bluuebunny/crossref_metadata_2025 huggingface dataset:
Media/Psychological Impact on Multiple Outbreaks of Emerging Infectious Diseases
Authors: Liu Rongsong , Wu Jianhong , Zhu Huaiping
Published: August 2007

We use a compartmental model to illustrate a possible mechanism for multiple outbreaks or even sustained periodic oscillations of emerging infectious diseases due to the psychological impact of the reported numbers of infectious and hospitalized individuals. This impact leads to the change of avoidance and contact patterns at both individual and community levels, and incorporating this impact using a simple nonlinear incidence function into the model shows qualitative differences of the transmission dynamics.
Model‐Based Analysis and Optimization of the Mapping of Cortical Sources in the Spontaneous Scalp EEG
Authors: Sazonov Andrei V. , Bergmans Jan W. M. , Cluitmans Pierre J. M. , Griep Paul A. M. , Arends Johan B. A. M. , Boon Paul A. J. M.
Published: August 2007

The mapping of brain sources into the scalp electroencephalogram (EEG) depends on volume conduction properties of the head and on an electrode montage involving a reference. Mathematically, this source mapping (SM) is fully determined by an observation function (OF) matrix. This paper analyses the OF‐matrix for a generation model for the desynchronized spontaneous EEG. The model involves a four‐shell spherical volume conductor containing dipolar sources that are mutually uncorrelated so as to reflect the desynchronized EEG. The reference is optimized in order to minimize the impact in the SM of the sources located distant from the electrodes. The resulting reference is called the localized reference (LR). The OF‐matrix is analyzed in terms of the relative power contribution of the sources and the cross‐channel correlation coefficient for five existing references as well as for the LR. It is found that the Hjorth Laplacian reference is a fair approximation of the LR, and thus is close to optimum for practical intents and purposes. The other references have a significantly poorer performance. Furthermore, the OF‐matrix is analyzed for limits to the spatial resolution for the EEG. These are estimated to be around 2 cm.
On Oscillatory Pattern of Malaria Dynamics in a Population with Temporary Immunity
Authors: Tumwiine J. , Mugisha J. Y. T. , Luboobi L. S.
Published: August 2007

We use a model to study the dynamics of malaria in the human and mosquito population to explain the stability patterns of malaria. The model results show that the disease‐free equilibrium is globally asymptotically stable and occurs whenever the basic reproduction number, R0 is less than unity. We also note that when R0>1, the disease‐free equilibrium is unstable and the endemic equilibrium is stable. Numerical simulations show that recoveries and temporary immunity keep the populations at oscillation patterns and eventually converge to a steady state.
New markers for murine memory B cells that define mutated and unmutated subsets
Authors: Anderson Shannon M. , Tomayko Mary M. , Ahuja Anupama , Haberman Ann M. , Shlomchik Mark J.
Published: August 2007

The study of murine memory B cells has been limited by small cell numbers and the lack of a definitive marker. We have addressed some of these difficulties with hapten-specific transgenic (Tg) mouse models that yield relatively large numbers of antigen-specific memory B cells upon immunization. Using these models, along with a 5-bromo-2′-deoxyuridine (BrdU) pulse-label strategy, we compared memory cells to their naive precursors in a comprehensive flow cytometric survey, thus revealing several new murine memory B cell markers. Most interestingly, memory cells were phenotypically heterogeneous. Particularly surprising was the finding of an unmutated memory B cell subset identified by the expression of CD80 and CD35. We confirmed these findings in an analogous V region knock-in mouse and/or in non-Tg mice. There also was anatomic heterogeneity, with BrdU+ memory cells residing not just in the marginal zone, as had been thought, but also in splenic follicles. These studies impact the current understanding of murine memory B cells by identifying new phenotypes and by challenging assumptions about the location and V region mutation status of memory cells. The apparent heterogeneity in the memory compartment implies either different origins and/or different functions, which we discuss.
Requirement for T-bet in the aberrant differentiation of unhelped memory CD8+ T cells
Authors: Intlekofer Andrew M. , Takemoto Naofumi , Kao Charlly , Banerjee Arnob , Schambach Felix , Northrop John K. , Shen Hao , Wherry E. John , Reiner Steven L.
Published: August 2007

Immunity to intracellular pathogens requires dynamic balance between terminal differentiation of short-lived, cytotoxic effector CD8+ T cells and self-renewal of central–memory CD8+ T cells. We now show that T-bet represses transcription of IL-7Rα and drives differentiation of effector and effector–memory CD8+ T cells at the expense of central–memory cells. We also found T-bet to be overexpressed in CD8+ T cells that differentiated in the absence of CD4+ T cell help, a condition that is associated with defective central–memory formation. Finally, deletion of T-bet corrected the abnormal phenotypic and functional properties of “unhelped” memory CD8+ T cells. T-bet, thus, appears to function as a molecular switch between central– and effector–memory cell differentiation. Antagonism of T-bet may, therefore, represent a novel strategy to offset dysfunctional programming of memory CD8+ T cells.
β-Scorpion Toxin Modifies Gating Transitions in All Four Voltage Sensors of the Sodium Channel
Authors: Campos Fabiana V. , Chanda Baron , Beirão Paulo S.L. , Bezanilla Francisco
Published: August 2007

Several naturally occurring polypeptide neurotoxins target specific sites on the voltage-gated sodium channels. Of these, the gating modifier toxins alter the behavior of the sodium channels by stabilizing transient intermediate states in the channel gating pathway. Here we have used an integrated approach that combines electrophysiological and spectroscopic measurements to determine the structural rearrangements modified by the β-scorpion toxin Ts1. Our data indicate that toxin binding to the channel is restricted to a single binding site on domain II voltage sensor. Analysis of Cole-Moore shifts suggests that the number of closed states in the activation sequence prior to channel opening is reduced in the presence of toxin. Measurements of charge–voltage relationships show that a fraction of the gating charge is immobilized in Ts1-modified channels. Interestingly, the charge–voltage relationship also shows an additional component at hyperpolarized potentials. Site-specific fluorescence measurements indicate that in presence of the toxin the voltage sensor of domain II remains trapped in the activated state. Furthermore, the binding of the toxin potentiates the activation of the other three voltage sensors of the sodium channel to more hyperpolarized potentials. These findings reveal how the binding of β-scorpion toxin modifies channel function and provides insight into early gating transitions of sodium channels.
KCNE1 and KCNE3 Stabilize and/or Slow Voltage Sensing S4 Segment of KCNQ1 Channel
Authors: Nakajo Koichi , Kubo Yoshihiro
Published: August 2007

KCNQ1 is a voltage-dependent K+ channel whose gating properties are dramatically altered by association with auxiliary KCNE proteins. For example, KCNE1, which is mainly expressed in heart and inner ear, markedly slows the activation kinetics of KCNQ1. Whether the voltage-sensing S4 segment moves differently in the presence of KCNE1 is not yet known, however. To address that question, we systematically introduced cysteine mutations, one at a time, into the first half of the S4 segment of human KCNQ1. A226C was found out as the most suited mutant for a methanethiosulfonate (MTS) accessibility analysis because it is located at the N-terminal end of S4 segment and its current was stable with repetitive stimuli in the absence of MTS reagent. MTS accessibility analysis revealed that the apparent second order rate constant for modification of the A226C mutant was state dependent, with faster modification during depolarization, and was 13 times slower in the presence of KCNE1 than in its absence. In the presence of KCNE3, on the other hand, the second order rate constant for modification was not state dependent, indicating that the C226 residue was always exposed to the extracellular milieu, even at the resting membrane potential. Taken together, these results suggest that KCNE1 stabilizes the S4 segment in the resting state and slows the rate of transition to the active state, while KCNE3 stabilizes the S4 segment in the active state. These results offer new insight into the mechanism of KCNQ1 channel modulation by KCNE1 and KCNE3.
Improved model-based, platform-independent feature extraction for mass spectrometry
Authors: Noy Karin , Fasulo Daniel
Published: August 2007

Motivation: Mass spectrometry (MS) is increasingly being used for biomedical research. The typical analysis of MS data consists of several steps. Feature extraction is a crucial step since subsequent analyses are performed only on the detected features. Current methodologies applied to low-resolution MS, in which features are peaks or wavelet functions, are parameter-sensitive and inaccurate in the sense that peaks and wavelet functions do not directly correspond to the underlying molecules under observation. In high-resolution MS, the model-based approach is more appealing as it can provide a better representation of the MS signals by incorporating information about peak shapes and isotopic distributions. Current model-based techniques are computationally expensive; various algorithms have been proposed to improve the computational efficiency of this paradigm. However, these methods cannot deal well with overlapping features, especially when they are merged to create one broad peak. In addition, no method has been proven to perform well across different MS platforms.

Results: We suggest a new model-based approach to feature extraction in which spectra are decomposed into a mixture of distributions derived from peptide models. By incorporating kernel-based smoothing and perceptual similarity for matching distributions, our statistical framework improves existing methodologies in terms of computational efficiency and the accuracy of the results. Our model is parameterized by physical properties and is therefore applicable to different MS instruments and settings. We validate our approach on simulated data, and show that the performance is higher than commonly used tools on real high- and low-resolution MS, and MS/MS data sets.

Contact:  daniel.fasulo@siemens.com

Supplementary information: Supplementary data are available at Bioinformatics online.
pIPHULA—parallel inference of population parameters using a likelihood approach
Authors: Schmidt Heiko A. , von Haeseler Arndt , Buschbom Jutta
Published: August 2007

Summary: pIPHULA is the parallel program to estimate the parameters of a realistic model of population growth.

Availability: pIPHULA (http://www.cibiv.at/software/piphula) is written in ISO C, parallel and sequential executables run on UNIX/Linux, Windows and MacOS systems. For (free) MPI libraries see http://en.wikipedia.org/wiki/Message_Passing_Interface.

Contact:  heiko.schmidt@univie.ac.at or ha.schmidt@web.de

Supplementary information: Supplementary data are available at Bioinformatics online.
PhylArray: phylogenetic probe design algorithm for microarray
Authors: Militon Cécile , Rimour Sébastien , Missaoui Mohieddine , Biderre Corinne , Barra Vincent , Hill David , Moné Anne , Gagne Geneviève , Meier Harald , Peyretaillade Eric , Peyret Pierre
Published: August 2007

Motivation: Microbial diversity is still largely unknown in most environments, such as soils. In order to get access to this microbial ‘black-box’, the development of powerful tools such as microarrays are necessary. However, the reliability of this approach relies on probe efficiency, in particular sensitivity, specificity and explorative power, in order to obtain an image of the microbial communities that is close to reality.

Results: We propose a new probe design algorithm that is able to select microarray probes targeting SSU rRNA at any phylogenetic level. This original approach, implemented in a program called ‘PhylArray’, designs a combination of degenerate and non-degenerate probes for each target taxon. Comparative experimental evaluations indicate that probes designed with PhylArray yield a higher sensitivity and specificity than those designed by conventional approaches. Applying the combined PhyArray/GoArrays strategy helps to optimize the hybridization performance of short probes. Finally, hybridizations with environmental targets have shown that the use of the PhylArray strategy can draw attention to even previously unknown bacteria.

Availability:  http://fc.isima.fr/~rimour/phylarray/

Contact:  pierre.peyret@univ-bpclermont.fr

Supplementary information: Supplementary data are available at Bioinformatics online.
Expression ratio evaluation in two-colour microarray experiments is significantly improved by correcting image misalignment
Authors: Tang Thomas , François Nicolas , Glatigny Annie , Agier Nicolas , Mucchielli Marie-Hélène , Aggerbeck Lawrence , Delacroix Hervé
Published: August 2007

Motivation: Two-colour microarrays are widely used to perform transcriptome analysis. In most cases, it appears that the ‘red’ and ‘green’ images resulting from the scan of a microarray slide are slightly shifted one with respect to the other. To increase the robustness of the measurement of the fluorescent emission intensities, multiple acquisitions with the same or different PMT gains can be used. In these cases, a systematic correction of image shift is required.

Results: To accurately detect this shift, we first developed an approach using cross-correlation. Second, we evaluated the most appropriate interpolation method to be used to derive the registered image. Then, we quantified the effects of image shifts on spot quality, using two different quality estimators. Finally, we measured the benefits associated with a systematic image registration. In this study, we demonstrate that registering the two images prior to data extraction provides a more reliable estimate of the two colours’ ratio and thus increases the accuracy of measurements of variations in gene expression.

Availability:  http://bioinfome.cgm.cnrs-gif.fr/

Contact:  tang@cgm.cnrs-gif.fr
Compared to What? A Comment on “A Robust Transformation Procedure for Interpreting Political Text” by Martin and Vanberg
Authors: Benoit Kenneth , Laver Michael
Published: August 2007

In “A Robust Transformation Procedure,” Martin and Vanberg (2007, hereafter MV) propose a new method for rescaling the raw virgin text scores produced by the “Wordscores” procedure of Laver, Benoit, and Garry (2003, hereafter LBG). Their alternative method addresses two deficiencies they argue exist with the transformation of virgin text scores proposed by LBG: First, that the LBG transformation is sensitive to the selection of virgin texts, and second, that it distorts the reference metric by failing to recover the original reference scores when reference texts are scored and transformed as if they were virgin texts. Their proposed alternative is “robust” in the sense that it avoids both shortcomings. Not only is MV's transformation a welcome contribution to the Wordscores project but also the critical analysis on which it is based brings to light a number of assumptions and choices that face the analyst seeking to estimate actors' policy positions using statistical analyses of the texts they generate. When first describing the possibility of rescaling the raw virgin text estimates, we emphasized that our

particular approach to rescaling is not fundamental to our word-scoring technique but, rather, is a matter of substantive research design unrelated to the validity of the raw virgin text scores… Other transformations are of course possible. (LBG, 316)

To explore more fully into the assumptions and choices behind alternative transformations and the research designs which motivate them, we offer the following comments.
Climate-driven range expansion of a critically endangered top predator in northeast Atlantic waters
Authors: Wynn Russell B , Josey Simon A , Martin Adrian P , Johns David G , Yésou Pierre
Published: August 2007

Global climate change is driving rapid distribution shifts in marine ecosystems; these are well established for lower trophic levels, but are harder to quantify for migratory top predators. By analysing a 25-year sightings-based dataset, we found evidence for rapid northwards range expansion of the critically endangered Balearic shearwater
Puffinus mauretanicus
in northeast Atlantic waters. A 0.6°C sea surface temperature increase in the mid-1990s is interpreted as an underlying controlling factor, while simultaneous northward shifts of plankton and prey fish species suggests a strong bottom-up control. Our results have important conservation implications and provide new evidence for climate-driven regime shift in Atlantic ecosystems.
Promotion of ecosystem carbon sequestration by invasive predators
Authors: Wardle David A , Bellingham Peter J , Fukami Tadashi , Mulder Christa P.H
Published: August 2007

Despite recent interest in understanding the effects of human-induced global change on carbon (C) storage in terrestrial ecosystems, most studies have overlooked the influence of a major element of global change, namely biological invasions. We quantified ecosystem C storage, both above- and below-ground, on each of 18 islands off the coast of New Zealand. Some islands support high densities of nesting seabirds, while others have been invaded by predatory rats and host few seabirds. Our results show that, by preying upon seabirds, rats have indirectly enhanced C sequestration in live plant biomass by 104%, reduced C sequestration in non-living pools by 26% and increased total ecosystem C storage by 37%. Given the current worldwide distribution of rats and other invasive predatory mammals, and the consequent disappearance of seabird colonies, these predators may be important determinants of ecosystem C sequestration.
Sons are made from old stores: sperm storage effects on sex ratio in a lizard
Authors: Olsson Mats , Schwartz Tonia , Uller Tobias , Healey Mo
Published: August 2007

Sperm storage is a widespread phenomenon across taxa and mating systems but its consequences for central fitness parameters, such as sex ratios, has rarely been investigated. In Australian painted dragon lizards (
Ctenophorus pictus
), we describe elsewhere that male reproductive success via sperm competition is largely an effect of sperm storage. That is, sperm being stored in the female reproductive tract out-compete more recently inseminated sperm in subsequent ovarian cycles. Here we look at the consequences of such sperm storage for sex allocation in the same species, which has genetic sex determination. We show that stored sperm have a 23% higher probability of producing sons than daughters. Thus, shifts in sex ratio, for example over the reproductive season, can partly be explained by different survival of son-producing sperm or some unidentified female mechanism taking effect during prolonged storage.
Symbiotic complexity: discovery of a fifth symbiont in the attine ant–microbe symbiosis
Authors: Little Ainslie E.F , Currie Cameron R
Published: August 2007

The fungus-growing ant–microbe mutualism is a classic example of organismal complexity generated through symbiotic association. The ants have an ancient obligate mutualism with fungi they cultivate for food. The success of the mutualism is threatened by specialized fungal parasites (
Escovopsis
) that consume the cultivated fungus. To defend their nutrient-rich garden against infection, the ants have a second mutualism with bacteria (
Pseudonocardia
), which produce antibiotics that inhibit the garden parasite
Escovopsis
. Here we reveal the presence of a fourth microbial symbiont associated with fungus-growing ants: black yeasts (Ascomycota;
Phialophora
). We show that black yeasts are commonly associated with fungus-growing ants, occurring throughout their geographical distribution. Black yeasts grow on the ants' cuticle, specifically localized to where the mutualistic bacteria are cultured. Molecular phylogenetic analyses reveal that the black yeasts form a derived monophyletic lineage associated with the phylogenetic diversity of fungus growers. The prevalence, distribution, localization and monophyly indicate that the black yeast is a fifth symbiont within the attine ant–microbe association, further exemplifying the complexity of symbiotic associations.
Ancient human mtDNA genotypes from England reveal lost variation over the last millennium
Authors: Töpf A.L , Gilbert M.T.P , Fleischer R.C , Hoelzel A.R
Published: August 2007

We analysed the historical genetic diversity of human populations in Europe at the mtDNA control region for 48 ancient Britons who lived betweencaAD 300 and 1000, and compared these with 6320 modern mtDNA genotypes from England and across Europe and the Middle East. We found that the historical sample shows greater genetic diversity than for modern England and other modern populations, indicating the loss of diversity over the last millennium. The pattern of haplotypic diversity was clearly European in the ancient sample, representing each of the modern haplogroups. There was also increased representation of one of the ancient haplotypes in modern populations. We consider these results in the context of possible selection or stochastic processes.
Steady diversification of derived liverworts under Tertiary climatic fluctuations
Authors: Wilson Rosemary , Heinrichs Jochen , Hentschel Jörn , Gradstein S.Robbert , Schneider Harald
Published: August 2007

Tropical forests contain the majority of extant plant diversity and their role as a cradle and/or museum of biodiversity is an important issue in our attempts to assess the long-term consequences of global climate change for terrestrial biomes. Highly diverse groups of liverworts are an often ignored but extremely common element in rainforests, and thus their evolution may shed light on the ecological robustness of rainforest biomes to climate fluctuations. We record a remarkable constant accumulation of diversity through time for the most species-rich family of liverworts, Lejeuneaceae, inferred by divergence time estimates. The observed pattern supports the recently developed concept of a dual role of the tropics as both a museum and a cradle of biodiversity.
Rare and fleeting: an example of interspecific recombination in animal mitochondrial DNA
Authors: Ciborowski Kate L , Consuegra Sofía , García de Leániz Carlos , Beaumont Mark A , Wang Jinliang , Jordan William C
Published: August 2007

Recombination is thought to occur only rarely in animal mitochondrial DNA (mtDNA). However, detection of mtDNA recombination requires that cells become heteroplasmic through mutation, intramolecular recombination or ‘leakage’ of paternal mtDNA. Interspecific hybridization increases the probability of detecting mtDNA recombinants due to higher levels of sequence divergence and potentially higher levels of paternal leakage. During a study of historical variation in Atlantic salmon (Salmo salar) mtDNA, an individual with a recombinant haplotype containing sequence from both Atlantic salmon and brown trout (Salmo trutta) was detected. The individual was not an F1 hybrid but it did have an unusual nuclear genotype which suggested that it was a later-generation backcross. No other similar recombinant haplotype was found from the same population or three neighbouring Atlantic salmon populations in 717 individuals collected during 1948–2002. Interspecific recombination may increase mtDNA variability within species and can have implications for phylogenetic studies.
First human-caused extinction of a cetacean species?
Authors: Turvey Samuel T , Pitman Robert L , Taylor Barbara L , Barlow Jay , Akamatsu Tomonari , Barrett Leigh A , Zhao Xiujiang , Reeves Randall R , Stewart Brent S , Wang Kexiong , Wei Zhuo , Zhang Xianfeng , Pusser L.T , Richlen Michael , Brandon John R , Wang Ding
Published: August 2007

The Yangtze River dolphin or baiji (
Lipotes vexillifer
), an obligate freshwater odontocete known only from the middle-lower Yangtze River system and neighbouring Qiantang River in eastern China, has long been recognized as one of the world's rarest and most threatened mammal species. The status of the baiji has not been investigated since the late 1990s, when the surviving population was estimated to be as low as 13 individuals. An intensive six-week multi-vessel visual and acoustic survey carried out in November–December 2006, covering the entire historical range of the baiji in the main Yangtze channel, failed to find any evidence that the species survives. We are forced to conclude that the baiji is now likely to be extinct, probably due to unsustainable by-catch in local fisheries. This represents the first global extinction of a large vertebrate for over 50 years, only the fourth disappearance of an entire mammal family since AD 1500, and the first cetacean species to be driven to extinction by human activity. Immediate and extreme measures may be necessary to prevent the extinction of other endangered cetaceans, including the sympatric Yangtze finless porpoise (
Neophocaena phocaenoides asiaeorientalis
).
Annulonemertes
(phylum Nemertea): when segments do not count
Authors: Sundberg Per , Strand Malin
Published: August 2007

We estimated the phylogenetic position of the pseudosegmented ribbon worm
Annulonemertes minusculus
to test proposed evolutionary hypotheses to explain these body constrictions. The analysis is based on 18S rDNA sequences and shows that the species belongs to an apomorphic clade of hoplonemertean species. The segmentation has no phylogenetic bearing as previously discussed, but is a derived character probably coupled to the species' interstitial habitat.
Genetic bottlenecks and successful biological invasions: the case of a recent Lessepsian migrant
Authors: Golani Daniel , Azzurro Ernesto , Corsini-Foka Maria , Falautano Manuela , Andaloro Franco , Bernardi Giacomo
Published: August 2007

Our current understanding of the mechanisms that lead to successful biological invasions is limited. Although adaptations play a central role in biological invasions, genetic studies have so far failed to produce a unified theory. The bluespotted cornetfish, a recent Red Sea invader in the Mediterranean Sea via the Suez Canal, provides an ideal case study for research in the mechanisms of invasive genetics. In this study, we show that the invading bluespotted cornetfish underwent a severe population bottleneck that reduced the genetic diversity of this immigrant to only two mitochondrial haplotypes. Although loss of genetic diversity is considered detrimental to the need to adapt to new environments, bluespotted cornetfish experienced an unprecedented success and rapid spread across the Mediterranean.
Increasing abundance of bowhead whales in West Greenland
Authors: Heide-Jørgensen Mads Peter , Laidre Kristin , Borchers David , Samarra Filipa , Stern Harry
Published: August 2007

In April 2006, a dedicated survey of bowhead whales (Balaena mysticetus) was conducted on the former whaling ground in West Greenland to determine the current wintering population abundance. This effort included a double platform aerial survey design, satellite tracking of the movements of nine whales, and estimation of high-resolution surface time from 14 whales instrumented with time–depth recorders. Bowhead whales were estimated to spend an average of 24% (cv=0.03) of the time at or above 2 m depth, the maximum depth at which they can be seen on the trackline. This resulted in a fully corrected abundance estimate of 1229 (95% CI: 495–2939) bowhead whales when the availability factor was applied and sightings missed by observers were corrected. This surprisingly large population estimate is puzzling given that the change in abundance cannot be explained by a recent or rapid growth in population size. One possible explanation is that the population, which demonstrates high age and sex segregation, has recently attained a certain threshold size elsewhere, and a higher abundance of mature females appears on the winter and spring feeding ground in West Greenland. This in combination with the latest severe reduction in sea ice facilitating access to coastal areas might explain the surprising increase in bowhead whale abundance in West Greenland.
Male crickets adjust ejaculate quality with both risk and intensity of sperm competition
Authors: Simmons Leigh W , Denholm Amy , Jackson Chantelle , Levy Esther , Madon Ewa
Published: August 2007

Sperm competition theory predicts that males should increase their expenditure on the ejaculate with increasing risk of sperm competition, but decrease their expenditure with increasing intensity. There is accumulating evidence for sperm competition theory, based on examinations of testes size and/or the numbers of sperm ejaculated. However, recent studies suggest that ejaculate quality can also be subject to selection by sperm competition. We used experimental manipulations of the risk and intensity of sperm competition in the cricket,
Teleogryllus oceanicus
. We found that males produced ejaculates with a greater percentage of live sperm when they had encountered a rival male prior to mating. However, when mating with a female that presented a high intensity of sperm competition, males did not respond to risk, but produced ejaculates with a reduced percentage of live sperm. Our data suggest that males exhibit a fine-tuned hierarchy of responses to these cues of sperm competition.
Absence of contagious yawning in children with autism spectrum disorder
Authors: Senju Atsushi , Maeda Makiko , Kikuchi Yukiko , Hasegawa Toshikazu , Tojo Yoshikuni , Osanai Hiroo
Published: August 2007

This study is the first to report the disturbance of contagious yawning in individuals with autism spectrum disorder (ASD). Twenty-four children with ASD as well as 25 age-matched typically developing (TD) children observed video clips of either yawning or control mouth movements. Yawning video clips elicited more yawns in TD children than in children with ASD, but the frequency of yawns did not differ between groups when they observed control video clips. Moreover, TD children yawned more during or after the yawn video clips than the control video clips, but the type of video clips did not affect the amount of yawning in children with ASD. Current results suggest that contagious yawning is impaired in ASD, which may relate to their impairment in empathy. It supports the claim that contagious yawning is based on the capacity for empathy.
Complexity and variation in loggerhead sea turtle life history
Authors: McClellan Catherine M , Read Andrew J
Published: August 2007

Juvenile loggerhead sea turtles spend more than a decade in the open ocean before returning to neritic waters to mature and reproduce. It has been assumed that this transition from an oceanic to neritic existence is a discrete ontogenetic niche shift. We tested this hypothesis by tracking the movements of large juveniles collected in a neritic foraging ground in North Carolina, USA. Our work shows that the shift from the oceanic to neritic waters is both complex and reversible; some individuals move back into coastal waters and then return to the open ocean for reasons that are still unclear, sometimes for multiple years. These findings have important consequences for efforts to protect these threatened marine reptiles from mortality in both coastal and open-ocean fisheries.
Two waves of diversification in mammals and reptiles of Baja California revealed by hierarchical Bayesian analysis
Authors: Leaché Adam D , Crews Sarah C , Hickerson Michael J
Published: August 2007

Many species inhabiting the Peninsular Desert of Baja California demonstrate a phylogeographic break at the mid-peninsula, and previous researchers have attributed this shared pattern to a single vicariant event, a mid-peninsular seaway. However, previous studies have not explicitly considered the inherent stochasticity associated with the gene-tree coalescence for species preceding the time of the putative mid-peninsular divergence. We use a Bayesian analysis of a hierarchical model to test for simultaneous vicariance across co-distributed sister lineages sharing a genealogical break at the mid-peninsula. This Bayesian method is advantageous over traditional phylogenetic interpretations of biogeography because it considers the genetic variance associated with the coalescent and mutational processes, as well as the among-lineage demographic differences that affect gene-tree coalescent patterns. Mitochondrial DNA data from six small mammals and six squamate reptiles do not support the perception of a shared vicariant history among lineages exhibiting a north–south divergence at the mid-peninsula, and instead support two events differentially structuring genetic diversity in this region.
A stochastic model for ecological systems with strong nonlinear response to environmental drivers: application to two water-borne diseases
Authors: Codeço Claudia Torres , Lele Subhash , Pascual Mercedes , Bouma Menno , Ko Albert I
Published: August 2007

Ecological systems with threshold behaviour show drastic shifts in population abundance or species diversity in response to small variation in critical parameters. Examples of threshold behaviour arise in resource competition theory, epidemiological theory and environmentally driven population dynamics, to name a few. Although expected from theory, thresholds may be difficult to detect in real datasets due to stochasticity, finite population size and confounding effects that soften the observed shifts and introduce variability in the data. Here, we propose a modelling framework for threshold responses to environmental drivers that allows for a flexible treatment of the transition between regimes, including variation in the sharpness of the transition and the variance of the response. The model assumes two underlying stochastic processes whose mixture determines the system's response. For environmentally driven systems, the mixture is a function of an environmental covariate and the response may exhibit strong nonlinearity. When applied to two datasets for water-borne diseases, the model was able to capture the effect of rainfall on the mean number of cases as well as the variance. A quantitative description of this kind of threshold behaviour is of more general application to predict the response of ecosystems and human health to climate change.
Statistically stored, geometrically necessary and grain boundary dislocation densities: microstructural representation and modelling
Authors: Rezvanian O , Zikry M.A , Rajendran A.M
Published: August 2007

A unified physically based microstructural representation of f.c.c. crystalline materials has been developed and implemented to investigate the microstructural behaviour of f.c.c. crystalline aggregates under inelastic deformations. The proposed framework is based on coupling a multiple-slip crystal plasticity formulation to three distinct dislocation densities, which pertain to statistically stored dislocations (SSDs), geometrically necessary dislocations (GNDs) and grain boundary dislocations. This interrelated dislocation density formulation is then coupled to a specialized finite element framework to study the evolving heterogeneous microstructure and the localized phenomena that can contribute to failure initiation as a function of inelastic crystalline deformation. The GND densities are used to understand where crystallographic, non-crystallographic and cellular microstructures form and the nature of their dislocation composition. The SSD densities are formulated to represent dislocation cell microstructures to obtain predictions related to the inhomogeneous distribution of SSDs. The effects of the lattice misorientations at the grain boundaries (GBs) have been included by accounting for the densities of the misfit dislocations at the GBs that accommodate these misorientations. By directly accounting for the misfit dislocations, the strength of the boundary regions can be more accurately represented to account for phenomena associated with the effects of the GB strength on intergranular deformation heterogeneities, stress localization and the nucleation of failure surfaces at critical regions, such as triple junctions.
Measurements of sound propagation in narrow tubes
Authors: Yazaki T , Tashiro Y , Biwa T
Published: August 2007

The propagation of sound in hollow tubes is a fundamental theme common to many areas of classical acoustics. Kirchhoff's theory explaining the propagation of sound in a circular tube is now playing an important role as a starting point in studying sound in porous media. This paper reports on measurements of the phase velocity and attenuation coefficient in the narrow regions of tubes, where the sound undergoes anomalous dispersion and is seen to slow down remarkably to the extent that a runner can pass ahead of it. Kirchhoff's theory can be verified by experiment over a wide range of thermodynamical conditions, from isentropic to isothermal.
Breeding experience and population density affect the ability of a songbird to respond to future climate variation
Authors: Wilson Scott , Norris D. Ryan , Wilson Amy G , Arcese Peter
Published: August 2007

Predicting how populations respond to climate change requires an understanding of whether individuals or cohorts within populations vary in their response to climate variation. We used mixed-effects models on a song sparrow (Melospiza melodia) population in British Columbia, Canada, to examine differences among females and cohorts in their average breeding date and breeding date plasticity in response to the El Niño Southern Oscillation. Climatic variables, age and population density were strong predictors of timing of breeding, but we also found considerable variation among individual females and cohorts. Within cohorts, females differed markedly in their breeding date and cohorts also differed in their average breeding date and breeding date plasticity. The plasticity of a cohort appeared to be due primarily to an interaction between the environmental conditions (climate and density) experienced at different ages rather than innate inter-cohort differences. Cohorts that expressed higher plasticity in breeding date experienced warmer El Niño springs in their second or third breeding season, suggesting that prior experience affects how well individuals responded to abnormal climatic conditions. Cohorts born into lower density populations also expressed higher plasticity in breeding date. Interactions between age, experience and environmental conditions have been reported previously for long-lived taxa. Our current results indicate that similar effects operate in a short-lived, temperate songbird.
Parental prey selection affects risk-taking behaviour and spatial learning in avian offspring
Authors: Arnold Kathryn E , Ramsay Scot L , Donaldson Christine , Adam Aileen
Published: August 2007

Early nutrition shapes life history. Parents should, therefore, provide a diet that will optimize the nutrient intake of their offspring. In a number of passerines, there is an often observed, but unexplained, peak in spider provisioning during chick development. We show that the proportion of spiders in the diet of nestling blue tits,
Cyanistes caeruleus
, varies significantly with the age of chicks but is unrelated to the timing of breeding or spider availability. Moreover, this parental prey selection supplies nestlings with high levels of taurine particularly at younger ages. This amino acid is known to be both vital and limiting for mammalian development and consequently found in high concentrations in placenta and milk. Based on the known roles of taurine in mammalian brain development and function, we then asked whether by supplying taurine-rich spiders, avian parents influence the stress responsiveness and cognitive function of their offspring. To test this, we provided wild blue tit nestlings with either a taurine supplement or control treatment once daily from the ages of 2–14 days. Then pairs of size- and sex-matched siblings were brought into captivity for behavioural testing. We found that juveniles that had received additional taurine as neonates took significantly greater risks when investigating novel objects than controls. Taurine birds were also more successful at a spatial learning task than controls. Additionally, those individuals that succeeded at a spatial learning task had shown intermediate levels of risk taking. Non-learners were generally very risk-averse controls. Early diet therefore has downstream impacts on behavioural characteristics that could affect fitness via foraging and competitive performance. Fine-scale prey selection is a mechanism by which parents can manipulate the behavioural phenotype of offspring.
Sensorimotor experience enhances automatic imitation of robotic action
Authors: Press Clare , Gillmeister Helge , Heyes Cecilia
Published: August 2007

Recent research in cognitive neuroscience has found that observation of human actions activates the ‘mirror system’ and provokes automatic imitation to a greater extent than observation of non-biological movements. The present study investigated whether this human bias depends primarily on phylogenetic or ontogenetic factors by examining the effects of sensorimotor experience on automatic imitation of non-biological robotic, stimuli. Automatic imitation of human and robotic action stimuli was assessed before and after training. During these test sessions, participants were required to execute a pre-specified response (e.g. to open their hand) while observing a human or robotic hand making a compatible (opening) or incompatible (closing) movement. During training, participants executed opening and closing hand actions while observing compatible (group CT) or incompatible movements (group IT) of a robotic hand. Compatible, but not incompatible, training increased automatic imitation of robotic stimuli (speed of responding on compatible trials, compared with incompatible trials) and abolished the human bias observed at pre-test. These findings suggest that the development of the mirror system depends on sensorimotor experience, and that, in our species, it is biased in favour of human action stimuli because these are more abundant than non-biological action stimuli in typical developmental environments.
Mass-dependent predation risk and lethal dolphin–porpoise interactions
Authors: MacLeod R , MacLeod C.D , Learmonth J.A , Jepson P.D , Reid R.J , Deaville R , Pierce G.J
Published: August 2007

In small birds, mass-dependent predation risk (MDPR) is known to make the trade-off between avoiding starvation and avoiding predation dependent on individual mass. This occurs because carrying increased fat reserves not only reduces starvation risk but also results in a higher predation risk due to reduced escape flight performance and/or the increased foraging exposure needed to maintain a higher body mass. In principle, the theory of MDPR could also apply to any animal capable of storing energy reserves to reduce starvation and whose escape performance decreases with increasing mass. We used a unique situation along certain parts of coastal Britain, where harbour porpoises (
Phocoena phocoena
) are pursued and killed but crucially not eaten by bottlenose dolphins (
Tursiops truncatus
), to investigate whether a MDPR effect can occur in non-avian species. We show that where high levels of dolphin ‘predation’ occur, porpoises carry significantly less energy reserves than would otherwise be expected and this equates to reducing by approximately 37% the length of time that a porpoise could survive without feeding. These results provide the first evidence that a mass-dependent starvation–predation risk trade-off may be a general ecological principle that can apply to widely different animal types rather than, as is currently thought, only to birds.
Contrasting responses of bumble bees to feeding conspecifics on their familiar and unfamiliar flowers
Authors: Kawaguchi Lina G , Ohashi Kazuharu , Toquenaga Yukihiko
Published: August 2007

Animals exploiting their familiar food items often avoid spatio-temporal aggregation with others by avoiding scents, less rewarding areas or visual contacts, thereby minimizing competition or interference when resources are replenished slowly in patches. When animals are searching or assessing available food sources, however, they may benefit from reducing sampling costs by following others at food sites. Therefore, animals may adjust their responses to others depending on their familiarity with foraging situations. Here, we conducted field experiments to test whether nectar-collecting bumble bees make this adjustment. We allowed free-foraging bees to choose between two inflorescences, one occupied by a conspecific bee and another unoccupied. When bees were presented with flowers of a familiar type, they avoided occupied inflorescences. In contrast, bees visited an occupied inflorescence when the flower type was unfamiliar. To our knowledge, this is the first report suggesting that animals adjust their responses to feeding conspecifics depending on their familiarity with food sources. Such behavioural flexibilities should allow foragers to both explore and exploit their environments efficiently.
Encountering competitors reduces clutch size and increases offspring size in a parasitoid with female–female fighting
Authors: Goubault Marlène , Mack Alexandra F.S , Hardy Ian C.W
Published: August 2007

Understanding the size of clutches produced by only one parent may require a game-theoretic approach: clutch size may affect offspring fitness in terms of future competitive ability. If larger clutches generate smaller offspring and larger adults are more successful in acquiring and retaining resources, clutch size optima should be reduced when the probability of future competitive encounters is higher. We test this using
Goniozus nephantidis
, a gregarious parasitoid wasp in which the assumption of size-dependent resource acquisition is met via female–female contests for hosts. As predicted, smaller clutches are produced by mothers experiencing competition, due to fewer eggs being matured and to a reduced proportion of matured eggs being laid. As assumed, smaller clutches generate fewer but larger offspring. We believe this is the first direct evidence for pre-ovipositional and game-theoretic clutch size adjustment in response to an intergenerational fitness effect when clutches are produced by a single individual.