Jonas Reijniers

Biomimetic Sonar System Performing Spectrum-Based Localization

In this paper, we study echolocation by spectral analysis as a biomimetic, i.e., inspired by bats, mechanism to observe a realistic environment. We propose a method to localize, i.e., to estimate the distance and bearing of reflectors, on the basis of a time-frequency representation of the returned echo similar to the one derived by the bats cochlea. The sonar system consists of a central transmitter, and two receivers pointing plusmn5deg outward. The method proposed reconstructs the environment by comparing the returned echoes with binaural spectral templates corresponding with echoes from different angles. We further show that a distance matrix defined on the set of templates can be used as a measure of their accuracy and reliability for localization purposes. We include experimental results that validate the system and indicate that it can deal with the complex echo signals received when confronted with realistic reflectors, i.e., possibly consisting of a large number of closely spaced scatterers.

Simulated head related transfer function of the phyllostomid bat Phyllostomus discolor

UNLABELLED This paper presents a calculation of the head related transfer function (HRTF) for the frontal hemisphere of the phyllostomid bat Phyllostomus discolor using an acoustic field simulation tool based on the boundary element method. From the calculated HRTF results, binaural interaural intensity differences (IIDs) are derived. THE RESULTS Region of highest sensitivity, HRTF patterns, and IID patterns are shown to be in good agreement with earlier experimental measurements on other specimens of the same bat species, i.e., the differences are within the interspecies variability range. Next, it is argued that the proposed simulation method offers distinct advantages over acoustic measurements on real bat specimens. To illustrate this, it is shown how computer manipulation of the virtual morphology model allows a more detailed comprehension of bat spatial hearing by investigating the effects of different head parts on the HRTF. From this analysis it is concluded that for this species the pinna has a significantly larger effect on the HRTF and IID patterns than the head itself. This conclusion argues in favor of a series of recent simulation studies based on pinna morphology only [R. Muller, J. Acoust. Soc. Am. 116, 3701-3712 (2004); Muller et al., ibid 119, 4083-4092 (2006)].

A curve of thresholds governs plague epizootics in Central Asia.

A core concept of infectious disease epidemiology is the abundance threshold, below which an infection is unable to invade or persist. There have been contrasting theoretical predictions regarding the nature of this threshold for vector-borne diseases, but for infections with an invertebrate vector, it is common to assume a threshold defined by the ratio of vector and host abundances. Here, we show in contrast, both from field data and model simulations, that for plague (Yersinia pestis) in Kazakhstan, the invasion threshold quantity is based on the product of its host (Rhombomys opimus) and vector (mainly Xenopsylla spp.) abundances, resulting in a combined threshold curve with hyperbolic shape. This shape implies compensation between host and vector abundances in permitting infection, which has important implications for disease control. Realistic joint thresholds, supported by data, should promote improved understanding, prediction and management of disease occurrence in this and other vector-borne disease systems.

A Novel Method to Reduce Time Investment When Processing Videos from Camera Trap Studies

Camera traps have proven very useful in ecological, conservation and behavioral research. Camera traps non-invasively record presence and behavior of animals in their natural environment. Since the introduction of digital cameras, large amounts of data can be stored. Unfortunately, processing protocols did not evolve as fast as the technical capabilities of the cameras. We used camera traps to record videos of Eurasian beavers (Castor fiber). However, a large number of recordings did not contain the target species, but instead empty recordings or other species (together non-target recordings), making the removal of these recordings unacceptably time consuming. In this paper we propose a method to partially eliminate non-target recordings without having to watch the recordings, in order to reduce workload. Discrimination between recordings of target species and non-target recordings was based on detecting variation (changes in pixel values from frame to frame) in the recordings. Because of the size of the target species, we supposed that recordings with the target species contain on average much more movements than non-target recordings. Two different filter methods were tested and compared. We show that a partial discrimination can be made between target and non-target recordings based on variation in pixel values and that environmental conditions and filter methods influence the amount of non-target recordings that can be identified and discarded. By allowing a loss of 5% to 20% of recordings containing the target species, in ideal circumstances, 53% to 76% of non-target recordings can be identified and discarded. We conclude that adding an extra processing step in the camera trap protocol can result in large time savings. Since we are convinced that the use of camera traps will become increasingly important in the future, this filter method can benefit many researchers, using it in different contexts across the globe, on both videos and photographs.

Density thresholds for Mopeia virus invasion and persistence in its host **Mastomys natalensis**

Well-established theoretical models predict host density thresholds for invasion and persistence of parasites with a density-dependent transmission. Studying such thresholds in reality, however, is not obvious because it requires long-term data for several fluctuating populations of different size. We developed a spatially explicit and individual-based SEIR model of Mopeia virus in multimammate mice Mastomys natalensis. This is an interesting model system for studying abundance thresholds because the host is the most common African rodent, populations fluctuate considerably and the virus is closely related to Lassa virus but non-pathogenic to humans so can be studied safely in the field. The simulations show that, while host density clearly is important, sharp thresholds are only to be expected for persistence (and not for invasion), since at short time-spans (as during invasion), stochasticity is determining. Besides host density, also the spatial extent of the host population is important. We observe the repeated local occurrence of herd immunity, leading to a decrease in transmission of the virus, while even a limited amount of dispersal can have a strong influence in spreading and re-igniting the transmission. The model is most sensitive to the duration of the infectious stage, the size of the home range and the transmission coefficient, so these are important factors to determine experimentally in the future.

The CIRCE head: a biomimetic sonar system

The investigation of biomimetic perception is part of the broader research field of biorobotics which aims to investigate biological sensorimotor control systems by building robot models of them. The intent of bio-inspired engineering is to distil from the principles found in successful nature-tested mechanisms specific ”crucial functions” [1]. In addition to its interest for engineers, we believe that the CIRCE biomimetic sonar system, a robotic system which reproduces, at a functional level, the echolocation system of bats, is a unique experimental tool for biologists to systematically investigate how the world is not just perceived but actively explored by bats.

Plague epizootic cycles in Central Asia

Infection thresholds, widely used in disease epidemiology, may operate on host abundance and, if present, on vector abundance. For wildlife populations, host and vector abundances often vary greatly across years and consequently the threshold may be crossed regularly, both up- and downward. Moreover, vector and host abundances may be interdependent, which may affect the infection dynamics. Theory predicts that if the relevant abundance, or combination of abundances, is above the threshold, then the infection is able to spread; if not, it is bound to fade out. In practice, though, the observed level of infection may depend more on past than on current abundances. Here, we study the temporal dynamics of plague (Yersinia pestis infection), its vector (flea) and its host (great gerbil) in the PreBalkhash region in Kazakhstan. We describe how host and vector abundances interact over time and how this interaction drives the dynamics of the system around the infection threshold, consequently affecting the proportion of plague-infected sectors. We also explore the importance of the interplay between biological and detectability delays in generating the observed dynamics.

Spatial distribution patterns of plague hosts : point pattern analysis of the burrows of great gerbils in Kazakhstan

Abstract Aim The spatial structure of a population can strongly influence the dynamics of infectious diseases, yet rarely is the underlying structure quantified. A case in point is plague, an infectious zoonotic disease caused by the bacterium Yersinia pestis. Plague dynamics within the Central Asian desert plague focus have been extensively modelled in recent years, but always with strong uniformity assumptions about the distribution of its primary reservoir host, the great gerbil (Rhombomys opimus). Yet, while clustering of this species’ burrows due to social or ecological processes could have potentially significant effects on model outcomes, there is currently nothing known about the spatial distribution of inhabited burrows. Here, we address this knowledge gap by describing key aspects of the spatial patterns of great gerbil burrows in Kazakhstan. Location Kazakhstan. Methods Burrows were classified as either occupied or empty in 98 squares of four different sizes: 200 m (side length), 250 m, 500 m and 590–1020 m. We used Ripleys K statistic to determine whether and at what scale there was clustering of occupied burrows, and semi‐variograms to quantify spatial patterns in occupied burrows at scales of 250 m to 9 km. Results Significant spatial clustering of occupied burrows occurred in 25% and 75% of squares of 500 m and 590–1020 m, respectively, but not in smaller squares. In clustered squares, the clustering criterion peaked around 250 m. Semi‐variograms showed that burrow density was auto‐correlated up to a distance of 7 km and occupied density up to 2.5 km. Main conclusions These results demonstrate that there is statistically significant spatial clustering of occupied burrows and that the uniformity assumptions of previous plague models should be reconsidered to assess its significance for plague transmission. This field evidence will allow for more realistic approaches to disease ecology models for both this system and for other structured host populations.

Estimating Time of Infection Using Prior Serological and Individual Information Can Greatly Improve Incidence Estimation of Human and Wildlife Infections.

Diseases of humans and wildlife are typically tracked and studied through incidence, the number of new infections per time unit. Estimating incidence is not without difficulties, as asymptomatic infections, low sampling intervals and low sample sizes can introduce large estimation errors. After infection, biomarkers such as antibodies or pathogens often change predictably over time, and this temporal pattern can contain information about the time since infection that could improve incidence estimation. Antibody level and avidity have been used to estimate time since infection and to recreate incidence, but the errors on these estimates using currently existing methods are generally large. Using a semi-parametric model in a Bayesian framework, we introduce a method that allows the use of multiple sources of information (such as antibody level, pathogen presence in different organs, individual age, season) for estimating individual time since infection. When sufficient background data are available, this method can greatly improve incidence estimation, which we show using arenavirus infection in multimammate mice as a test case. The method performs well, especially compared to the situation in which seroconversion events between sampling sessions are the main data source. The possibility to implement several sources of information allows the use of data that are in many cases already available, which means that existing incidence data can be improved without the need for additional sampling efforts or laboratory assays.

Information generated by the moving pinnae of Rhinolophus rouxi: tuning of the morphology at different harmonics.

Bats typically emit multi harmonic calls. Their head morphology shapes the emission and hearing sound fields as a function of frequency. Therefore, the sound fields are markedly different for the various harmonics. As the sound field provides bats with all necessary cues to locate objects in space, different harmonics might provide them with variable amounts of information about the location of objects. Also, the ability to locate objects in different parts of the frontal hemisphere might vary across harmonics. This paper evaluates this hypothesis in R. rouxi, using an information theoretic framework. We estimate the reflector position information transfer in the echolocation system of R. rouxi as a function of frequency. This analysis shows that localization performance reaches a global minimum and a global maximum at the two most energetic frequency components of R. rouxi call indicating tuning of morphology and harmonic structure. Using the fundamental the bat is able to locate objects in a large portion of the frontal hemisphere. In contrast, using the 1 overtone, it can only locate objects, albeit with a slightly higher accuracy, in a small portion of the frontal hemisphere by reducing sensitivity to echoes from outside this region of interest. Hence, different harmonic components provide the bat either with a wide view or a focused view of its environment. We propose these findings can be interpreted in the context of the foraging behaviour of R. rouxi, i.e., hunting in cluttered environments. Indeed, the focused view provided by the 1 overtone suggests that at this frequency its morphology is tuned for clutter rejection and accurate localization in a small region of interest while the finding that overall localization performance is best at the fundamental indicates that the morphology is simultaneously tuned to optimize overall localization performance at this frequency.