Searching for motifs in the behaviour of larval Drosophila melanogaster and Caenorhabditis elegans reveals continuity between behavioural states

We present a novel method for the unsupervised discovery of behavioural motifs in larval Drosophila melanogaster and Caenorhabditis elegans. A motif is defined as a particular sequence of postures that recurs frequently. The animal''s changing posture is represented by an eigenshape time series, and we look for motifs in this time series. To find motifs, the eigenshape time series is segmented, and the segments clustered using spline regression. Unlike previous approaches, our method can classify sequences of unequal duration as the same motif. The behavioural motifs are used as the basis of a probabilistic behavioural annotator, the eigenshape annotator (ESA). Probabilistic annotation avoids rigid threshold values and allows classification uncertainty to be quantified. We apply eigenshape annotation to both larval Drosophila and C. elegans and produce a good match to hand annotation of behavioural states. However, we find many behavioural events cannot be unambiguously classified. By comparing the results with ESA of an artificial agent''s behaviour, we argue that the ambiguity is due to greater continuity between behavioural states than is generally assumed for these organisms.     

Use of multiple modes of flight subsidy by a soaring terrestrial bird,the golden eagle Aquila chrysaetos,when on migration

Large birds regularly use updrafts to subsidize flight. Although most research on soaring bird flight has focused on use of thermal updrafts, there is evidence suggesting that many species are likely to use multiple modes of subsidy. We tested the degree to which a large soaring species uses multiple modes of subsidy to provide insights into the decision-making that underlies flight behaviour. We statistically classified more than 22 000 global positioning satellite–global system for mobile communications telemetry points collected at 30-s intervals to identify the type of subsidized flight used by 32 migrating golden eagles during spring in eastern North America. Eagles used subsidized flight on 87% of their journey. They spent 41.9% ± 1.5 (, range: 18–56%) of their subsidized northbound migration using thermal soaring, 45.2% ± 2.1 (12–65%) of time gliding between thermals, and 12.9% ± 2.2 (1–55%) of time using orographic updrafts. Golden eagles responded to the variable local-scale meteorological events they encountered by switching flight behaviour to take advantage of multiple modes of subsidy. Orographic soaring occurred more frequently in morning and evening, earlier in the migration season, and when crosswinds and tail winds were greatest. Switching between flight modes allowed migration for relatively longer periods each day and frequent switching behaviour has implications for a better understanding of avian flight behaviour and of the evolution of use of subsidy in flight.     

Mapping the stereotyped behaviour of freely moving fruit flies

A frequent assumption in behavioural science is that most of an animal''s activities can be described in terms of a small set of stereotyped motifs. Here, we introduce a method for mapping an animal''s actions, relying only upon the underlying structure of postural movement data to organize and classify behaviours. Applying this method to the ground-based behaviour of the fruit fly, Drosophila melanogaster, we find that flies perform stereotyped actions roughly 50% of the time, discovering over 100 distinguishable, stereotyped behavioural states. These include multiple modes of locomotion and grooming. We use the resulting measurements as the basis for identifying subtle sex-specific behavioural differences and revealing the low-dimensional nature of animal motions.     

A metapopulation modelling framework for gonorrhoea and other sexually transmitted infections in heterosexual populations

Gonorrhoea continues to be a public health problem in the UK, and is the second most common bacterial sexually transmitted infection (STI) after chlamydia. In the UK, gonorrhoea is disproportionately concentrated in epidemiologically distinct subpopulations, with much higher incidence rates in young people, some ethnic minorities and inner city subpopulations. The original model of STI transmission proposed by Hethcote and Yorke explained some of these features through the concept of the ‘core group’. Since then, several authors have modified the original model approach to include multiple sexual activity classes, but found this modelling approach to be inadequate when applied to low-prevalence settings such as the UK. We present a metapopulation framework for modelling gonorrhoea and other STIs. The model proposes that the epidemiology of gonorrhoea is largely driven by subpopulations with higher than average concentrations of individuals with high sexual risk activity. We show how this conceptualization of gonococcal epidemiology overcomes key limitations associated with some of the prior efforts to model gonorrhoea. We also use the model to explain several epidemiological features of gonorrhoea, such as its asymmetric distribution across subpopulations, and the contextual risk experienced by members of at-risk subpopulations. Finally, we extend the model to explain the distribution of other STIs, using chlamydia as an example of a more ubiquitous bacterial STI.     

Mechanistic analysis of the search behaviour of Caenorhabditis elegans

A central question in movement research is how animals use information and movement to promote encounter success. Current random search theory identifies reorientation patterns as key to the compromise between optimizing encounters for both nearby and faraway targets, but how the balance between intrinsic motor programmes and previous environmental experience determines the occurrence of these reorientation behaviours remains unknown. We used high-resolution tracking and imaging data to describe the complete motor behaviour of Caenorhabditis elegans when placed in a novel environment (one in which food is absent). Movement in C. elegans is structured around different reorientation behaviours, and we measured how these contributed to changing search strategies as worms became familiar with their new environment. This behavioural transition shows that different reorientation behaviours are governed by two processes: (i) an environmentally informed ‘extrinsic’ strategy that is influenced by recent experience and that controls for area-restricted search behaviour, and (ii) a time-independent, ‘intrinsic’ strategy that reduces spatial oversampling and improves random encounter success. Our results show how movement strategies arise from a balance between intrinsic and extrinsic mechanisms, that search behaviour in C. elegans is initially determined by expectations developed from previous environmental experiences, and which reorientation behaviours are modified as information is acquired from new environments.     

The effect of individual variation on the structure and function of interaction networks in harvester ants

Social insects exhibit coordinated behaviour without central control. Local interactions among individuals determine their behaviour and regulate the activity of the colony. Harvester ants are recruited for outside work, using networks of brief antennal contacts, in the nest chamber closest to the nest exit: the entrance chamber. Here, we combine empirical observations, image analysis and computer simulations to investigate the structure and function of the interaction network in the entrance chamber. Ant interactions were distributed heterogeneously in the chamber, with an interaction hot-spot at the entrance leading further into the nest. The distribution of the total interactions per ant followed a right-skewed distribution, indicating the presence of highly connected individuals. Numbers of ant encounters observed positively correlated with the duration of observation. Individuals varied in interaction frequency, even after accounting for the duration of observation. An ant''s interaction frequency was explained by its path shape and location within the entrance chamber. Computer simulations demonstrate that variation among individuals in connectivity accelerates information flow to an extent equivalent to an increase in the total number of interactions. Individual variation in connectivity, arising from variation among ants in location and spatial behaviour, creates interaction centres, which may expedite information flow.     

A dynamical model for the Utricularia trap

We propose a model that captures the dynamics of a carnivorous plant, Utricularia inflata. This plant possesses tiny traps for capturing small aquatic animals. Glands pump water out of the trap, yielding a negative pressure difference between the plant and its surroundings. The trap door is set into a meta-stable state and opens quickly as an extra pressure is generated by the displacement of a potential prey. As the door opens, the pressure difference sucks the animal into the trap. We write an ODE model that captures all the physics at play. We show that the dynamics of the plant is quite similar to neuronal dynamics and we analyse the effect of a white noise on the dynamics of the trap.     

Conventional Cells—The Last Step Toward General Acceptance of Standard Conventional Cells for the Reporting of Crystallographic Data

In 1969, a seminal section on reduced forms and conventional cells was published in the International Tables for X-Ray Crystallography. The section contains a table that gives a metric classification of the 44 reduced forms. In 2001, this table with appropriate revisions was republished in the Journal of Research of the National Institute of Standards and Technology. An especially valuable feature of the table is that it defines and allows the user to determine a standard conventional cell. Since 1969, there has been an evolution toward acceptance and widespread use of such conventional cells. An inspection of the articles in key crystallographic journals reveals that most cells follow the conventions. However, one major exception remains—the centered monoclinic lattices. In approximately one-third of these cases, non-conventional C-centered cells are used, apparently to avoid the use of I-centered cells. It is recommended that the crystallographic community routinely use the I-centered conventional cell in such cases.     

Surface wettability of plasma SiOx:H nanocoating-induced endothelial cells' migration and the associated FAK-Rho GTPases signalling pathways

Vascular endothelial cell (EC) adhesion and migration are essential processes in re-endothelialization of implanted biomaterials. There is no clear relationship and mechanism between EC adhesion and migration behaviour on surfaces with varying wettabilities. As model substrates, plasma SiO_x:H nanocoatings with well-controlled surface wettability (with water contact angles in the range of 98.5 ± 2.3° to 26.3 ± 4.0°) were used in this study to investigate the effects of surface wettability on cell adhesion/migration and associated protein expressions in FAK-Rho GTPases signalling pathways. It was found that EC adhesion/migration showed opposite behaviour on the hydrophilic and hydrophobic surfaces (i.e. hydrophobic surfaces promoted EC migration but were anti-adhesions). The number of adherent ECs showed a maximum on hydrophilic surfaces, while cells adhered to hydrophobic surfaces exhibited a tendency for cell migration. The focal adhesion kinase (FAK) inhibitor targeting the Y-397 site of FAK could significantly inhibit cell adhesion/migration, suggesting that EC adhesion and migration on surfaces with different wettabilities involve (p)FAK and its downstream signalling pathways. Western blot results suggested that the FAK-Rho GTPases signalling pathways were correlative to EC migration on hydrophobic plasma SiO_x:H surfaces, but uncertain to hydrophilic surfaces. This work demonstrated that surface wettability could induce cellular behaviours that were associated with different cellular signalling events.     

Characterization of the phosphatic mineral of the barnacle Ibla cumingi at atomic level by solid-state nuclear magnetic resonance: comparison with other phosphatic biominerals

Ibliform barnacles are among the few invertebrate animals harnessing calcium phosphate to construct hard tissue. The ³¹P solid-state NMR (SSNMR) signal from the shell plates of Ibla cumingi (Iblidae) is broader than that of bone, and shifted by ca 1 ppm to low frequency. ¹H–³¹P heteronuclear correlation (HETCOR) experiments show a continuum of different phosphorus/phosphate atomic environments, close to hydrogen populations with resonance frequencies between ca 10 and 20 ppm. Associated ¹H and ³¹P chemical shifts argue the coexistence of weakly (high ³¹P frequency, low ¹H frequency) to more strongly (lower ³¹P frequency, higher ¹H frequency) hydrogen-bonded hydrogen phosphate-like molecular/ionic species. There is no resolved signal from discrete OH⁻ ions. ¹³C SSNMR shows chitin, protein and other organic biomolecules but, unlike bone, there are no significant atomic scale organic matrix–mineral contacts. The poorly ordered hydrogen phosphate-like iblid mineral is strikingly different, structurally and compositionally, from both vertebrate bone mineral and the more crystalline fluoroapatite of the linguliform brachiopods. It probably represents a previously poorly characterized calcium phosphate biomineral, the evolution of which may have reflected either the chemical conditions of ancestral seas or the mechanical advantages of phosphatic biomineralization over a calcium carbonate equivalent.     

Invasion,persistence and control in epidemic models for plant pathogens: the effect of host demography

Many epidemiological models for plant disease include host demography to describe changes in the availability of susceptible tissue for infection. We compare the effects of using two commonly used formulations for host growth, one linear and the other nonlinear, upon the outcomes for invasion, persistence and control of pathogens in a widely used, generic model for botanical epidemics. The criterion for invasion, reflected in the basic reproductive number, R₀, is unaffected by host demography: R₀ is simply a function of epidemiological parameters alone. When, however, host growth is intrinsically nonlinear, unexpected results arise for persistence and the control of disease. The endemic level of infection (I_∞) also depends upon R₀. We show, however, that the sensitivity of I_∞ to changes in R₀ > 1 depends upon which underlying epidemiological parameter is changed. Increasing R₀ by shortening the infectious period results in a monotonic increase in I_∞. If, however, an increase in R₀ is driven by increases in transmission rates or by decreases in the decay of free-living inoculum, I_∞ first increases (R₀ < 2), but then decreases (R₀ > 2). This counterintuitive result means that increasing the intensity of control can result in more endemic infection.     

Tilted cellulose arrangement as a novel mechanism for hygroscopic coiling in the stork's bill awn

The sessile nature of plants demands the development of seed-dispersal mechanisms to establish new growing loci. Dispersal strategies of many species involve drying of the dispersal unit, which induces directed contraction and movement based on changing environmental humidity. The majority of researched hygroscopic dispersal mechanisms are based on a bilayered structure. Here, we investigate the motility of the stork''s bill (Erodium) seeds that relies on the tightening and loosening of a helical awn to propel itself across the surface into a safe germination place. We show that this movement is based on a specialized single layer consisting of a mechanically uniform tissue. A cell wall structure with cellulose microfibrils arranged in an unusually tilted helix causes each cell to spiral. These cells generate a macroscopic coil by spiralling collectively. A simple model made from a thread embedded in an isotropic foam matrix shows that this cellulose arrangement is indeed sufficient to induce the spiralling of the cells.     

A combined within-host and between-hosts modelling framework for the evolution of resistance to antimalarial drugs

The spread of drug resistance represents a significant challenge to many disease control efforts. The evolution of resistance is a complex process influenced by transmission dynamics between hosts as well as infection dynamics within these hosts. This study aims to investigate how these two processes combine to impact the evolution of resistance in malaria parasites. We introduce a stochastic modelling framework combining an epidemiological model of Plasmodium transmission and an explicit within-human infection model for two competing strains. Immunity, treatment and resistance costs are included in the within-host model. We show that the spread of resistance is generally less likely in areas of intense transmission, and therefore of increased competition between strains, an effect exacerbated when costs of resistance are higher. We also illustrate how treatment influences the spread of resistance, with a trade-off between slowing resistance and curbing disease incidence. We show that treatment coverage has a stronger impact on disease prevalence, whereas treatment efficacy primarily affects resistance spread, suggesting that coverage should constitute the primary focus of control efforts. Finally, we illustrate the importance of feedbacks between modelling scales. Overall, our results underline the importance of concomitantly modelling the evolution of resistance within and between hosts.     

Analytical methods for quantifying environmental connectivity for the control and surveillance of infectious disease spread

The sustained transmission and spread of environmentally mediated infectious diseases is governed in part by the dispersal of parasites, disease vectors and intermediate hosts between sites of transmission. Functional geospatial models can be used to quantify and predict the degree to which environmental features facilitate or limit connectivity between target populations, yet typical models are limited in their geographical and analytical approach, providing simplistic, global measures of connectivity and lacking methods to assess the epidemiological implications of fine-scale heterogeneous landscapes. Here, functional spatial models are applied to problems of surveillance and control of the parasitic blood fluke Schistosoma japonicum and its intermediate snail host Oncomelania haupensis in western China. We advance functional connectivity methods by providing an analytical framework to (i) identify nodes of transmission where the degree of connectedness to other villages, and thus the potential for disease spread, is higher than is estimated using Euclidean distance alone and (ii) (re)organize transmission sites into disease surveillance units based on second-order relationships among nodes using non-Euclidean distance measures, termed effective geographical distance (EGD). Functional environmental models are parametrized using ecological information on the target organisms, and pair-wise distributions of inter-node EGD are estimated. A Monte Carlo rank product analysis is presented to identify nearby nodes under alternative distance models. Nodes are then iteratively embedded into EGD space and clustered using a k-means algorithm to group villages into ecologically meaningful surveillance groups. A consensus clustering approach is taken to derive the most stable cluster structure. The results indicate that novel relationships between nodes are revealed when non-Euclidean, ecologically determined distance measures are used to quantify connectivity in heterogeneous landscapes. These connections are not evident when analysing nodes in Euclidean space, and thus surveillance and control activities planned using Euclidean distance measures may be suboptimal. The methods developed here provide a quantitative framework for assessing the effectiveness of ecologically grounded surveillance systems and of control and prevention strategies for environmentally mediated diseases.     

Requirements for the Development of Bacillus Anthracis Spore Reference Materials Used to Test Detection Systems

Bacillus anthracis spores have been used as biological weapons and the possibility of their further use requires surveillance systems that can accurately and reliably detect their presence in the environment. These systems must collect samples from a variety of matrices, process the samples, and detect the spores. The processing of the sample may include removal of inhibitors, concentration of the target, and extraction of the target in a form suitable for detection. Suitable reference materials will allow the testing of each of these steps to determine the sensitivity and specificity of the detection systems. The development of uniform and well-characterized reference materials will allow the comparison of different devices and technologies as well as assure the continued performance of detection systems. This paper discusses the special requirements of reference materials for Bacillus anthracis spores that could be used for testing detection systems. The detection of Bacillus anthracis spores is based on recognition of specific characteristics (markers) on either the spore surface or in the nucleic acids (DNA). We have reviewed the specific markers and their relevance to characterization of reference materials. We have also included the approach for the characterization of candidate reference materials that we are developing at the NIST laboratories. Additional applications of spore reference materials would include testing sporicidal treatments, techniques for sampling the environment, and remediation of spore-contaminated environments.     

Suitability of European climate for the Asian tiger mosquito Aedes albopictus: recent trends and future scenarios

The Asian tiger mosquito (Aedes albopictus) is an invasive species that has the potential to transmit infectious diseases such as dengue and chikungunya fever. Using high-resolution observations and regional climate model scenarios for the future, we investigated the suitability of Europe for A. albopictus using both recent climate and future climate conditions. The results show that southern France, northern Italy, the northern coast of Spain, the eastern coast of the Adriatic Sea and western Turkey were climatically suitable areas for the establishment of the mosquito during the 1960–1980s. Over the last two decades, climate conditions have become more suitable for the mosquito over central northwestern Europe (Benelux, western Germany) and the Balkans, while they have become less suitable over southern Spain. Similar trends are likely in the future, with an increased risk simulated over northern Europe and slightly decreased risk over southern Europe. These distribution shifts are related to wetter and warmer conditions favouring the overwintering of A. albopictus in the north, and drier and warmer summers that might limit its southward expansion.     

Proposed extension of the SINTAP/FITNET thin wall option based on a simple method for reference load determination

A “correct” limit or yield load is an essential element of flaw assessment procedures of the R6 or SINTAP/FITNET type. In this paper the authors propose a definition of this quantity which is based on the SINTAP option 3 failure assessment function. This “reference load” can be determined for any component geometry by finite element analysis. The method is applied to two kinds of thin walled structures (notched plates and curved stiffened panels) and the results demonstrate that the approach is a suitable extension of the existing thin wall module.     

Spontaneous formation of Ge nanocrystals with the capping layer of Si3N4 by N2 implantation and rapid thermal annealing

We studied Ge nanocrystals (nc-Ge) formed by bombarding Ge(100) surface with N₂⁺ gas followed by rapid thermal annealing (RTA). After initial N₂⁺ implantation, near-edge x-ray absorption fine structure and x-ray photoelectron spectroscopy (XPS) data showed formation of molecule-like N₂ species and chemically metastable Ge nitrides (GeN_x). The RTA transformed these into hemispherical nc-Ge of 10-25 nm in the diameter as clearly seen in transmission electron microscope images. XPS confirmed that the surface of the nc-Ge was covered with Ge₃N₄ layer and underlying layer is also mostly likely Ge₃N₄. This simple process of forming isolated nc-Ge with Ge₃N₄ surrounding layer can be useful in non-volatile memory applications.     

Thermally responsive polymeric hydrogel brushes: synthesis, physical properties and use for the culture of chondrocytes

Hydrogel brushes are materials composed of a water-swollen network, which contains polymer chains that are grafted with another polymer. Using a thermally responsive polymer, poly(N-isopropyl acrylamide) (polyNIPAM), as the graft component we are able to maintain the critical solution temperature (Tcrit), independent of the overall composition of the material, at approximately 32 degrees C. The change in swelling at Tcrit is a function of the amount of polyNIPAM in the system. However, there is a much smaller change in the surface contact angles at Tcrit. PolyNIPAM-based materials have generated considerable interest, as 'smart' substrates for the culture of cells and here, we show the utility of hydrogel brushes in cell culture. Chondrocytes attached to the hydrogel brushes and yielded viable cell cultures. Moreover, the chondrocytes could be released from the hydrogel brushes without the use of proteases by reducing the temperature of the cultures to below Tcrit to induce a change in the conformation of the polyNIPAM chain at Tcrit. The importance of the crosslink hydrogel component is illustrated by significant changes in cell attachment/cell viability as the crosslink density is changed.