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.

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.

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.

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.

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.

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.

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.

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.

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.

4-Hydroxybenzyl modification of the highly teratogenic retinoid, 4-[(1E)-2-(5,5,8,8-tetramethyl-5,6,7,8-tetrahydro-2-naphthalenyl)-1-propen-1-yl]benzoic acid (TTNPB), yields a compound that induces apoptosis in breast cancer cells and shows reduced teratogenicity.

Retinoids are a class of compounds with structural similarity to vitamin A. These compounds inhibit the proliferation of many cancer cell lines but have had limited medical application as they are often toxic at therapeutic levels. Efforts to synthesize retinoids with a greater therapeutic index have met with limited success. 4-[(1E)-2-(5,5,8,8-tetramethyl-5,6,7,8-tetrahydro-2-naphthalenyl)-1-propen-1-yl]benzoic acid (TTNPB) is one of the most biologically active all-trans-retinoic acid (atRA) analogues and is highly teratogenic. In this study, we show that modification of the TTNPB carboxyl group with an N-(4-hydroxyphenyl)amido (4HPTTNPB) or a 4-hydroxybenzyl (4HBTTNPB) group changes the activity of the compound in cell culture and in vivo. Unlike TTNPB, both compounds induce apoptosis in cancer cells and bind poorly to the retinoic acid receptors (RARs). Like the similarly modified all-trans-retinoic acid (atRA) analogues N-(4-hydroxyphenyl)retinamide (4-HPR/fenretinide) and 4-hydroxybenzylretinone (4-HBR), 4HBTTNPB is a potent activator of components of the ER stress pathway. The amide-linked analogue, 4HPTTNPB, is less toxic to developing embryos than the parent TTNPB, and most significantly, the 4-hydroxybenzyl-modified compound (4HBTTNPB) that cannot be hydrolyzed in vivo to the parent TTNPB compound is nearly devoid of teratogenic liability.

Putative audio recordings of the Ivory-billed Woodpecker (Campephilus principalis).

Putative audio recordings of the Ivory-billed Woodpecker (Campephilus principalis) are presented along with discussions of the videos from which they were extracted and the observations that were made when these data were obtained. On two occasions, high-pitched calls were heard coming from the direction of a bird that was identified in the field as an Ivory-billed Woodpecker. These calls seem to match the description of an alarm call that was reported in the 1930s. One of the videos captured a series of the high-pitched calls, which sound similar to the Blue Jay (Cyanocitta cristata) bell call but do not match published sonograms of that call. A putative double knock, which is characteristic of the Ivory-billed Woodpecker, was captured in another video a little over a minute before a large bird with characteristics consistent with an Ivory-billed Woodpecker flew into view. Since it is extremely difficult to observe this critically endangered species, information on audio clues could have an impact on its conservation.

Experimental testing of the noise-canceling processor.

Signal-processing techniques for localizing an acoustic source buried in noise are tested in a tank experiment. Noise is generated using a discrete source, a bubble generator, and a sprinkler. The experiment has essential elements of a realistic scenario in matched-field processing, including complex source and noise time series in a waveguide with water, sediment, and multipath propagation. The noise-canceling processor is found to outperform the Bartlett processor and provide the correct source range for signal-to-noise ratios below -10 dB. The multivalued Bartlett processor is found to outperform the Bartlett processor but not the noise-canceling processor.

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.

Genetic and pathologic aspects of retinoic acid-induced limb malformations in the mouse.

Because all-trans retinoic acid (atRA) is teratogenic in all species tested and many of the specific defects induced are common across the phylogenetic spectrum, it would be logical to predict that murine strain differences in teratology to this agent are minimal. However, for specific defects, strain susceptibilities are vastly different. Studies with atRA have shown stark differences between C57BL/6 and SWV mouse strains in susceptibility to postaxial forelimb ectrodactyly and ectopic hindlimb formation, with the C57 strain being more susceptible for both defects. Various approaches were used to determine why these strains differ in susceptibility, but the mechanisms remain unknown. Hindlimb duplications were hypothesized to be caused by the formation of ectopic posterior body axes. For forelimb ectrodactyly, a locus on chromosome 11, Rafar, has linkage to the strain difference, and mRNA localization has shown that specific genes (Fgf8, Dlx3, Bmp4, and Sp8) in the postaxial preAER (prior to formation of the apical ectodermal ridge) of the developing limb bud (the site of the defect) were downregulated hours after atRA administration more in the susceptible C57 than in the SWV strain. Because both atRA and divalent cadmium induce postaxial forelimb ectrodactyly (right-sided predominance) at a high rate in C57BL/6 and low in the SWV strain, there is debate as to whether they share a common mechanism. These teratogens cause a greater-than-additive level of forelimb ectrodactyly when coadministered at low doses, but cadmium does not induce ectopic hindlimb formation. The hypothesis is that these agents have separate molecular pathologic pathways that converge to perturb a common anatomic structure.

Sensitivity to cadmium-chloride-induced forelimb ectrodactyly is independent of the p53 gene-dosage in the C57BL/6J mouse.

BACKGROUND: The p53 pathway plays an important role in the regulation of apoptosis, osteoblast differentiation, skeletal development, and teratogenic sensitivity. The administration of cadmium chloride (CdCl(2)) on gestational day 9 in susceptible mouse strains causes postaxial forelimb ectrodactyly in a percentage of fetuses through unknown mechanisms. In this study, the hypothesis that the p53 gene dosage might affect the incidence or severity of CdCl(2)-induced forelimb ectrodactyly was examined. METHODS: Heterozygous p53-null female mice, on the C57BL/6J background known to be sensitive to CdCl(2)-induced forelimb ectrodactyly, were mated with heterozygous males and then treated with a single intraperitoneal (ip) dose of CdCl(2) (4 mg x kg(-1)) at embryonic day (ED) 9. Embryos and fetuses, genotyped using DNA isolated from the yolk sacs, were collected at ED10 and examined for the pattern of cell death in the limb buds or collected at ED18 and examined for limb malformations. RESULTS: In the wild type and heterozygous p53 embryonic limb buds, CdCl(2)-induced apoptosis involved mesenchymal cells as well as the apical ectodermal ridge (AER), whereas CdCl(2)-induced apoptosis was restricted mainly to the AER in the homozygous p53-null limb buds. No difference in the incidence or severity of forelimb ectrodactyly in the embryos of different p53 genotypes was observed. CONCLUSION: Despite the fact that CdCl(2) induced both p53-dependent (in the mesenchyme) and p53-independent (in the AER) cell death in the developing limb bud, CdCl(2)-induced ectrodactyly was independent of the p53 gene dosage at the studied time point.

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.