Directionality of nose-emitted echolocation calls from bats without a nose leaf (Plecotus auritus).

All echolocating bats and whales measured to date emit a directional bio-sonar beam that affords them a number of advantages over an omni-directional beam, i.e. reduced clutter, increased source level and inherent directional information. In this study, we investigated the importance of directional sound emission for navigation through echolocation by measuring the sonar beam of brown long-eared bats, Plecotus auritusPlecotus auritus emits sound through the nostrils but has no external appendages to readily facilitate a directional sound emission as found in most nose emitters. The study shows that P. auritus, despite lacking an external focusing apparatus, emits a directional echolocation beam (directivity index=13 dB) and that the beam is more directional vertically (-6 dB angle at 22 deg) than horizontally (-6 dB angle at 35 deg). Using a simple numerical model, we found that the recorded emission pattern is achievable if P. auritus emits sound through the nostrils as well as the mouth. The study thus supports the hypothesis that a directional echolocation beam is important for perception through echolocation and we propose that animals with similarly non-directional emitter characteristics may facilitate a directional sound emission by emitting sound through both the nostrils and the mouth.

From "ear" to there: a review of biorobotic models of auditory processing in lizards.

The peripheral auditory system of lizards has been extensively studied, because of its remarkable directionality. In this paper, we review the research that has been performed on this system using a biorobotic approach. The various robotic implementations developed to date, both wheeled and legged, of the auditory model exhibit strong phonotactic performance for two types of steering mechanisms-a simple threshold decision model and Braitenberg sensorimotor cross-couplings. The Braitenberg approach removed the need for a decision model, but produced relatively inefficient robot trajectories. Introducing various asymmetries in the auditory model reduced the efficiency of the robot trajectories, but successful phonotaxis was maintained. Relatively loud noise distractors degraded the trajectory efficiency and above-threshold noise resulted in unsuccessful phonotaxis. Machine learning techniques were applied to successfully compensate for asymmetries as well as noise distractors. Such techniques were also successfully used to construct a representation of auditory space, which is crucial for sound localisation while remaining stationary as opposed to phonotaxis-based localisation. The peripheral auditory model was furthermore found to adhere to an auditory scaling law governing the variation in frequency response with respect to physical ear separation. Overall, the research to date paves the way towards investigating the more fundamental topic of auditory metres versus auditory maps, and the existing robotic implementations can act as tools to compare the two approaches.

A spatial compression technique for head-related transfer function interpolation and complexity estimation.

A head-related transfer function (HRTF) model employing Legendre polynomials (LPs) is evaluated as an HRTF spatial complexity indicator and interpolation technique in the azimuth plane. LPs are a set of orthogonal functions derived on the sphere which can be used to compress an HRTF dataset by transforming it into a lower dimensional space. The LP compression technique was applied to various HRTF datasets, both real and synthetic, to determine how much different HRTFs can be compressed with respect to their structural complexity and their spatial resolution. The spatial complexity of different datasets was evaluated quantitatively by defining an HRTF spatial complexity index, which considers the rate of change in HRTF power spectrum with respect to spatial position. The results indicate that the compression realized by the LP technique is largely independent of the number of spatial samples in the HRTF dataset, while compressibility tracks the HRTF spatial complexity index so that more LP coefficients are needed to represent an HRTF dataset with a larger complexity index. The slope of the complexity index with respect to sub-sampling density can be used as a predictor for high interpolation error.

Carbon dioxide fixation and sulfate sequestration by a supramolecular trigonal bipyramid.

The subcomponent self-assembly of a bent dialdehyde ligand and different cationic and anionic templates led to the formation of two new metallosupramolecular architectures: a Fe(II) 4 L6 molecular rectangle was isolated following reaction of the ligand with iron(II) tetrafluoroborate, and a M5 L6 trigonal bipyramidal structure was constructed from either zinc(II) tetrafluoroborate or cadmium(II) trifluoromethanesulfonate. The spatially constrained arrangement of the three equatorial metal ions in the M5 L6 structures was found to induce small-molecule transformations. Atmospheric carbon dioxide was fixed as carbonate and bound to the equatorial metal centers in both the Zn5 L6 and Cd5 L6 assemblies, and sulfur dioxide was hydrated and bound as the sulfite dianion in the Zn5 L6 structure. Subsequent in situ oxidation of the sulfite dianion resulted in a sulfate dianion bound within the supramolecular pocket.

Ultrasonic recording system without intrinsic limits.

Today state-of-the-art bioacoustic research requires high-sample-rate, multi-channel, and often long-term recording systems. Commercial systems are very costly. This paper proposes and demonstrates an ultrasonic recording system design that is arbitrarily scalable. The system is modular and based on retail components and open source software/hardware. Each module has four microphones and modules can be combined to extend the coverage area, obtain higher spatial recording resolution, and/or add recording redundancy. The system is designed to have no inherent scalability limits. The system has been deployed in four different test settings. The first setup tests the system's ability to make medium-term recordings (1 to 2 min) with many microphones. The second setup tests the robustness of the system, being deployed throughout the Danish winter with only minor issues. The third setup integrates the system in a mobile robot as an echolocating guidance system, while the fourth setup demonstrates full-spectrum transducer calibration. In most respects this system's hardware specification surpasses all competitors on the market at a quarter of the price. Tests demonstrate that large deployments are feasible and accurate ultrasonic measurements can be obtained.

Compression of head-related transfer function using autoregressive-moving-average models and Legendre polynomials.

Head-related transfer functions (HRTFs) are generally large datasets, which can be an important constraint for embedded real-time applications. A method is proposed here to reduce redundancy and compress the datasets. In this method, HRTFs are first compressed by conversion into autoregressive-moving-average (ARMA) filters whose coefficients are calculated using Prony's method. Such filters are specified by a few coefficients which can generate the full head-related impulse responses (HRIRs). Next, Legendre polynomials (LPs) are used to compress the ARMA filter coefficients. LPs are derived on the sphere and form an orthonormal basis set for spherical functions. Higher-order LPs capture increasingly fine spatial details. The number of LPs needed to represent an HRTF, therefore, is indicative of its spatial complexity. The results indicate that compression ratios can exceed 98% while maintaining a spectral error of less than 4 dB in the recovered HRTFs.

Drone exploration of bat echolocation: A UAV-borne multimicrophone array to study bat echolocation.

Multimicrophone array techniques offer crucial insight into bat echolocation, yet they severely undersample the environments bats operate in as they are limited in geographic placement and mobility. UAVs are excellent candidates to greatly increase the environments in which such arrays can be deployed, but the impact of UAV noise on recording quality and the UAV's behavioral impact on the bats may affect usability. We developed a UAV-borne multimicrophone setup capable of recording bat echolocation across diverse environments. We quantify and mitigate the impact of UAV noise on the recording setup and test the recording capability of the array by recording four common Danish bat species: Pipistrellus pygmaeus, Myotis daubentonii, Eptesicus serotinus, and Nyctalus noctula. The UAV produces substantial noise at ultrasonic frequencies relevant to many bat species. However, suspending the array 30 m below the UAV attenuates the noise to levels below the self-noise of our recording system at 20 kHz and above, and we successfully record and acoustically localize all four bat species. The behavioral impact of the UAV is minimal as all four species approached the array to within 1 m and all emitted recordable feeding buzzes. UAV-borne multimicrophone arrays will allow us to quantify bat echolocation in hitherto unexplored habitats and provide crucial insight into how bats operate their sonar across their entire natural habitat.

Driving singing behaviour in songbirds using a multi-modal, multi-agent virtual environment.

Interactive biorobotics provides unique experimental potential to study the mechanisms underlying social communication but is limited by our ability to build expressive robots that exhibit the complex behaviours of birds and small mammals. An alternative to physical robots is to use virtual environments. Here, we designed and built a modular, audio-visual 2D virtual environment that allows multi-modal, multi-agent interaction to study mechanisms underlying social communication. The strength of the system is an implementation based on event processing that allows for complex computation. We tested this system in songbirds, which provide an exceptionally powerful and tractable model system to study social communication. We show that pair-bonded zebra finches (Taeniopygia guttata) communicating through the virtual environment exhibit normal call timing behaviour, males sing female directed song and both males and females display high-intensity courtship behaviours to their mates. These results suggest that the environment provided is sufficiently natural to elicit these behavioral responses. Furthermore, as an example of complex behavioral annotation, we developed a fully unsupervised song motif detector and used it to manipulate the virtual social environment of male zebra finches based on the number of motifs sung. Our virtual environment represents a first step in real-time automatic behaviour annotation and animal-computer interaction using higher level behaviours such as song. Our unsupervised acoustic analysis eliminates the need for annotated training data thus reducing labour investment and experimenter bias.

Reconstruction of the signal produced by a directional sound source from remote multi-microphone recordings.

A mathematical method for reconstructing the signal produced by a directional sound source from knowledge of the same signal in the far field, i.e., microphone recordings, is developed. The key idea is to compute inverse filters that compensate for the directional filtering of the signal by the sound source directivity, using a least-square error optimization strategy. Previous work pointed out how the method strongly depends on arrival times of signal in the microphone recordings. Two strategies are used in this paper for calculating the time shifts that are afterward taken as inputs, together with source directivity, for the reconstruction. The method has been tested in a laboratory environment, where ground truth was available, with a Polaroid transducer as source. The reconstructions are similar with both strategies. The performance of the method also depends on source orientation.

A method for estimating the orientation of a directional sound source from source directivity and multi-microphone recordings: principles and application.

Taking into account directivity of real sound sources makes it possible to try solving an interesting and biologically relevant problem: estimating the orientation in three-dimensional space of a directional sound source. The source, of known directivity, produces a broadband signal (in the ultrasonic range, in this application) that is recorded by microphones whose position with respect to source is known. An analytical method to process the recorded signals and estimate source orientation is developed in this paper. Experiments testing method performance in estimating source orientation were performed both in a laboratory environment with a Polaroid transducer as source and in a flight room with a Myotis daubentonii bat. In the first case, results showed the estimation method to be accurate and pointed out its limitations. The latter case is significant as an example biological application of the method for extracting behavioral features from bats; results are compared with alternative calculations based on microphone root-mean-square (rms)-pressure values.

A computational fluid dynamics model of viscous coupling of hairs.

Arrays of arthropod filiform hairs form highly sensitive mechanoreceptor systems capable of detecting minute air disturbances, and it is unclear to what extent individual hairs interact with one another within sensor arrays. We present a computational fluid dynamics model for one or more hairs, coupled to a rigid-body dynamics model, for simulating both biological (e.g., a cricket cercal hair) and artificial MEMS-based systems. The model is used to investigate hair-hair interaction between pairs of hairs and quantify the extent of so-called viscous coupling. The results show that the extent to which hairs are coupled depends on the mounting properties of the hairs and the frequency at which they are driven. In particular, it is shown that for equal length hairs, viscous coupling is suppressed when they are driven near the natural frequency of the undamped system and the damping coefficient at the base is small. Further, for certain configurations, the motion of a hair can be enhanced by the presence of nearby hairs. The usefulness of the model in designing artificial systems is discussed.

Artificial intelligence and robotics in high throughput post-genomics.

The shift of post-genomics towards a systems approach has offered an ever-increasing role for artificial intelligence (AI) and robotics. Many disciplines (e.g. engineering, robotics, computer science) bear on the problem of automating the different stages involved in post-genomic research with a view to developing quality assured high-dimensional data. We review some of the latest contributions of AI and robotics to this end and note the limitations arising from the current independent, exploratory way in which specific solutions are being presented for specific problems without regard to how these could be eventually integrated into one comprehensible integrated intelligent system.

An analysis of neural models for walking control.

A large space of different neural models exists from simple mathematical abstractions to detailed biophysical representations with strongly differing levels of complexity and biological relevance. Previous comparisons between models have looked at biological realism or mathematical tractability rather than expressive power. This paper, however, investigates whether more sophisticated models are better suited to a complex sensorimotor control task than simpler ones, or whether the more general nature of groups of the simpler neurons allows them to collectively solve complex tasks better despite their individual simplicity. Many models have been proposed or used for sensorimotor control tasks such as the control of locomotion. Four such neural models with varying levels of complexity were chosen. Controllers made of networks of each neural type were evolved to generate locomotion in a simulated dynamically stable four-legged robot using a genetic algorithm. The problem domain was chosen as one for which no simple solution could be hand crafted and which, with its tight sensorimotor coupling, had strongly time-dependent properties as is common in many biological control tasks. Analysis of the results shows that the most complex and biologically based model is significantly better at walking control, even producing recognizable gaits.

Clustering Emergency Department patients - an assessment of group normality.

This paper presents an investigation into clustering of vital signs from Emergency Department patients with an intention of uncovering distinct thresholds for groups of patients. Emergency Department clinicians have to deal with an enormous spectrum of symptoms and diseases. The variety in patients is a cause for false alarms which greatly burden clinicians. Better targeted alarm thresholds may mitigate the risk of alarm fatigue. The study is based on vital signs from a prospective cohort study at a Danish Hospital coupled with health registry data, and utilizes k-means clustering and novel evaluation metrics for cluster assessment. All combinations of 5 key vital signs are clustered in a range from 2..20. We evaluate the clustering of respiration and arterial peripheral oxygen saturation for k=7. The study fails to identify distinct groups, but does uncover relevant traits and contribute with an evaluation strategy for further studies.

Multi-stability and pattern-selection in oscillatory networks with fast inhibition and electrical synapses.

A model or hybrid network consisting of oscillatory cells interconnected by inhibitory and electrical synapses may express different stable activity patterns without any change of network topology or parameters, and switching between the patterns can be induced by specific transient signals. However, little is known of properties of such signals. In the present study, we employ numerical simulations of neural networks of different size composed of relaxation oscillators, to investigate switching between in-phase (IP) and anti-phase (AP) activity patterns. We show that the time windows of susceptibility to switching between the patterns are similar in 2-, 4- and 6-cell fully-connected networks. Moreover, in a network (N = 4, 6) expressing a given AP pattern, a stimulus with a given profile consisting of depolarizing and hyperpolarizing signals sent to different subpopulations of cells can evoke switching to another AP pattern. Interestingly, the resulting pattern encodes the profile of the switching stimulus. These results can be extended to different network architectures. Indeed, relaxation oscillators are not only models of cellular pacemakers, bursting or spiking, but are also analogous to firing-rate models of neural activity. We show that rules of switching similar to those found for relaxation oscillators apply to oscillating circuits of excitatory cells interconnected by electrical synapses and cross-inhibition. Our results suggest that incoming information, arriving in a proper time window, may be stored in an oscillatory network in the form of a specific spatio-temporal activity pattern which is expressed until new pertinent information arrives.

Kinase peptide specificity: improved determination and relevance to protein phosphorylation.

Specificity of phosphorylation is critical to signal transduction. Recent emphasis on colocalization of substrate and kinase has eclipsed emphasis on peptide specificity, i.e., kinase preference for particular amino acids surrounding the phosphorylation site. We describe an approach to determining peptide specificity by using positional scanning of biotinylated oriented peptide libraries and insights emerging from those determinations. We accurately determine preference (or disfavor) for residues at a given substrate position (such as P+2) by comparison of in vitro phosphorylation of peptide libraries differing by a single residue at that position. By analysis of all positions near the phosphorylation site, position-specific scoring matrices are generated and used both to understand the basis of specificity and to predict phosphorylation. PKC-delta and -zeta predictions have been validated rigorously by comparisons with measured phosphorylation. The results demonstrate specificity and sensitivity (80-90%) much better than the previous predictive method. These predictions can be accessed at http://mpr.nci.nih.gov. The accuracy of the specificity determination allows identification of an important difference in peptide specificity between these closely related kinases; Ile/Leu at the P-1 position is disfavored by PKC-zeta but not PKC-delta. Our findings and visual representation of peptide specificity highlight the importance of disfavored residues. Finally, analysis of 124 experimentally determined PKC sites from the literature demonstrates a very strong role of peptide specificity in many of those sites. Thus, position-specific scoring matrices generated by this method provide a foundation for quantitative analyses of kinase specificity and improved predictions of previously determined physiologically relevant phosphorylation sites.

Chemokine stimulation of human peripheral blood T lymphocytes induces rapid dephosphorylation of ERM proteins, which facilitates loss of microvilli and polarization.

Lymphocyte microvilli mediate initial rolling-adhesion along endothelium but are lost during transmigration from circulation to tissue. However, the mechanism for resorption of lymphocyte microvilli remains unexplored. We show that chemokine stimulation of human peripheral blood T (PBT) cells is sufficient to induce rapid resorption of microvilli. Microvilli in other cells are regulated by ezrin/radixin/moesin (ERM) proteins, which link the plasma membrane to the cortical F-actin cytoskeleton; maintenance of these linkages requires ERM activation, reflected by phosphorylation at a specific carboxy-terminal threonine residue. Carboxyphosphorylated-ERM (cpERM) proteins in resting PBT cells show a punctate peripheral distribution consistent with localization to microvilli. cpERM dephosphorylation begins within seconds of stimulation by chemokines (stromal derived factor 1 alpha [SDF-1 alpha] or secondary lymphoid tissue cytokine), and ERM proteins lose their punctate distribution with kinetics paralleling the loss of microvilli. The cpERM proteins are preferentially associated with the cytoskeleton at rest and this association is lost with chemokine-induced dephosphorylation. Transfection studies show that a dominant-negative ERM construct destroys microvilli, whereas a construct mimicking cpERM facilitates formation of microvilli, retards chemokine-induced loss of microvilli, and markedly impairs chemokine-induced polarization. Thus, chemokine induces rapid dephosphorylation and inactivation of cpERM, which may in turn facilitate 2 aspects of cytoskeletal reorganization involved in lymphocyte recruitment: loss of microvilli and polarization.