A model-based approach to designing developmental toxicology experiments using sea urchin embryos.

The key aim of this paper is to suggest a more quantitative approach to designing a dose-response experiment, and more specifically, a concentration-response experiment. The work proposes a departure from the traditional experimental design to determine a dose-response relationship in a developmental toxicology study. It is proposed that a model-based approach to determine a dose-response relationship can provide the most accurate statistical inference for the underlying parameters of interest, which may be estimating one or more model parameters or pre-specified functions of the model parameters, such as lethal dose, at maximal efficiency. When the design criterion or criteria can be determined at the onset, there are demonstrated efficiency gains using a more carefully selected model-based optimal design as opposed to an ad-hoc empirical design. As an illustration, a model-based approach was theoretically used to construct efficient designs for inference in a developmental toxicity study of sea urchin embryos exposed to trimethoprim. This study compares and contrasts the results obtained using model-based optimal designs versus an ad-hoc empirical design.

Application of image processing to evidence for the persistence of the Ivory-billed Woodpecker (Campephilus principalis).

Image processing is used to enhance apparent field marks in video footage that was obtained during three encounters with birds that were identified in the field as Ivory-billed Woodpeckers (Campephilus principalis). Previous analysis of the videos was based on characteristics that are resolved in the raw footage, such as flight path, wing motion, flap rate, behaviors, field marks, and body proportions. Adjusting parameters such as brightness, contrast, and color reveals features consistent with the left dorsal stripe, black leading edges on the dorsal surfaces of the wings, and a red crest that would be consistent with a male of the species. It may be possible to extract additional features from other parts of the videos by applying more advanced processing that allows greater control and analysis of the parameters.

Acoustic recordings and modeling under seasonally varying sea ice.

Acoustic data from the Canada Basin Acoustic Propagation Experiment are discussed. These recordings were obtained under seasonally varying sea ice to the north of Alaska during a period of 154 days. They contain signals from sources that were deployed at ranges of 17.5, 29.6, and 237.8 km and ambient sounds from marine mammals and ice-related events. After the area was covered with ice, the amplitude of receptions from the most distant source gradually decreased as scattering features on the underside of the ice developed during fracturing, drifting, ridging, and rafting events. Improvements are presented for an Arctic acoustic model that is based on the parabolic equation method, and the approach is applied to a problem in which variable ice thickness acts as a loss mechanism by scattering energy out of the waveguide. Some of the recordings have a harmonic signature that is believed to be associated with the resonances of ice floes rubbing together, but variations in the harmonics over short time scales cannot be explained in terms of the resonances of an isolated floe. This behavior may be related to the coupling of vibrations at contact points that vary during the relative motions of floes.

Bird Tissues from Museum Collections Are Reliable for Assessing Avian Haemosporidian Diversity.

Birds harbor a diverse group of haemosporidian parasites that reproduce and develop in the host blood cells, muscle tissue, and various organs, which can cause negative effects on the survival and reproduction of their avian hosts. Characterization of the diversity, distribution, host specificity, prevalence patterns, and phylogenetic relationships of these parasites is critical to the study of avian host-parasite ecology and evolution and for understanding and preventing epidemics in wild bird populations. Here, we tested whether muscle and liver samples collected as part of standard ornithological museum expeditions can be examined to study the diversity and distributions of haemosporidians in the same way as blood collected from individual birds that are typically banded and released. We used a standard molecular diagnostic screening method for mitochondrial DNA (cytochrome b) of the parasites and found that blood, muscle, and liver collected from the same host individual provide similar estimates of prevalence and diversity of haemosporidians from the genera Parahaemoproteus and Leucocytozoon. Although we found higher prevalence for the genus Plasmodium when we screened blood vs. liver and muscle samples, the estimates of the diversity of Plasmodium from different tissue types are not affected at the community level. Given these results, we conclude that for several reasons existing museum genetic resources collections are valuable data sources for the study of haemosporidians. First, ornithological museum collections around the world house tens of thousands of vouchered tissue samples collected from remote regions of the world. Second, the host specimens are vouchered and thus host identification and phenotype are permanently documented in databased archives with a diversity of associated ancillary data. Thus, not only can identifications be confirmed but also a diversity of morphological measurements and data can be measured and accessed for these host specimens in perpetuity.

Avian host composition, local speciation and dispersal drive the regional assembly of avian malaria parasites in South American birds.

Identifying the ecological factors that shape parasite distributions remains a central goal in disease ecology. These factors include dispersal capability, environmental filters and geographic distance. Using 520 haemosporidian parasite genetic lineages recovered from 7,534 birds sampled across tropical and temperate South America, we tested (a) the latitudinal diversity gradient hypothesis and (b) the distance-decay relationship (decreasing proportion of shared species between communities with increasing geographic distance) for this host-parasite system. We then inferred the biogeographic processes influencing the diversity and distributions of this cosmopolitan group of parasites across South America. We found support for a latitudinal gradient in diversity for avian haemosporidian parasites, potentially mediated through higher avian host diversity towards the equator. Parasite similarity was correlated with climate similarity, geographic distance and host composition. Local diversification in Amazonian lineages followed by dispersal was the most frequent biogeographic events reconstructed for haemosporidian parasites. Combining macroecological patterns and biogeographic processes, our study reveals that haemosporidian parasites are capable of circumventing geographic barriers and dispersing across biomes, although constrained by environmental filtering. The contemporary diversity and distributions of haemosporidian parasites are mainly driven by historical (speciation) and ecological (dispersal) processes, whereas the parasite community assembly is largely governed by host composition and to a lesser extent by environmental conditions.

Publisher Correction: Periodic and transient motions of large woodpeckers.

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.

Periodic and transient motions of large woodpeckers.

Two types of periodic and transient motions of large woodpeckers are considered. A drumming woodpecker may be modeled as a harmonic oscillator with a periodic forcing function. The transient behavior that occurs after the forcing is turned off suggests that the double knocks of Campephilus woodpeckers may be modeled in terms of a harmonic oscillator with an impulsive forcing, and this hypothesis is consistent with audio and video recordings. Wingbeats are another type of periodic and transient motion of large woodpeckers. A model for the flap rate in cruising flight is applied to the Pileated Woodpecker (Dryocopus pileatus) and the Ivory-billed Woodpecker (Campephilus principalis). During a brief transient just after taking off, the wing motion and flap rate of a large woodpecker may not be the same as in cruising flight. These concepts are relevant to videos that contain evidence for the persistence of the Ivory-billed Woodpecker.

Video evidence and other information relevant to the conservation of the Ivory-billed Woodpecker (Campephilus principalis).

Despite the publication of three independent papers that reported sightings of the Ivory-billed Woodpecker (Campephilus principalis), its preservation became a controversial topic because nobody has been able to obtain a distinct photo, which is considered the standard form of evidence for documenting birds. An analysis based on a combination of factors related to habitat and behavior suggests that the expected waiting time for obtaining a distinct photo of an Ivory-billed Woodpecker is several orders of magnitude greater than it would be for a more typical baseline species of comparable rarity. Given these difficulties and the time pressure involved to ensure the conservation of this species, this paper discusses the need to use a different approach for an exceptional case. Presented here are three videos that show birds with flights, behaviors, field marks, and other characteristics that are consistent with the Ivory-billed Woodpecker but no other species inhabiting the region.

Integrating the context-appropriate balanced attention model and reinforcement sensitivity theory: Towards a domain-general personality process model.

Over the last 40 years or more the personality literature has been dominated by trait models based on the Big Five (B5). Trait-based models describe personality at the between-person level but cannot explain the within-person mental mechanisms responsible for personality. Nor can they adequately account for variations in emotion and behavior experienced by individuals across different situations and over time. An alternative, yet understated, approach to personality architecture can be found in neurobiological theories of personality, most notably reinforcement sensitivity theory (RST). In contrast to static trait-based personality models like the B5, RST provides a more plausible basis for a personality process model, namely, one that explains how emotions and behavior arise from the dynamic interaction between contextual factors and within-person mental mechanisms. In this article, the authors review the evolution of a neurobiologically based personality process model based on RST, the response modulation model and the context-appropriate balanced attention model. They argue that by integrating this complex literature, and by incorporating evidence from personality neuroscience, one can meaningfully explain personality at both the within- and between-person levels. This approach achieves a domain-general architecture based on RST and self-regulation that can be used to align within-person mental mechanisms, neurobiological systems and between-person measurement models. (PsycINFO Database Record

Prevalence of avian haemosporidian parasites is positively related to the abundance of host species at multiple sites within a region.

Parasite prevalence is thought to be positively related to host population density owing to enhanced contagion. However, the relationship between prevalence and local abundance of multiple host species is underexplored. We surveyed birds and their haemosporidian parasites (genera Plasmodium and Haemoproteus) at multiple sites across eastern North America to test whether the prevalence of these parasites in a host species at a particular site is related to that host's local abundance. Prevalence was positively related to host abundance within most sites, although the effect was stronger and more consistent for Plasmodium than for Haemoproteus. In contrast, prevalence was not related to variation in the abundance of most individual host species among sites across the region. These results suggest that parasite prevalence partly reflects the relative abundances of host species in local assemblages. However, three nonnative host species had low prevalence despite being relatively abundant at one site, as predicted by the enemy release hypothesis.

Local host specialization, host-switching, and dispersal shape the regional distributions of avian haemosporidian parasites.

The drivers of regional parasite distributions are poorly understood, especially in comparison with those of free-living species. For vector-transmitted parasites, in particular, distributions might be influenced by host-switching and by parasite dispersal with primary hosts and vectors. We surveyed haemosporidian blood parasites (Plasmodium and Haemoproteus) of small land birds in eastern North America to characterize a regional parasite community. Distributions of parasite populations generally reflected distributions of their hosts across the region. However, when the interdependence between hosts and parasites was controlled statistically, local host assemblages were related to regional climatic gradients, but parasite assemblages were not. Moreover, because parasite assemblage similarity does not decrease with distance when controlling for host assemblages and climate, parasites evidently disperse readily within the distributions of their hosts. The degree of specialization on hosts varied in some parasite lineages over short periods and small geographic distances independently of the diversity of available hosts and potentially competing parasite lineages. Nonrandom spatial turnover was apparent in parasite lineages infecting one host species that was well-sampled within a single year across its range, plausibly reflecting localized adaptations of hosts and parasites. Overall, populations of avian hosts generally determine the geographic distributions of haemosporidian parasites. However, parasites are not dispersal-limited within their host distributions, and they may switch hosts readily.

Treatment of ice cover and other thin elastic layers with the parabolic equation method.

The parabolic equation method is extended to handle problems involving ice cover and other thin elastic layers. Parabolic equation solutions are based on rational approximations that are designed using accuracy constraints to ensure that the propagating modes are handled properly and stability constrains to ensure that the non-propagating modes are annihilated. The non-propagating modes are especially problematic for problems involving thin elastic layers. It is demonstrated that stable results may be obtained for such problems by using rotated rational approximations [Milinazzo, Zala, and Brooke, J. Acoust. Soc. Am. 101, 760-766 (1997)] and generalizations of these approximations. The approach is applied to problems involving ice cover with variable thickness and sediment layers that taper to zero thickness.

Treatment of a sloping fluid-solid interface and sediment layering with the seismo-acoustic parabolic equation.

The parabolic equation method is extended to handle problems in seismo-acoustics that have multiple fluid and solid layers, continuous depth dependence within layers, and sloping interfaces between layers. The medium is approximated in terms of a series of range-independent regions, and a single-scattering approximation is used to compute transmitted fields across the vertical interfaces between regions. The approach is implemented in terms of a set of dependent variables that is well suited to piecewise continuous depth dependence in the elastic parameters, but one of the fluid-solid interface conditions in that formulation involves a second derivative that complicates the treatment of sloping interfaces. This issue is resolved by using a non-centered, four-point difference formula for the second derivative. The approach is implemented using a matrix decomposition that is efficient when the parameters of the medium have a general dependence within the upper layers of the sediment but only depend on depth in the water column and deep within the sediment.

Two parabolic equations for propagation in layered poro-elastic media.

Parabolic equation methods for fluid and elastic media are extended to layered poro-elastic media, including some shallow-water sediments. A previous parabolic equation solution for one model of range-independent poro-elastic media [Collins et al., J. Acoust. Soc. Am. 98, 1645-1656 (1995)] does not produce accurate solutions for environments with multiple poro-elastic layers. First, a dependent-variable formulation for parabolic equations used with elastic media is generalized to layered poro-elastic media. An improvement in accuracy is obtained using a second dependent-variable formulation that conserves dependent variables across interfaces between horizontally stratified layers. Furthermore, this formulation expresses conditions at interfaces using no depth derivatives higher than first order. This feature should aid in treating range dependence because convenient matching across interfaces is possible with discretized derivatives of first order in contrast to second order.

Nonuniform depth grids in parabolic equation solutions.

The parabolic wave equation is solved using a finite-difference solution in depth that involves a nonuniform grid. The depth operator is discretized using Galerkin's method with asymmetric hat functions. Examples are presented to illustrate that this approach can be used to improve efficiency for problems in ocean acoustics and seismo-acoustics. For shallow water problems, accuracy is sensitive to the precise placement of the ocean bottom interface. This issue is often addressed with the inefficient approach of using a fine grid spacing over all depth. Efficiency may be improved by using a relatively coarse grid with nonuniform sampling to precisely position the interface. Efficiency may also be improved by reducing the sampling in the sediment and in an absorbing layer that is used to truncate the computational domain. Nonuniform sampling may also be used to improve the implementation of a single-scattering approximation for sloping fluid-solid interfaces.

The checkered history of checkerboard distributions.

To address the idea that the process of interspecific competition can be inferred from data on geographical distribution alone and that evidence from geographical distribution implies an important role for interspecific competition in shaping ecological communities, we reexamine the occurrence of "true checkerboard" distributions among the land and freshwater birds in three Melanesian archipelagoes: Vanuatu, the Bismarck Archipelago, and the Solomon Islands. We use the most recently published distributional records and explicitly include the geography of the distributions of species within each archipelago. We use the overlap of convex hulls to estimate the overlap in the geographic range for each pair of species in each of these archipelagoes. We define a "true checkerboard" to consist of a pair of species with exclusive island-by-island distributions, but that have overlapping geographical ranges. To avoid the "dilution effect," we follow Diamond and Gilpin in focusing only on congeneric and within-guild species pairs as potential competitors. Few, if any, "true checkerboards" exist in these archipelagoes that could possibly have been influenced by competitive interactions, and even "true checkerboards" can arise for reasons other than interspecific competition. The similarity between related species pairs (congeneric and within-guild pairs) and unrelated species pairs in their deviation from expectation of the number of islands shared and the overlap of their geographic ranges indicates that these are not distinct statistical populations, but rather a single population of species pairs. Our result, which is based on an examination of the distributional data alone, is consistent with the interpretation that, in these avifaunas, the distributions of congeneric, within-guild, and unrelated species pairs are shaped by a common set of biological and physical environmental processes.

A single-scattering correction for the seismo-acoustic parabolic equation.

An efficient single-scattering correction that does not require iterations is derived and tested for the seismo-acoustic parabolic equation. The approach is applicable to problems involving gradual range dependence in a waveguide with fluid and solid layers, including the key case of a sloping fluid-solid interface. The single-scattering correction is asymptotically equivalent to a special case of a single-scattering correction for problems that only have solid layers [Küsel et al., J. Acoust. Soc. Am. 121, 808-813 (2007)]. The single-scattering correction has a simple interpretation (conservation of interface conditions in an average sense) that facilitated its generalization to problems involving fluid layers. Promising results are obtained for problems in which the ocean bottom interface has a small slope.

Single-scattering parabolic equation solutions for elastic media propagation, including Rayleigh waves.

The parabolic equation method with a single-scattering correction allows for accurate modeling of range-dependent environments in elastic layered media. For problems with large contrasts, accuracy and efficiency are gained by subdividing vertical interfaces into a series of two or more single-scattering problems. This approach generates several computational parameters, such as the number of interface slices, an iteration convergence parameter τ, and the number of iterations n for convergence. Using a narrow-angle approximation, the choices of n=1 and τ=2 give accurate solutions. Analogous results from the narrow-angle approximation extend to environments with larger variations when slices are used as needed at vertical interfaces. The approach is applied to a generic ocean waveguide that includes the generation of a Rayleigh interface wave. Results are presented in both frequency and time domains.

Experimental testing of the variable rotated elastic parabolic equation.

A series of laboratory experiments was conducted to obtain high-quality data for acoustic propagation in shallow water waveguides with sloping elastic bottoms. Accurate modeling of transmission loss in these waveguides can be performed with the variable rotated parabolic equation method. Results from an earlier experiment with a flat or sloped slab of polyvinyl chloride (PVC) demonstrated the necessity of accounting for elasticity in the bottom and the ability of the model to produce benchmark-quality agreement with experimental data [J. M. Collis et al., J. Acoust. Soc. Am. 122, 1987-1993 (2007)]. This paper presents results of a second experiment, using two PVC slabs joined at an angle to create a waveguide with variable bottom slope. Acoustic transmissions over the 100-300 kHz band were received on synthetic horizontal arrays for two source positions. The PVC slabs were oriented to produce three different simulated waveguides: flat bottom followed by downslope, upslope followed by flat bottom, and upslope followed by downslope. Parabolic equation solutions for treating variable slopes are benchmarked against the data.