Statistical models for animal telemetry data with applications to harbor seals in the Gulf of Alaska

2017 Spring.Includes bibliographical references.Much is known about the general biology and natural history of harbor seals (Phoca vitulina), but questions remain about the aquatic and terrestrial space use of these marine mammals. This is in large part because methods for examining the spatial ecology of harbor seals are poorly developed. The objective of this dissertation is to pair existing telemetry data with contemporary spatio-temporal modeling to quantify the space use and resource selection of harbor seals in the coastal waters of southern Alaska. Recent extensions to models for analyzing animal telemetry data address complications such as autocorrelation and telemetry measurement error; however, additional challenges remain, especially in the context of analyzing Argos satellite telemetry data collected on marine mammals like harbor seals. For example, existing methods assume elliptical (or circular) patterns of measurement error, even though Argos satellite telemetry devices impose more complicated error structures on the data. Constraints, or barriers, to animal movement present another complication. Harbor seals and other marine mammals are constrained to move within the marine environment, and mechanistic models that do not adhere to movement barriers yield unreliable inference. Therefore, a primary goal of this research is to develop statistical tools that account for these nuances and provide rigorous, ecologically relevant inference. Even though the models presented in this dissertation were specifically developed with Argos satellite telemetry data and harbor seals in mind, the methods are general and can be applied to other species and types of telemetry data. This dissertation consists of five chapters. In Chapter 1, I briefly discuss the general biology of harbor seals, focusing on what is known about their spatial habits in Alaska. I then summarize trends in Alaskan harbor seal abundance, a topic that motivated my research as well as the work of many others. I describe the existing Alaska Department of Fish and Game telemetry data sets that are available for examining harbor seal spatial ecology, commonly-used statistical methods for analyzing animal telemetry data, and conclude with the objectives of my research and an outline for the remainder of the dissertation. In Chapter 2, I propose an approach for obtaining resource selection inference from animal location data that accounts for complicated error structures, movement constraints, and temporally autocorrelated observations. The model consists of two general components: a model for the true, but unobserved, animal locations that reflects prior knowledge about constraints to animal movement, and a model for the observed telemetry locations that is conditional on the true locations. I apply the model to simulated data, showing that it outperforms common ad hoc approaches used when confronted with telemetry measurement error and movement constraints. I then apply the framework to obtain inference concerning aquatic resource selection and space use for harbor seals near Kodiak Island, Alaska. Chapters 3 and 4 shift the focus from inference concerning aquatic space use and resource selection, to inference concerning the use of coastal resources (i.e., haul-out sites) by harbor seals. In Chapter 3, I present a fully model-based approach for estimating the location of central places (e.g., haul-out sites, dens, nests, etc.) from telemetry data that accounts for multiple sources of uncertainty and uses all of the available locational data. The model consists of an observation model to account for large telemetry measurement error and animal movement, and a highly flexible mixture model (a Dirichlet process) to identify the location of central places. Ancillary behavioral data (e.g., harbor seal dive data obtained from the satellite-linked depth recorders) are also incorporated into the modeling framework to obtain inference concerning temporal patterns in central place use. Based on the methods developed in Chapter 3, I present a comprehensive analysis of the spatio-temporal patterns of haul-out use for harbor seals near Kodiak Island in Chapter 4. Chapter 4 also extends previously developed methods to examine the affect of covariates on haul-out site selection and to obtain population-level inference concerning haul-out use. I conclude, in Chapter 5, with some general thoughts about analyzing animal telemetry data, as well as potential future research directions

Implementation of an Advanced Training Program to Increase Nurses’ Knowledge of Continuous Renal Replacement Therapy Management

Background: Continuous renal replacement therapy (CRRT) is a complex, life-preserving treatment for unstable patients who require hemodialysis in the intensive care unit (ICU). Nurses responsible for managing the CRRT machine in this large academic medical center’s cardiovascular ICU (CVICU) complete a one-hour basic training course focused on setting up the machine, responding to basic alarms, and changing out the CRRT circuit when necessary. Staff nurses, advanced practice providers (APPs), and nursing administrators agree that training is insufficient. Research evidence supports rigorous staff training as essential to improving the quality of CRRT delivery. Purpose: This Doctor of Nursing Practice (DNP) project purposed to implement an advanced CRRT training program for nurses and APPs in the hospital’s CVICU to (a) increase participants’ CRRT knowledge and to improve management and troubleshooting skills; (b) improve CRRT delivery in the CVICU; (c) evaluate participants’ perception of training program effectiveness. Intervention: An advanced CRRT training program was implemented. Participants attended a four-hour CRRT training course provided by the clinical educator for the CRRT machine manufacturer. Methods: To assess the impact of the intervention on CRRT knowledge, participants completed a CRRT knowledge test before and after the training course. To assess the impact of the intervention on CRRT delivery, post-intervention data from the CRRT machines was compared to pre-intervention data for the following CRRT-specific outcomes of interest: downtime, dosing target accuracy, filter life, number of unnecessary filter changes, filters used per treatment day, and filter expense. To assess the impact of the intervention on perceived competency, participants were asked to complete pre- and post-intervention surveys. Statistical analyses were performed to compare pre-intervention to post-intervention data. Results: The advanced CRRT training course was attended by 25 participants. Participants had a statistically significant increase in knowledge as evidenced by the difference between pre- (59.37%, SD=8.46%) and post-intervention (82.54%, SD=6.63%) CRRT knowledge test scores (p=Conclusions: Implementation of an advanced training program is an essential first step toward increasing nurses’ knowledge and improving CRRT management and troubleshooting skills

Comparing linkage designs based on land facets to linkage designs based on focal species

Least-cost modeling for focal species is the most widely used method for designing conservation corridors and linkages. However, these designs depend on today's land covers, which will be altered by climate change. We recently proposed an alternative approach based on land facets (recurring landscape units of relatively uniform topography and soils). The rationale is that corridors with high continuity of individual land facets will facilitate movement of species associated with each facet today and in the future. Conservation practitioners might like to know whether a linkage design based on land facets is likely to provide continuity of modeled breeding habitat for species needing connectivity today, and whether a linkage for focal species provides continuity and interspersion of land facets. To address these questions, we compared linkages designed for focal species and land facets in three landscapes in Arizona, USA. We used two variables to measure linkage utility, namely distances between patches of modeled breeding habitat for 5–16 focal species in each linkage, and resistance profiles for focal species and land facets between patches connected by the linkage. Compared to focal species designs, linkage designs based on land facets provided as much or more modeled habitat connectivity for 25 of 28 species-landscape combinations, failing only for the three species with the most narrowly distributed habitat. Compared to land facets designs, focal species linkages provided lower connectivity for about half the land facets in two landscapes. In areas where a focal species approach to linkage design is not possible, our results suggest that conservation practitioners may be able to implement a land facets approach with some confidence that the linkage design would serve most potential focal species. In areas where focal species designs are possible, we recommend using the land facet approach to complement, rather than replace, focal species approaches

Assessing radiative transfer models trained by numerical weather forecasts using sun-tracking radiometric measurements for satellite link characterization up to W band

Radio communications, and in particular Earth-to-satellite links, are worldwide used for delivering digital services. The bandwidth demand of such services is increasing accordingly to the advent of more advanced applications (e.g., multimedia services, deep-space explorations, etc.) thus pushing the scientific community toward the investigation of channel carriers at higher frequencies. When using carrier frequencies above X band, the main drawback is how to tackle the impact of tropospheric processes (i.e., rain, cloud, water vapor). This work assesses the joint use of weather forecast models, radiative transfer models and Sun-tracking radiometric measurements to explore their potential benefits in predicting path attenuation and sky noise temperature for slant paths at frequencies between K and W band, thus paving the way to the optimization of satellite link-budgets

Conservation implications of sea turtle nesting trends: elusive recovery of a globally important loggerhead population

Abstract Understanding population status and trends is important for developing and evaluating management and conservation actions for threatened species. Monitoring population status of marine organisms is especially challenging. Because sea turtles come ashore to lay their eggs and nests are easily counted, these counts are commonly used as an index of abundance and population trends. Nest counts do not provide a direct index of adult female population abundance because females typically lay more than one nest per year and most do not reproduce every year. This study attempts for the first time to investigate the likelihood that observed fluctuations of nest counts represent inter‐annual changes of the adult female population by accounting for uncertainty in reproductive rate parameters. We analyzed 30 yr of reproductive data from the largest nesting loggerhead sea turtle population worldwide, breeding in Florida (USA), and for the three Recovery Units and seven Management Units therein. Nest counts followed a general non‐monotonic trend with wide fluctuations that corresponded to decreasing and increasing trends during short intervals. When we accounted for uncertainty in both clutch frequency and remigration interval, there was no evidence for an increasing or a declining trend in the breeding female population across the entire period. Despite extensive conservation efforts and protections for loggerheads in Florida and the wider USA, we did not find evidence of a strong population recovery. We recommend maintaining a high level of protection, addressing persistent anthropogenic threats, continued collection of rigorous nest‐count data, and monitoring reproductive parameters to better link nest counts to adult female population abundance. Our results demonstrate the need for caution in using nest counts as a direct proxy for adult female population status, as it may lead to unsupported conclusions potentially detrimental to conservation. Therefore, we recommend to always translating nest trends to at least adult female trends, including uncertainty in reproductive parameters. Our approach can be exported to other populations, even where reproductive parameters are not available. Applying high parameter uncertainty obtained from other populations can help identifying unequivocal population changes; that is, nest trends unlikely justified by uncertainty and poor knowledge of reproductive parameters

An effective approach to choosing project, program and portfolio management software at a large and geographically diverse company

Thesis (M.B.A.)--Massachusetts Institute of Technology, Sloan School of Management; and, (S.M.)--Massachusetts Institute of Technology, Engineering Systems Division; in conjunction with the Leaders for Manufacturing Program at MIT, 2009.Includes bibliographical references (leaves 72-77).Selecting and deploying an IT tool can be very complicated and expensive. This paper studies a particular approach to choosing project, program and portfolio management software at one large and geographically diverse company in the Electronics Manufacturing Services (EMS) industry, Voltaform. Though there are many ways to approach this task, significant thought should go into which one is chosen for each particular company and its situation. This document addresses the approach taken at VoltaForm as well as the reasoning behind it. It describes developing a business case focused on end user needs for the new software, including the detailed data analysis techniques used to evaluate the end user needs. It also describes certain aspects of the deployment of the software once chosen. The purpose of this paper is to provide guidance and examples for anyone faced with a similar task.by Missy M. Brost.S.M.M.B.A

Cloning and functional characterization of the fatty acid elongase 1 (FAE1) gene from high erucic Crambe abyssinica cv. Prophet.

A genomic fatty acid elongation 1 (FAE1) clone was isolated from Crambe abyssinica. The genomic clone corresponds to a 1521-bp open reading frame, which encodes a protein of 507 amino acids. In yeast cells expression of CrFAE led to production of new very long chain monounsaturated fatty acids such as eicosenoic (20:1(delta11)) and erucic (22:1(delta13)) acids. Seed-specific expression in Arabidopsis thaliana resulted in up to a 12-fold increase in the proportion of erucic acid. On the other hand, in transgenic high-erucic Brassica carinata plants, the proportion of erucic acid was as high as 51.9% in the best transgenic line, a net increase of 40% compared to wild type. These results indicate that the CrFAE gene encodes a condensing enzyme involved in the biosynthesis of very long-chain fatty acids utilizing monounsaturated and saturated acyl substrates, with a strong capability for improving the erucic acid content

Constrained 2-D/3-D Registration for Motion Compensation in AFib Ablation Procedures

Abstract. Fluoroscopic overlay images rendered from pre-operative vol-umetric data can provide additional guidance for physicians during catheter ablation procedures for treatment of atrial fibrillation (AFib). As these overlay images are compromised by cardiac and respiratory motion, mo-tion compensation methods have been proposed. The approaches so far either require simultaneous biplane imaging for 3-D motion compensa-tion or, in case of mono-plane X-ray imaging, provide only a limited 2-D functionality. To overcome the downsides of the previously suggested methods, we propose a new approach that facilitates full 3-D motion compensation even if only mono-plane X-ray views are available. To this end, we use constrained model-based 2-D/3-D registration to track a circumferential mapping catheter which is commonly used during AFib catheter ablation procedures. Our approach yields an average 2-D track-ing error of 0.6 mm and an average 3-D tracking error of 2.1 mm.

Turbulent flow at 190 m height above London during 2006-2008: A climatology and the applicability of similarity theory

Flow and turbulence above urban terrain is more complex than above rural terrain, due to the different momentum and heat transfer characteristics that are affected by the presence of buildings (e.g. pressure variations around buildings). The applicability of similarity theory (as developed over rural terrain) is tested using observations of flow from a sonic anemometer located at 190.3 m height in London, U.K. using about 6500 h of data. Turbulence statistics—dimensionless wind speed and temperature, standard deviations and correlation coefficients for momentum and heat transfer—were analysed in three ways. First, turbulence statistics were plotted as a function only of a local stability parameter z/Λ (where Λ is the local Obukhov length and z is the height above ground); the σ_i/u_* values (i = u, v, w) for neutral conditions are 2.3, 1.85 and 1.35 respectively, similar to canonical values. Second, analysis of urban mixed-layer formulations during daytime convective conditions over London was undertaken, showing that atmospheric turbulence at high altitude over large cities might not behave dissimilarly from that over rural terrain. Third, correlation coefficients for heat and momentum were analyzed with respect to local stability. The results give confidence in using the framework of local similarity for turbulence measured over London, and perhaps other cities. However, the following caveats for our data are worth noting: (i) the terrain is reasonably flat, (ii) building heights vary little over a large area, and (iii) the sensor height is above the mean roughness sublayer depth