Leslie B. Hart

Health of Common Bottlenose Dolphins (Tursiops truncatus) in Barataria Bay, Louisiana, Following the Deepwater Horizon Oil Spill

The oil spill resulting from the explosion of the Deepwater Horizon drilling platform initiated immediate concern for marine wildlife, including common bottlenose dolphins in sensitive coastal habitats. To evaluate potential sublethal effects on dolphins, health assessments were conducted in Barataria Bay, Louisiana, an area that received heavy and prolonged oiling, and in a reference site, Sarasota Bay, Florida, where oil was not observed. Dolphins were temporarily captured, received a veterinary examination, and were then released. Dolphins sampled in Barataria Bay showed evidence of hypoadrenocorticism, consistent with adrenal toxicity as previously reported for laboratory mammals exposed to oil. Barataria Bay dolphins were 5 times more likely to have moderate-severe lung disease, generally characterized by significant alveolar interstitial syndrome, lung masses, and pulmonary consolidation. Of 29 dolphins evaluated from Barataria Bay, 48% were given a guarded or worse prognosis, and 17% were considered poor or grave, indicating that they were not expected to survive. Disease conditions in Barataria Bay dolphins were significantly greater in prevalence and severity than those in Sarasota Bay dolphins, as well as those previously reported in other wild dolphin populations. Many disease conditions observed in Barataria Bay dolphins are uncommon but consistent with petroleum hydrocarbon exposure and toxicity.

Skin Lesions on Common Bottlenose Dolphins (Tursiops truncatus) from Three Sites in the Northwest Atlantic, USA

Skin disease occurs frequently in many cetacean species across the globe; methods to categorize lesions have relied on photo-identification (photo-id), stranding, and by-catch data. The current study used photo-id data from four sampling months during 2009 to estimate skin lesion prevalence and type occurring on bottlenose dolphins (Tursiops truncatus) from three sites along the southeast United States coast [Sarasota Bay, FL (SSB); near Brunswick and Sapelo Island, GA (BSG); and near Charleston, SC (CHS)]. The prevalence of lesions was highest among BSG dolphins (P = 0.587) and lowest in SSB (P = 0.380), and the overall prevalence was significantly different among all sites (p<0.0167). Logistic regression modeling revealed a significant reduction in the odds of lesion occurrence for increasing water temperatures (OR = 0.92; 95%CI:0.906–0.938) and a significantly increased odds of lesion occurrence for BSG dolphins (OR = 1.39; 95%CI:1.203–1.614). Approximately one-third of the lesioned dolphins from each site presented with multiple types, and population differences in lesion type occurrence were observed (p<0.05). Lesions on stranded dolphins were sampled to determine the etiology of different lesion types, which included three visually distinct samples positive for herpesvirus. Although generally considered non-fatal, skin disease may be indicative of animal health or exposure to anthropogenic or environmental threats, and photo-id data provide an efficient and cost-effective approach to document the occurrence of skin lesions in free-ranging populations.

The scalable modeling system: directive-based code parallelization for distributed and shared memory computers

A directive-based parallelization tool called the Scalable Modeling System (SMS) is described. The user inserts directives in the form of comments into existing Fortran code. SMS translates the code and directives into a parallel version that runs efficiently on shared and distributed memory high-performance computing platforms including the SGI Origin, IBM SP2, Cray T3E, Sun, and Alpha and Intel clusters. Twenty directives are available to support operations including array re-declarations, inter-process communications, loop translations, and parallel I/O operations. SMS also provides tools to support incremental parallelization and debugging that significantly reduces code parallelization time from months to weeks of effort. SMS is intended for applications using regular structured grids that are solved using finite difference approximation or spectral methods. It has been used to parallelize 10 atmospheric and oceanic models, but the tool is sufficiently general that it can be applied to other structured grids codes. Recent performance comparisons demonstrate that the Eta, Hybrid Coordinate Ocean model and Regional Ocean Modeling System model, parallelized using SMS, perform as well or better than their OpenMP or Message Passing Interface counterparts.

Lacaziosis and lacaziosis-like prevalence among wild, common bottlenose dolphins Tursiops truncatus from the west coast of Florida, USA.

Lacaziosis (lobomycosis; Lacazia loboi) is a fungal skin disease that naturally occurs only in humans and dolphins. The first reported case of lacaziosis in a bottlenose dolphin Tursiops truncatus occurred in 1970 in Sarasota Bay, Florida, USA, and subsequent photo-ID monitoring of the Sarasota Bay dolphin population has revealed persistence of the disease. The objectives of this study were to estimate lacaziosis prevalence (P) in 2 bottlenose dolphin populations on the west coast of Florida (Sarasota Bay and Charlotte Harbor) and compare disease occurrence to other published estimates of lacaziosis in dolphin populations across the globe. Historic photographic records of dolphins captured and released for health assessment purposes (Sarasota Bay) and photo-ID studies (Charlotte Harbor) were screened for evidence of lesions consistent with lacaziosis. Health assessment data revealed a prevalence of lacaziosis in the Sarasota Bay bottlenose dolphin population between 2 and 3%, and analyses of photo-ID data provided a lacaziosis-like prevalence estimate of 2% for Charlotte Harbor dolphins. With the exception of lacaziosis prevalence estimates for dolphins inhabiting the Indian River Lagoon (P = 0.068; P = 0.12), no statistically significant differences were seen among Sarasota Bay, Charlotte Harbor, and other published estimates. Although lacaziosis is a rare disease among these dolphin populations, studies that assess disease burden among different populations can assist with the surveillance of this zoonotic pathogen.

Adrenal Hormones in Common Bottlenose Dolphins (Tursiops truncatus): Influential Factors and Reference Intervals

Inshore common bottlenose dolphins (Tursiops truncatus) are exposed to a broad spectrum of natural and anthropogenic stressors. In response to these stressors, the mammalian adrenal gland releases hormones such as cortisol and aldosterone to maintain physiological and biochemical homeostasis. Consequently, adrenal gland dysfunction results in disruption of hormone secretion and an inappropriate stress response. Our objective herein was to develop diagnostic reference intervals (RIs) for adrenal hormones commonly associated with the stress response (i.e., cortisol, aldosterone) that account for the influence of intrinsic (e.g., age, sex) and extrinsic (e.g., time) factors. Ultimately, these reference intervals will be used to gauge an individual’s response to chase-capture stress and could indicate adrenal abnormalities. Linear mixed models (LMMs) were used to evaluate demographic and sampling factors contributing to differences in serum cortisol and aldosterone concentrations among bottlenose dolphins sampled in Sarasota Bay, Florida, USA (2000–2012). Serum cortisol concentrations were significantly associated with elapsed time from initial stimulation to sample collection (p<0.05), and RIs were constructed using nonparametric methods based on elapsed sampling time for dolphins sampled in less than 30 minutes following net deployment (95% RI: 0.91–4.21 µg/dL) and following biological sampling aboard a research vessel (95% RI: 2.32–6.68 µg/dL). To examine the applicability of the pre-sampling cortisol RI across multiple estuarine stocks, data from three additional southeast U.S. sites were compared, revealing that all of the dolphins sampled from the other sites (N = 34) had cortisol concentrations within the 95th percentile RI. Significant associations between serum concentrations of aldosterone and variables reported in previous studies (i.e., age, elapsed sampling time) were not observed in the current project (p<0.05). Also, approximately 16% of Sarasota Bay bottlenose dolphin aldosterone concentrations were below the assay’s detection limit (11 pg/mL), thus hindering the ability to derive 95th percentile RIs. Serum aldosterone concentrations from animals sampled at the three additional sites were compared to the detection limit, and the proportion of animals with low aldosterone concentrations was not significantly different than an expected prevalence of 16%. Although this study relied upon long-term, free-ranging bottlenose dolphin health data from a single site, the objective RIs can be used for future evaluation of adrenal function among individuals sampled during capture-release health assessments.

Modeling lacaziosis lesion progression in common bottlenose dolphins Tursiops truncatus using long-term photographic records.

Lacaziosis (lobomycosis) is a skin disease caused by Lacazia loboi, occurring naturally only in humans and dolphins. Attempts to culture the pathogen in vitro have been unsuccessful, and inoculation studies of lacaziosis development in mice have provided only limited, short-term data on the progression and propagation of L. loboi. The present study used photographic data from long-term photo-identification and health assessment projects to model and quantify the progression of lacaziosis lesions in 3 common bottlenose dolphins Tursiops truncatus from Sarasota Bay, Florida, USA. Dorsal fin images throughout each animals sighting history were examined for lesion growth, and the proportion of lesion coverage in each photograph was estimated using image analysis tools in Adobe Photoshop. The progression of lacaziosis lesions and lesion growth rates were modeled using a non-linear monomolecular growth model. As data on lacaziosis development and advancement are limited in humans and laboratory animals, dolphins with a long-term case history of the disease may serve as a good animal model to better understand lacaziosis progression. Furthermore, this study demonstrates the utility of long-term population monitoring data for tracking the progression of a poorly understood disease that is relevant to both dolphin and human health.

Parallelizing Operational Weather Forecast Models for Portable and Fast Execution

This paper describes a high-level library (The Nearest Neighbor Tool, NNT) that has been used to parallelize operational weather prediction models. NNT is part of the Scalable Modeling System (SMS), developed at the Forecast Systems Laboratory (FSL). Programs written in NNT rely on SMSs run-time system and port between a wide range of computing platforms, performing well in multiprocessor systems. We show, using examples from operational weather models, how large Fortran 77 codes can be parallelized using NNT. We compare the ease of programmability of NNT and High Performance Fortran (HPF). We also discuss optimizations like data movement overlap (in interprocessor communication and I/O operations), and the minimization of data exchanges through the use of redundant computations. We show that although HPF provides a simpler programming interface, NNT allows for program optimizations that increase performance considerably and still keeps a simple user interface. These optimizations have proven essential to run weather prediction models in real time, and HPF compilers should incorporate them in order to meet operational demands. Throughout the paper, we present performance results of weather models running on a network of workstations, the Intel Paragon, and the SGI Challenge. Finally, we study the cost of programming global address space architectures with NNTs local address space paradigm.

Lacaziosis-like Disease Among Bottlenose Dolphins Tursiops truncatus Photographed in Golfo Dulce, Costa Rica

Lacaziosis (also known as lobomycosis) is a chronic dermal disease caused by the fungal agent Lacazia loboi, which affects both humans and dolphins. Photographic data have been used to identify lacaziosis-like disease (LLD) among dolphins in the waters of North and South America, and here we report LLD in bottlenose dolphins Tursiops truncatus off the coast of Costa Rica, the first reporting in Central American waters. During the periods of 1991 to 1992 and 2010 to 2011, 3 research teams conducted separate dolphin surveys in the Pacific tropical fiord Golfo Dulce, and each documented skin lesions in the resident population of bottlenose dolphins. Photo-ID records were used to identify LLD-affected bottlenose dolphins and to assess their lesions. Findings showed between 13.2 and 16.1% of the identified dolphins exhibited lesions grossly resembling lacaziosis. By combining efforts and cross-referencing photographic data, the teams explored the presence of LLD in Golfo Dulce over a time gap of approximately 20 yr. Our findings expand the geographical range of the disease and offer insight into its longevity within a given population of dolphins.

PERFORMANCE AND PORTABILITY IN PARALLEL COMPUTING: A WEATHER FORECAST VIEW

We have developed a high level library, the Nearest Neighbor Tool (NNT), to facilitate the coding of finite difference approximation weather prediction models on parallel computers. NNT provides portability and ease of programming and at the same time optimizes performance by allowing the overlap of computation and communication to tolerate the latency of remote data moves. In this paper we describe NNT and the implementation of the Well Posed Topographic model (WPT), a finite difference approximation weather prediction model. We present a qualitative study of the performance of the code on various multiprocessors and evaluate the effectiveness of NNT.

Comparison of shared memory and distributed memory parallelisation strategies for grid-based weather forecast models

We have parallelized a grid-based weather forecast model called SEQN using two programming models: shared memory and message passing. By shared memory we mean programming in standard Fortran 77 with directives for parallelism, such as is found on the Kendall Square Research KSR1 parallel supercomputer. For message passing we used the distributed memory Intel Paragon. We have benchmarked both versions of the code on the respective machines, and have run the message passing version on the KSR1 in order to directly compare performance and evaluate the cost of portability. In addition we present first results from the KSR2.<<ETX>>