with that exhibited by the original arch model: the topological structures are the same, and Lyapunov exponents (and dimensions) are in good agreement.
Chaos computing: ideas and implementations
Authors: Ditto William L , Murali K , Sinha Sudeshna
Published: August 2007

We review the concept of the ‘chaos computing’ paradigm, which exploits the controlled richness of nonlinear dynamics to obtain flexible reconfigurable hardware. We demonstrate the idea with specific schemes and verify the schemes through proof-of-principle experiments.
In situ
monitoring of friction surfaces and their sequence pattern analysis
Authors: Kano S , Homma H , Sasaki S , Shimura H
Published: August 2007

Friction occurs between solid surfaces, and even sometimes on lubricated surfaces. To understand tribological subjects, it is important to know the changes that occur in friction surfaces. In this study, a laser strobe technique is applied to a friction surface observation. The recorded surface images were analysed using pattern-matching methods and their correlations are discussed. A test using pin-on-plate methods with carbon steels was performed using a reciprocating motion speed of 10 Hz for 4.9 N. A pulsed laser light (Nd:YAG SHG=532 nm, 5 ns per pulse) was irradiated onto the friction surface. It was induced using an optical microscope that was located just to the side of the pin. The laser pulse was synchronized with the plate motion, which was a trigger of the laser pulse. The surface image was stored for every cycle. These sequences were calculated and their correlations were analysed as a function of the surface pattern and the friction track size and shape. Analysis revealed that some groups were distinguishable as parameters of the damage size and shape.
In the Begining Science said…
Authors: Harvey Graham
Published: August 2007

From DNA to Dean: Reflections and Explorations of a Priest‐scientist, Arthur Peacocke

God and the Web of Creation, Ruth Page
Theologizing Film
Authors: Wollaston Isabel
Published: August 2007

Explorations in Theology and Film, Clive Marsh and Gaye Ortiz (eds)
A Hierarchical Modelling Framework for Identifying Unusual Performance in Health Care Providers
Authors: Ohlssen David I. , Sharples Linda D. , Spiegelhalter David J.
Published: August 2007

A wide variety of statistical methods have been proposed for detecting unusual performance in cross-sectional data on health care providers. We attempt to create a unified framework for comparing these methods, focusing on a clear distinction between estimation and hypothesis testing approaches, with the corresponding distinction between detecting ‘extreme’ and ‘divergent’ performance. When assuming a random-effects model the random-effects distribution forms the null hypothesis, and there appears little point in testing whether individual effects are greater or less than average. The hypothesis testing approach uses p-values as summaries and brings with it the standard problems of multiple testing, whether Bayesian or classical inference is adopted. A null random-effects formulation allows us to answer appropriate questions of the type: ‘is a particular provider worse than we would expect the true worst provider (but still part of the null distribution) to be'? We outline a broad three-stage strategy of exploratory detection of unusual providers, detailed modelling robust to potential outliers and confirmation of unusual performance, illustrated by using two detailed examples. The concepts are most easily handled within a Bayesian analytic framework using Markov chain Monte Carlo methods, but the basic ideas should be generally applicable.
The Size of Under-Reporting Bias in Recorded Transnational Terrorist Activity
Authors: Drakos Konstantinos
Published: August 2007

We address an apparent gap in the applied terrorism literature providing an estimate for the size of under-reporting in transnational terrorist activity. The method that is suggested is computationally straightforward and takes into account the stochastic interactions between terrorism, polity and press freedom in a manner that utilizes their sample properties. The outcome from the application of this metric is that underreporting bias is indeed present and quite sizable.