bluuebunny/crossref_metadata_2025 huggingface dataset:
Reproducibility of Distance and Direction Errors Associated with Forward, Backward, and Sideway Walking in the Context of Blind Navigation
Authors: Paquet Nicole , Rainville Constant , Lajoie Yves , Tremblay François
Published: March 2007

The ability to navigate without vision towards a previously seen target has been extensively studied, but its reliability over time has yet to be established. Our aims were to determine distance and direction errors made during blind navigation across four different directions involving three different gait patterns (stepping forward, stepping sideway, and stepping backward), and to establish the test – retest reproducibility of these errors. Twenty young healthy adults participated in two testing sessions separated by 7 days. They were shown targets located, respectively, 8 m ahead, 8 m behind, and 8 m to their right and left. With vision occluded by opaque goggles, they walked forward (target ahead), backward (target behind), and sideway (right and left targets) until they perceived to be on the target. Subjects were not provided with feedback about their performance. Walked distance, angular deviation, and body rotation were measured. The mean estimated distance error was similar across the four walking directions and ranged from 16 to 80 cm with respect to the 8 m target. In contrast, direction errors were significantly larger during sideway navigation (walking in the frontal plane: leftward, 10° ± 15° deviation; rightward, 18° ± 13°) than during forward and backward navigation (walking in the sagittal plane). In general, distance and direction errors were only moderately reproducible between the two sessions [intraclass correlation coefficients (ICCs) ranging from 0.682 to 0.705]. Among the four directions, rightward navigation showed the best reproducibility with ICCs ranging from 0.607 to 0.726, and backward navigation had the worst reliability with ICCs ranging from 0.094 to 0.554. These findings indicate that errors associated with blind navigation across different walking directions and involving different gait patterns are only moderately to poorly reproducible on repeated testing, especially for walking backward. The biomechanical constraints and increased cognitive loading imposed by changing the walking pattern to backward stepping may underlie the poor performance in this direction.
Single M13 bacteriophage tethering and stretching
Authors: Khalil Ahmad S. , Ferrer Jorge M. , Brau Ricardo R. , Kottmann Stephen T. , Noren Christopher J. , Lang Matthew J. , Belcher Angela M.
Published: March 2007

The ability to present biomolecules on the highly organized structure of M13 filamentous bacteriophage is a unique advantage. Where previously this viral template was shown to direct the orientation and nucleation of nanocrystals and materials, here we apply it in the context of single-molecule (SM) biophysics. Genetically engineered constructs were used to display different reactive species at each of the filament ends and along the major capsid, and the resulting hetero-functional particles were shown to consistently tether microscopic beads in solution. With this system, we report the development of a SM assay based on M13 bacteriophage. We also report the quantitative characterization of the biopolymer's elasticity by using an optical trap with nanometer-scale position resolution. Expanding the fluctuating rod limit of the wormlike chain to incorporate enthalpic polymer stretching yielded a model capable of accurately capturing the full range of extensions. Fits of the force-extension measurements gave a mean persistence length of ≈1,265 nm, lending SM support for a shorter filamentous bacteriophage persistence length than previously thought. Furthermore, a predicted stretching modulus roughly two times that of dsDNA, coupled with the system's linkage versatility and load-bearing capability, makes the M13 template an attractive candidate for use in tethered bead architectures.
Optimizing the control of disease infestations at the landscape scale
Authors: Forster Graeme A. , Gilligan Christopher A.
Published: March 2007

Using a contact-process model for the spread of crop disease over a regional scale, we examine the importance of the time scale for control with respect to the cost of the epidemic. The costs include the direct cost of treating infected sites as well as the indirect costs incurred through lost yield. We first use a mean-field approximation to derive analytical results for the optimal treatment regimes that minimize the total cost of the epidemic. We distinguish short- and long-term epidemics. and show that seasonal control (short time scale) requires extreme treatment, either treating all sites or none or switching between the two at some stage during the season. The optimal long-term strategy requires an intermediate level of control that results in near eradication of the disease. We also demonstrate the importance of incorporating economic constraints by deriving a critical relationship between the epidemiological and economic parameters that determine the qualitative nature of the optimal treatment strategy. The set of optimal strategies is summarized in a policy plot, which can be used to determine the nature of the optimal treatment regime given prior knowledge of the epidemiological and economic parameters. Finally, we test the robustness of the analytical results, derived from the mean-field approximation, on the spatially explicit contact process and demonstrate robustness to implementation errors and misestimation of crucial parameters.
Compatibility of basic social perceptions determines perceived attractiveness
Authors: Johnson Kerri L. , Tassinary Louis G.
Published: March 2007

The human body's shape and motion afford social judgments. The body's shape, specifically the waist-to-hip ratio, has been related to perceived attractiveness. Early reports interpreted this effect to be evidence for adaptation, a theory known generally as the waist-to-hip ratio hypothesis. Many of the predictions derived from this perspective have been empirically disconfirmed, leaving the issue of natural selection unresolved. Knowing the cognitive mechanisms undergirding the relationship between judgments of attractiveness and body cues is essential to understanding its evolution. Here we show that perceived attractiveness covaries with body shape and motion because they cospecify social percepts that are either compatible or incompatible. The body's shape and motion provoke basic social perceptions, biological sex and gender (i.e., masculinity/femininity), respectively. The compatibility of these basic percepts predicts perceived attractiveness. We report evidence for the importance of cue compatibility in five studies that used diverse stimuli (animations, static line-drawings, and dynamic line-drawings). Our results demonstrate how a proximal cognitive mechanism, itself likely the product of selection pressures, helps to reconcile previous contradictory findings.
Agostic interaction and intramolecular proton transfer from the protonation of dihydrogen ortho metalated ruthenium complexes
Authors: Toner Andrew , Matthes Jochen , Gründemann Stephan , Limbach Hans-Heinrich , Chaudret Bruno , Clot Eric , Sabo-Etienne Sylviane
Published: March 2007

Protonation of the ortho-metalated ruthenium complexes RuH(H2)(X)(PiPr3)2[X= 2-phenylpyridine (ph-py) (1), benzoquinoline (bq) (2)] and RuH(CO)(ph-py)(PiPr3)2(3) with [H(OEt2)2]+[BAr′4]−(BAr′4= [(3,5-(CF3)2C6H3)4B]) under H2atmosphere yields the corresponding cationic hydrido dihydrogen ruthenium complexes [RuH(H2)(H-X)(PiPr3)2][BAr′4] [X = phenylpyridine (ph-py) (1-H); benzoquinoline (bq) (2-H)] and the carbonyl complex [RuH(CO)(H-ph-py)(PiPr3)2][BAr′4] (3-H). The complexes accommodate an agostic CH interaction characterized by NMR and in the case of 1-H by x-ray diffraction. Fluxional processes involve the hydride and dihydrogen ligands in 1-H and 2-H and the rotation of the phenyl ring displaying the agostic interaction in 1-H and 3-H. NMR studies (lineshape analysis of the temperature-dependent NMR spectra) and density functional theory calculations are used to understand these processes. Under vacuum, one equivalent of dihydrogen can be removed from 1-H and 2-H leading to the formation of the corresponding cationic ortho-metalated complexes [Ru(H2)(THF)(X)(PiPr3)2]+[X= ph-py (1-THF), bq (2-THF)]. The reaction is fully reversible. Density functional theory calculations and NMR data give information about the reversible mechanism of CH activation in these ortho-metalated ruthenium complexes. Our study highlights the subtle interplay between key ligands such as hydrides, σ-dihydrogen, and agostic bonds, in CH activation processes.
Large seasonal swings in leaf area of Amazon rainforests
Authors: Myneni Ranga B. , Yang Wenze , Nemani Ramakrishna R. , Huete Alfredo R. , Dickinson Robert E. , Knyazikhin Yuri , Didan Kamel , Fu Rong , Negrón Juárez Robinson I. , Saatchi Sasan S. , Hashimoto Hirofumi , Ichii Kazuhito , Shabanov Nikolay V. , Tan Bin , Ratana Piyachat , Privette Jeffrey L. , Morisette Jeffrey T. , Vermote Eric F. , Roy David P. , Wolfe Robert E. , Friedl Mark A. , Running Steven W. , Votava Petr , El-Saleous Nazmi , Devadiga Sadashiva , Su Yin , Salomonson Vincent V.
Published: March 2007

Despite early speculation to the contrary, all tropical forests studied to date display seasonal variations in the presence of new leaves, flowers, and fruits. Past studies were focused on the timing of phenological events and their cues but not on the accompanying changes in leaf area that regulate vegetation–atmosphere exchanges of energy, momentum, and mass. Here we report, from analysis of 5 years of recent satellite data, seasonal swings in green leaf area of ≈25% in a majority of the Amazon rainforests. This seasonal cycle is timed to the seasonality of solar radiation in a manner that is suggestive of anticipatory and opportunistic patterns of net leaf flushing during the early to mid part of the light-rich dry season and net leaf abscission during the cloudy wet season. These seasonal swings in leaf area may be critical to initiation of the transition from dry to wet season, seasonal carbon balance between photosynthetic gains and respiratory losses, and litterfall nutrient cycling in moist tropical forests.
Strong effects of molecular topology on diffusion of entangled DNA molecules
Authors: Robertson Rae M. , Smith Douglas E.
Published: March 2007

When long polymers such as DNA are in a highly concentrated state they may become entangled, leading to restricted self-diffusion. Here, we investigate the effect of molecular topology on diffusion in concentrated DNA solutions and find surprisingly large effects, even with molecules of modest length and concentration. We measured the diffusion coefficients of linear and relaxed circular molecules by tracking the Brownian motion of single molecules with fluorescence microscopy. Four possible cases were compared: linear molecules surrounded by linear molecules, circular molecules surrounded by linear molecules, linear molecules surrounded by circles, and circles surrounded by circles. In measurements with 45-kbp DNA at 1 mg/ml, we found that circles diffused ≈100 times slower when surrounded by linear molecules than when surrounded by circles. In contrast, linear and circular molecules diffused at nearly the same rate when surrounded by circles, and circles diffused ≈10 times slower than linears when surrounded by linears. Thus, diffusion in entangled DNA solutions strongly depends on topology of both the diffusing molecule and the surrounding molecules. This effect also strongly depends on DNA concentration and length. The differences largely disappeared when the concentration was lowered to 0.1 mg/ml or when the DNA length was lowered to 6 kb. Present theories cannot fully explain these effects.
Synthesis and evaluation of transthyretin amyloidosis inhibitors containing carborane pharmacophores
Authors: Julius Richard L. , Farha Omar K. , Chiang Janet , Perry L. Jeanne , Hawthorne M. Frederick
Published: March 2007

Carboranes represent a potentially rich but underutilized class of inorganic and catabolism-inert pharmacophores. The regioselectivity and ease of derivatization of carboranes allows for facile syntheses of a wide variety of novel structures. The steric bulk, rigidity, and ease of B- and C-derivatization and lack of π-interactions associated with hydrophobic carboranes may be exploited to enhance the selectivity of previously identified bioactive molecules. Transthyretin (TTR) is a thyroxine-transport protein found in the blood that has been implicated in a variety of amyloid related diseases. Previous investigations have identified a variety of nonsteroidal antiinflammatory drugs (NSAIDs) and structurally related derivatives that imbue kinetic stabilization to TTR, thus inhibiting its dissociative fragmentation and subsequent aggregation to form putative toxic amyloid fibrils. However, the cyclooxygenase (COX) activity associated with these pharmaceuticals may limit their potential as long-term therapeutic agents for TTR amyloid diseases. Here, we report the synthesis and evaluation of carborane-containing analogs of the promising NSAID pharmaceuticals previously identified. The replacement of a phenyl ring in the NSAIDs with a carborane moiety greatly decreases their COX activity with the retention of similar efficacy as an inhibitor of TTR dissociation. The most promising of these compounds, 1-carboxylic acid-7-[3-fluorophenyl]-1,7-dicarba-
closo
-dodecaborane, showed effectively no COX-1 or COX-2 inhibition at a concentration more than an order of magnitude larger than the concentration at which TTR dissociation is nearly completely inhibited. This specificity is indicative of the potential for the exploitation of the unique properties of carboranes as potent and selective pharmacophores.
Inhibitory factors associated with anaphase-promoting complex/cylosome in mitotic checkpoint
Authors: Braunstein Ilana , Miniowitz Shirly , Moshe Yakir , Hershko Avram
Published: March 2007

The mitotic (or spindle assembly) checkpoint system ensures accurate chromosome segregation by preventing anaphase initiation until all chromosomes are correctly attached to the mitotic spindle. It affects the activity of the anaphase-promoting complex/cyclosome (APC/C), a ubiquitin ligase that targets inhibitors of anaphase initiation for degradation. The mechanisms by which this system regulates APC/C remain obscure. Some models propose that the system promotes sequestration of the APC/C activator Cdc20 by binding to the checkpoint proteins Mad2 and BubR1. A different model suggests that a mitotic checkpoint complex (MCC) composed of BubR1, Bub3, Cdc20, and Mad2 inhibits APC/C in mitotic checkpoint [Sudakin V, Chan GKT, Yen TJ (2001)
J Cell Biol
154:925–936]. We examined this problem by using extracts from nocodazole-arrested cells that reproduce some downstream events of the mitotic checkpoint system, such as lag kinetics of the degradation of APC/C substrate. Incubation of extracts with adenosine-5′-(γ-thio)triphosphate (ATP[γS]) stabilized the checkpoint-arrested state, apparently by stable thiophosphorylation of some proteins. By immunoprecipitation of APC/C from stably checkpoint-arrested extracts, followed by elution with increased salt concentration, we isolated inhibitory factors associated with APC/C. A part of the inhibitory material consists of Cdc20 associated with BubR1 and Mad2, and is thus similar to MCC. Contrary to the original MCC hypothesis, we find that MCC disassembles upon exit from the mitotic checkpoint. Thus, the requirement of the mitotic checkpoint system for the binding of Mad2 and BubR1 to Cdc20 may be for the assembly of the inhibitory complex rather than for Cdc20 sequestration.
Peripheral multidendritic sensory neurons are necessary for rhythmic locomotion behavior in
Drosophila
larvae
Authors: Song Wei , Onishi Maika , Jan Lily Yeh , Jan Yuh Nung
Published: March 2007

From breathing to walking, rhythmic movements encompass physiological processes important across the entire animal kingdom. It is thought by many that the generation of rhythmic behavior is operated by a central pattern generator (CPG) and does not require peripheral sensory input. Sensory feedback is, however, required to modify or coordinate the motor activity in response to the circumstances of actual movement. In contrast to this notion, we report here that sensory input is necessary for the generation of
Drosophila
larval locomotion, a form of rhythmic behavior. Blockage of all peripheral sensory inputs resulted in cessation of larval crawling. By conditionally silencing various subsets of larval peripheral sensory neurons, we identified the multiple dendritic (MD) neurons as the neurons essential for the generation of rhythmic peristaltic locomotion. By recording the locomotive motor activities, we further demonstrate that removal of MD neuron input disrupted rhythmic motor firing pattern in a way that prolonged the stereotyped segmental motor firing duration and prevented the propagation of posterior to anterior segmental motor firing. These findings reveal that MD sensory neuron input is a necessary component in the neural circuitry that generates larval locomotion.
The impact of armed conflict on protected-area efficacy in Central Africa
Authors: de Merode Emmanuel , Smith Kes Hillman , Homewood Katherine , Pettifor Richard , Rowcliffe Marcus , Cowlishaw Guy
Published: March 2007

What determines the vulnerability of protected areas, a fundamental component of biodiversity conservation, to political instability and warfare? We investigated the efficacy of park protection at Garamba National Park (Democratic Republic of Congo) before, during and after a period of armed conflict. Previous analysis has shown that bushmeat hunting in the park increased fivefold during the conflict, but then declined, in conjunction with changes in the sociopolitical structures (social institutions) that controlled the local bushmeat trade. We used park patrol records to investigate whether these changes were facilitated by a disruption to anti-poaching patrols. Contrary to expectation, anti-poaching patrols remained frequent during the conflict (as bushmeat offtake increased) and decreased afterwards (when bushmeat hunting also declined). These results indicate that bushmeat extraction was determined primarily by the social institutions. Although we found a demonstrable effect of anti-poaching patrols on hunting pressure, even a fourfold increase in patrol frequency would have been insufficient to cope with wartime poaching levels. Thus, anti-poaching patrols alone may not always be the most cost-effective means of managing protected areas, and protected-area efficacy might be enhanced by also working with those institutions that already play a role in regulating local natural-resource use.
Energetic reserves, leptin and testosterone: a refinement of the immunocompetence handicap hypothesis
Authors: Alonso-Alvarez C , Bertrand S , Sorci G
Published: March 2007

The immunocompetence handicap hypothesis (ICHH) assumes that testosterone (T), required for the expression of sexual traits, can also incur a cost due to its immunosuppressive properties. However, T-dependent immunosuppression could also arise as an indirect consequence of energy reallocation from the immune system to other metabolic demands. Leptin is mostly produced in lipogenic tissues and its circulating level is positively correlated with the amount of lipid reserves. Leptin also has an important role as immunoenhancer and we suggest that this hormone could play a role as a mediator of the immunosuppressive effect of testosterone. In particular, we propose that only the individuals able to maintain large lipid reserves (with high leptin levels), while sustaining high testosterone levels, might be able to develop sexual displays without an impairment of their immune defences. Here, we tested one of the assumptions underlying this extension of the ICHH: leptin administration should attenuate testosterone-induced immunosuppression. T-implanted and control male zebra finches (
Taeniopygia guttata
) received daily injections of leptin or phosphate buffered saline. T-implants initially depressed the phytohaemagglutinin-induced immune response. However, T-birds injected with leptin enhanced their immune response to the level of control birds. These results open a new perspective on the study of the ICHH.
Systematic placement of an enigmatic Southeast Asian taxon
Eupetes macrocerus
and implications for the biogeography of a main songbird radiation, the Passerida
Authors: Jønsson Knud A , Fjeldså Jon , Ericson Per G.P , Irestedt Martin
Published: March 2007

Biogeographic connections between Australia and other continents are still poorly understood although the plate tectonics of the Indo-Pacific region is now well described.
Eupetes macrocerus
is an enigmatic taxon distributed in a small area on the Malay Peninsula and on Sumatra and Borneo. It has generally been associated with
Ptilorrhoa
in New Guinea on the other side of Wallace's Line, but a relationship with the West African
Picathartes
has also been suggested. Using three nuclear markers, we demonstrate that
Eupetes
is the sister taxon of the South African genus
Chaetops
, and their sister taxon in turn being
Picathartes
, with a divergence in the Eocene. Thus, this clade is distributed in remote corners of Africa and Asia, which makes the biogeographic history of these birds very intriguing. The most parsimonious explanation would be that they represent a relictual basal group in the Passerida clade established after a long-distance dispersal from the Australo-Papuan region to Africa. Many earlier taxonomic arrangements may have been based on assumptions about relationships with similar-looking forms in the same, or adjacent, biogeographic regions, and revisions with molecular data may uncover such cases of neglect of ancient relictual patterns reflecting past connections between the continents.
Fractal rotation isolates mechanisms for form-dependent motion in human vision
Authors: Benton Christopher P , O'Brien Justin M.D , Curran W
Published: March 2007

Here, we describe a motion stimulus in which the quality of rotation is fractal. This makes its motion unavailable to the translation-based motion analysis known to underlie much of our motion perception. In contrast, normal rotation can be extracted through the aggregation of the outputs of translational mechanisms. Neural adaptation of these translation-based motion mechanisms is thought to drive the motion after-effect, a phenomenon in which prolonged viewing of motion in one direction leads to a percept of motion in the opposite direction. We measured the motion after-effects induced in static and moving stimuli by fractal rotation. The after-effects found were an order of magnitude smaller than those elicited by normal rotation. Our findings suggest that the analysis of fractal rotation involves different neural processes than those for standard translational motion. Given that the percept of motion elicited by fractal rotation is a clear example of motion derived from form analysis, we propose that the extraction of fractal rotation may reflect the operation of a general mechanism for inferring motion from changes in form.
The impact of prophylaxis of healthcare workers on influenza pandemic burden
Authors: Gardam Michael , Liang Dong , Moghadas Seyed M , Wu Jianhong , Zeng Qingling , Zhu Huaiping
Published: March 2007

Several models have rationalized the use of antiviral drugs as an early control measure for delaying the progression and limiting the size of outbreaks during an influenza pandemic. However, the strategy for use of these drugs is still under debate. We evaluated the impact of prophylaxis of healthcare workers (HCWs) through a mathematical model that considers attack rates in a range of 25–35% in the general population and 25–50% among HCWs. Simulations and uncertainty analysis using the demographics of the province of Ontario, Canada show that increasing prophylaxis coverage of HCWs has little impact on reducing the reproduction number of disease transmission and may not prevent the occurrence of an outbreak if expected. However, it does enable a high level of treatment, which substantially reduces morbidity and mortality in the population as a whole. Therefore, prophylaxis of HCWs should be considered an important part of public health efforts for minimizing influenza pandemic burden and its socio-economic disruption.
Metapopulation dynamics of
Escherichia coli
O157 in cattle: an exploratory model
Authors: Liu Wei-chung , Matthews Louise , Chase-Topping Margo , Savill Nick J , Shaw Darren J , Woolhouse Mark E.J
Published: March 2007

Livestock movement is thought to be a risk factor for the transmission of infectious diseases of farm animals. Simple mathematical models were constructed for the transmission of
Escherichia coli
serogroup O157 between Scottish cattle farms, and the models were used in a preliminary exploration of factors contributing to the levels of infection reported in the field. The results suggest that cattle movement can make a significant contribution to the observed prevalence of
E. coli
O157-positive farms, but is not by itself sufficient for the persistence of
E. coli
O157. The results also suggest that cattle movements involving infected farms with cattle shedding an exceptional amount of
E. coli
O157, ‘super-shedders’, also make a substantial contribution to the prevalence of infected farms. Simulations indicate that
E. coli
O157 could have reached the currently observed prevalence levels in less than a decade. Implications and findings from our models are discussed in relation to possible control of
E. coli
O157 in Scottish cattle.
Termites live in a material world: exploration of their ability to differentiate between food sources
Authors: Inta Ra , Lai Joseph C.S , Fu Eugene W , Evans Theodore A
Published: March 2007

Drywood termites are able to assess wood size using vibratory signals, although the exact mechanism behind this assessment ability is not known. Important vibratory characteristics such as the modal frequencies of a wooden block depend on its geometry and boundary conditions; however, they are also dependent on the material characteristics of the block, such as mass, density and internal damping. We report here on choice experiments that tested the ability of the drywood termite
Cryptotermes secundus
to assess wooden block size using a solid wooden block paired with a composite block, the latter made of either wood and aluminium or wood and rubber. Each composite block was constructed to match mass or low-frequency vibratory modes (i.e. fundamental frequency) of the solid wooden block. The termites always chose the blocks with more wood; they moved to the solid wooden blocks usually within a day and then tunnelled further into the solid wooden block by the end of the experiment. Termites offered composite blocks of wood and rubber matched for mass were the slowest to show a preference for the solid wooden block and this preference was the least definitive of any treatment, which indicated that mass and/or damping may play a role in food assessment. This result clearly shows that the termites were not fooled by composite blocks matched for mass or frequency, which implies that they probably employ more than a single simple measure in their food assessment strategy. This implies a degree of sophistication in their ability to assess their environment hitherto unknown. The potential importance of alternative features in the vibrational signals is discussed.
Characterizing an outbreak of vancomycin-resistant enterococci using hidden Markov models
Authors: McBryde E.S , Pettitt A.N , Cooper B.S , McElwain D.L.S
Published: March 2007

Background
. Antibiotic-resistant nosocomial pathogens can arise in epidemic clusters or sporadically. Genotyping is commonly used to distinguish epidemic from sporadic vancomycin-resistant enterococci (VRE). We compare this to a statistical method to determine the transmission characteristics of VRE.

Methods and findings
. A structured continuous-time hidden Markov model (HMM) was developed. The hidden states were the number of VRE-colonized patients (both detected and undetected). The input for this study was weekly point-prevalence data; 157 weeks of VRE prevalence. We estimated two parameters: one to quantify the cross-transmission of VRE and the other to quantify the level of VRE colonization from sporadic sources. We compared the results to those obtained by concomitant genotyping and phenotyping.

We estimated that 89% of transmissions were due to ward cross-transmission while 11% were sporadic. Genotyping found that 90% had identical glycopeptide resistance genes and 84% were identical or nearly identical on pulsed-field gel electrophoresis (PFGE).

There was some evidence, based on model selection criteria, that the cross-transmission parameter changed throughout the study period. The model that allowed for a change in transmission just prior to the outbreak and again at the peak of the outbreak was superior to other models. This model estimated that cross-transmission increased at week 120 and declined after week 135, coinciding with environmental decontamination.

Significance
. We found that HMMs can be applied to serial prevalence data to estimate the characteristics of acquisition of nosocomial pathogens and distinguish between epidemic and sporadic acquisition. This model was able to estimate transmission parameters despite imperfect detection of the organism. The results of this model were validated against PFGE and glycopeptide resistance genotype data and produced very similar results. Additionally, HMMs can provide information about unobserved events such as undetected colonization.
Culturally transmitted paternity beliefs and the evolution of human mating behaviour
Authors: Mesoudi Alex , Laland Kevin N
Published: March 2007

Recent anthropological findings document how certain lowland South American societies hold beliefs in ‘partible paternity’, which allow children to have more than one ‘biological’ father. This contrasts with Western beliefs in ‘singular paternity’, and biological reality, where children have just one father. Here, mathematical models are used to explore the coevolution of paternity beliefs and the genetic variation underlying human mating behaviour. A gene–culture coevolutionary model found that populations exposed to a range of selection regimes typically converge on one of two simultaneously stable equilibria; one where the population is monogamous and believes in singular paternity, and the other where the population is polygamous and believes in partible paternity. A second agent-based model, with alternative assumptions regarding the formation of mating consortships, broadly replicated this finding in populations with a strongly female-biased sex ratio, consistent with evidence for high adult male mortality in the region. This supports an evolutionary scenario in which ancestral South American populations with differing paternity beliefs were subject to divergent selection on genetically influenced mating behaviour, facilitated by a female-biased sex ratio, leading to the present-day associations of female control, partible paternity and polygamy in some societies, and male control, singular paternity and monogamy in others.
Alien predators are more dangerous than native predators to prey populations
Authors: Salo Pälvi , Korpimäki Erkki , Banks Peter B , Nordström Mikael , Dickman Chris R
Published: March 2007

Alien predators are widely considered to be more harmful to prey populations than native predators. To evaluate this expectation, we conducted a meta-analysis of the responses of vertebrate prey in 45 replicated and 35 unreplicated field experiments in which the population densities of mammalian and avian predators had been manipulated. Our results showed that predator origin (native versus alien) had a highly significant effect on prey responses, with alien predators having an impact double that of native predators. Also the interaction between location (mainland versus island) and predator origin was significant, revealing the strongest effects with alien predators in mainland areas. Although both these results were mainly influenced by the huge impact of alien predators on the Australian mainland compared with their impact elsewhere, the results demonstrate that introduced predators can impose more intense suppression on remnant populations of native species and hold them further from their predator-free densities than do native predators preying upon coexisting prey.
Evolution of frequency-dependent mate choice: keeping up with fashion trends
Authors: Kokko Hanna , Jennions Michael D , Houde Anne
Published: March 2007

The diversity of sexual traits favoured by females is enormous and, curiously, includes preferences for males with rare or novel phenotypes. We modelled the evolution of a preference for rarity that yielded two surprising results. First, a Fisherian ‘sexy son’ effect can boost female preferences to a frequency well above that predicted by mutation–selection balance, even if there are significant mortality costs for females. Preferences do not reach fixation, however, as they are subject to frequency-dependent selection: if choosy females are too common, then rare genotypes in one generation become common, and thus unattractive, in the offspring generation. Nevertheless, even at relatively low frequency, preferences maintain polymorphism in male traits. The second unexpected result is that the preferences can evolve to much higher frequencies if choice is hindered, such that females cannot always express their preferences. Our results emphasize the need to consider feedback where preferences determine the dynamics of male genotypes and vice versa. They also highlight the similarity between the arbitrariness of behavioural norms in models of social evolution with punishment (the so-called ‘folk theorem’) and the diversity of sexual traits that can be preferred simply because deviating from the norm produces unattractive offspring and is, in this sense, ‘punished’.
Sperm competition, alternative mating tactics and context-dependent fertilization success in the burying beetle,
Nicrophorus vespilloides
Authors: House Clarissa M , Hunt John , Moore Allen J
Published: March 2007

Fertilization success in sperm competition is often determined by laboratory estimates of the proportion of offspring sired by the first (
P
1
) or second (
P
2
) male that mates. However, inferences from such data about how sexual selection acts on male traits in nature may be misleading if fertilization success depends on the biological context in which it is measured. We used the sterile male technique to examine the paternity of the same male in two mating contexts in the burying beetle,
Nicrophorus vespilloides
, a species where males have alternative mating strategies based on the presence or absence of resources. We found no congruence in the paternity achieved by a given male when mating under different social conditions.
P
2
estimates were extremely variable under both conditions. Body size was unrelated to success in sperm competition away from a carcass but, most probably through pre-copulatory male–male competition, influenced fertilization success on a carcass. The contribution of sperm competition is therefore dependent on the conditions under which it is measured. We discuss our findings in relation to sperm competition theory and highlight the need to consider biological context in order to link copulation and fertilization success for competing males.
Empirical tests of the role of disruptive coloration in reducing detectability
Authors: Fraser Stewart , Callahan Alison , Klassen Dana , Sherratt Thomas N
Published: March 2007

Disruptive patterning is a potentially universal camouflage technique that is thought to enhance concealment by rendering the detection of body shapes more difficult. In a recent series of field experiments, artificial moths with markings that extended to the edges of their ‘wings’ survived at higher rates than moths with the same edge patterns inwardly displaced. While this result seemingly indicates a benefit to obscuring edges, it is possible that the higher density markings of the inwardly displaced patterns concomitantly reduced their extent of background matching. Likewise, it has been suggested that the mealworm baits placed on the artificial moths could have created differential contrasts with different moth patterns. To address these concerns, we conducted controlled trials in which human subjects searched for computer-generated moth images presented against images of oak trees. Moths with edge-extended disruptive markings survived at higher rates, and took longer to find, than all other moth types, whether presented sequentially or simultaneously. However, moths with no edge markings and reduced interior pattern density survived better than their high-density counterparts, indicating that background matching may have played a so-far unrecognized role in the earlier experiments. Our disruptively patterned non-background-matching moths also had the lowest overall survivorship, indicating that disruptive coloration alone may not provide significant protection from predators. Collectively, our results provide independent support for the survival value of disruptive markings and demonstrate that there are common features in human and avian perception of camouflage.
Regularization of the Kelvin–Helmholtz instability by surface tension
Authors: Ambrose David M
Published: March 2007

The Kelvin–Helmholtz instability is present in the motion of a vortex sheet without surface tension. This can be seen from the linearization of the equations of motion, and there have also been proofs of ill-posedness for the full nonlinear equations. In the presence of surface tension, the linearized equations no longer exhibit an instability, and it has been believed that the full equations should then be well-posed. In this paper, I sketch a proof that the vortex sheet with surface tension is well-posed in the case of both two- and three-dimensional fluids. The proof in the case of three-dimensional fluids is the joint work with Nader Masmoudi. The method is to first reformulate the problem using suitable variables and parametrizations, and then to perform energy estimates. The choice of variables and parametrizations in the two-dimensional case is the same as that of Hou
et al
. in a prior numerical work.
Wave breaking and shock waves for a periodic shallow water equation
Authors: Escher Joachim
Published: March 2007

This paper is devoted to the study of a recently derived periodic shallow water equation. We discuss in detail the blow-up scenario of strong solutions and present several conditions on the initial profile, which ensure the occurrence of wave breaking. We also present a family of global weak solutions, which may be viewed as global periodic shock waves to the equation under discussion.
Bi-Hamiltonian systems on the dual of the Lie algebra of vector fields of the circle and periodic shallow water equations
Authors: Kolev Boris
Published: March 2007

This paper is a survey article on bi-Hamiltonian systems on the dual of the Lie algebra of vector fields on the circle. Here, we investigate the special case where one of the structures is the canonical Lie–Poisson structure and the second one is constant. These structures, called affine or modified Lie–Poisson structures, are involved in the integrability of certain Euler equations that arise as models for shallow water waves.
Edge waves: theories past and present
Authors: Johnson R.S
Published: March 2007

The problem of edge waves as an example within classical water-wave theory is described by presenting an overview of some of the theories that have been offered for this phenomenon. The appropriate governing equations and boundary conditions are formulated, and then the important discoveries of Stokes and Ursell, concerning the travelling edge wave, are presented. (We do not address the corresponding problem of standing waves.) Thus, the linear problem and its spectrum are constructed; in addition, we also present the linear long-wave approximation to the problem, as well as Whitham's weakly nonlinear extension to Stokes' original theory. All these discussions are based on the same formulation of the problem, allowing an immediate comparison of the results, whether this be in terms of different approximations or whether the theory be for an irrotational flow or not.

Gerstner's exact solution of the water-wave problem is then briefly described, together with a transformation that produces an exact solution of the full equations for the edge wave. The form of this solution is then used as the basis for a multiple-scale description of the edge wave over a slowly varying depth; this leads to a version of the shallow-water equations which has an exact solution that corresponds to the edge wave. Some examples of the theoretical predictions for the run-up pattern are presented. We conclude with three variants of nonlinear model equations that may prove useful in the study of edge waves and, particularly, the interaction of different modes.
Look who's talking: communication and quorum sensing in the bacterial world
Authors: Williams Paul , Winzer Klaus , Chan Weng C , Cámara Miguel
Published: March 2007

For many years bacteria were considered primarily as autonomous unicellular organisms with little capacity for collective behaviour. However, we now appreciate that bacterial cells are in fact, highly communicative. The generic term ‘quorum sensing’ has been adopted to describe the bacterial cell-to-cell communication mechanisms which co-ordinate gene expression usually, but not always, when the population has reached a high cell density. Quorum sensing depends on the synthesis of small molecules (often referred to as pheromones or autoinducers) that diffuse in and out of bacterial cells. As the bacterial population density increases, so does the synthesis of quorum sensing signal molecules, and consequently, their concentration in the external environment rises. Once a critical threshold concentration has been reached, a target sensor kinase or response regulator is activated (or repressed) so facilitating the expression of quorum sensing-dependent genes. Quorum sensing enables a bacterial population to mount a co-operative response that improves access to nutrients or specific environmental niches, promotes collective defence against other competitor prokaryotes or eukaryotic defence mechanisms and facilitates survival through differentiation into morphological forms better able to combat environmental threats. Quorum sensing also crosses the prokaryotic–eukaryotic boundary since quorum sensing-dependent signalling can be exploited or inactivated by both plants and mammals.
Cell–cell communication in the plant pathogen
Agrobacterium tumefaciens
Authors: White Catharine E , Winans Stephen C
Published: March 2007

The plant pathogen
Agrobacterium tumefaciens
induces the formation of crown gall tumours at wound sites on host plants by directly transforming plant cells. This disease strategy benefits the bacteria as the infected plant tissue produces novel nutrients, called opines, that the colonizing bacteria can use as nutrients. Almost all of the genes that are required for virulence, and all of the opine uptake and utilization genes, are carried on large tumour-inducing (Ti) plasmids. The observation more than 25 years ago that specific opines are required for Ti plasmid conjugal transfer led to the discovery of a cell–cell signalling system on these plasmids that is similar to the LuxR–LuxI system first described in
Vibrio fischeri
. All Ti plasmids that have been described to date carry a functional LuxI-type
N
-acylhomoserine lactone synthase (TraI), and a LuxR-type signal receptor and transcriptional regulator called TraR. The
traR
genes are expressed only in the presence of specific opines called conjugal opines. The TraR–TraI system provides an important model for LuxR–LuxI-type systems, especially those found in the agriculturally important Rhizobiaceae family. In this review, we discuss current advances in the biochemistry and structural biology of the TraR–TraI system.
Quorum-sensing regulation in rhizobia and its role in symbiotic interactions with legumes
Authors: Sanchez-Contreras Maria , Bauer Wolfgang D , Gao Mengsheng , Robinson Jayne B , Allan Downie J
Published: March 2007

Legume-nodulating bacteria (rhizobia) usually produce
N
-acyl homoserine lactones, which regulate the induction of gene expression in a quorum-sensing (or population-density)-dependent manner. There is significant diversity in the types of quorum-sensing regulatory systems that are present in different rhizobia and no two independent isolates worked on in detail have the same complement of quorum-sensing genes. The genes regulated by quorum sensing appear to be rather diverse and many are associated with adaptive aspects of physiology that are probably important in the rhizosphere. It is evident that some aspects of rhizobial physiology related to the interaction between rhizobia and legumes are influenced by quorum sensing. However, it also appears that the legumes play an active role, both in terms of interfering with the rhizobial quorum-sensing systems and responding to the signalling molecules made by the bacteria. In this article, we review the diversity of quorum-sensing regulation in rhizobia and the potential role of legumes in influencing and responding to this signalling system.
The peptide pheromone-inducible conjugation system of
Enterococcus faecalis
plasmid pCF10: cell–cell signalling, gene transfer, complexity and evolution
Authors: Dunny Gary M
Published: March 2007

Expression of a large set of gene products required for conjugative transfer of the antibiotic resistance plasmid pCF10 is controlled by cell–cell communication between plasmid-free recipient cells and plasmid-carrying donor cells using a peptide mating pheromone cCF10. Most of the recent experimental analysis of this system has focused on the molecular events involved in initiation of the pheromone response in the donor cells, and on the mechanisms by which the donor cells control self-induction by endogenously produced pheromone. Recently, studies of the molecular machinery of conjugation encoded by the pheromone-inducible genes have been initiated. In addition, the system may serve as a useful bacterial model for addressing the evolution of biological complexity.
Antibiotics as signalling molecules
Authors: Yim Grace , Huimi Wang Helena , Davies FRS Julian
Published: March 2007

We present the argument that the majority of low-molecular-weight organic compounds made and secreted by microbes play roles as cell-signalling molecules in the environment. Of the large number of compounds isolated to date, only a small fraction have been shown to possess useful therapeutic antibiotic activity. However, most microbial metabolites modulate gene transcription at low concentrations, and this is proposed to be the primary effect of the compounds in the maintenance of microbial communities in the environment. Thus, microbial metabolites constitute a large collection of cell-signalling molecules that regulate gene expression in microbial populations and possibly the interactions of these populations with the surrounding organisms.