Going to the Zoo: Using Tags to Create Measures for Animal Health, Well-being and Welfare in a Managed Care Setting

This PhD investigates how animal-attached motion-sensitive electronic tags might create behavioural biomarkers for animal ‘state’. Such biomarkers could indicate good health, disease, and injuries as well as positive and negative affective states. Success could have widespread implications for the well-being of numerous species in managed care by optimising welfare practices. This work primarily involved loggerhead sea turtles, Caretta caretta, in different states of health at the Arca del Mar rehabilitation centre, Oceanogràfic, Valencia, Spain, however the potential of tags for various aquatic, aerial and terrestrial species is also considered. Initially, the concept of tag-derived behavioural biomarkers for health (TDBBs) was established, examining data from ‘healthy’ and ‘unhealthy’ rehabilitating sea turtles to identify potentially useful metrics for specific injuries and/or diseases. Then, potential TDBBs for ‘healthy’ turtles and those with gas emboli were created, with variance in body attitude, number of 45° turns per hour and mean angular velocity per hour showing the most promise to differentiate the two groups. TDBBs were also explored for welfare, giving ‘healthy’ turtles nutritional enrichment, demonstrating that enrichment procedures do not always affect captive animal behaviour. To consider welfare implications of captivity, the movement behaviour of free-living and managed-care loggerheads was compared to determine wild-type and captive behaviour overlap. Findings revealed significant differences in the variance in pitch, heading and absolute angular velocity as well as the number of turns per hour. The final research topic considered trajectory step length data (the distances travelled in between turns), derived from tags deployed on nine wild species, for informing enclosure size for captive animals. The findings revealed that existing enclosure size guidelines regularly only permitted animals to undertake a very small percentage (often less than 3 %) of the step lengths recorded from free-living conspecifics. Last, the potential of TDBBs is reviewed, with limitations and future research discussed

The 10 Research Topics in the Internet of Things

Since the term first coined in 1999 by Kevin Ashton, the Internet of Things (IoT) has gained significant momentum as a technology to connect physical objects to the Internet and to facilitate machine-to-human and machine-to-machine communications. Over the past two decades, IoT has been an active area of research and development endeavours by many technical and commercial communities. Yet, IoT technology is still not mature and many issues need to be addressed. In this paper, we identify 10 key research topics and discuss the research problems and opportunities within these topics.Comment: 10 pages. IEEE CIC 2020 vision pape

Learning in a Technology Enhanced World

Specht, M. (2009). Learning in a Technology Enhanced World: Context in Ubiquitous Learning Support. Inaugural Address. September, 11, 2009, Heerlen, The Netherlands: Open University of the Netherlands.In the following sections I will first outline what the current developments and trends in technology for the next five to ten years are and what their potential for enhancing learning is. OUN Second, I will describe how these developments and innovations already today influence the way we communicate, live, and learn. How the generation gap between digital natives and digital immigrants is leading to different perceptions of digital media and their use for learning and teaching. Third, I will outline some research on context and learning. I will describe examples of what I mean when I talk about context and I will give an overview of the usage of context in education and the key effects we can expect from contextualising technology enhancements for learning. What are the variables and design parameters we have to consider when we design contextualized learning in a technology enhanced world? In the fourth part I will introduce the model of ambient information channels that is a structuring metaphor for contextual learning technology. Last, I will highlight some key questions for a future research agenda in the field of contextual learning support and describe some research we are currently working on at the Centre of Learning Sciences and Technologies (CELSTEC) here at the Open University of the Netherlands

Integrative approaches in fragment-based drug discovery

This thesis combines experimental and computational methods to investigate aspects of fragment identification and elaboration in fragment-based ligand design, a promising approach for identifying small molecule drugs, to target the pharmacologically relevant bromodomain PHIP(2). The research covers various aspects of the process, from initial crystallographic fragment screening to validation of follow-up compounds. Chapters 1 and 2 provide an overview of relevant perspectives and methodologies in fragment-based drug discovery. Chapter 3 reports a crystallographic fragment screening against PHIP(2), resolving 47 fragments at the acetylated-lysine binding site, and evaluates the abilities of crowdsourced computational methods to replicate fragment binding and crystallographic poses. This chapter highlights the challenges associated with using computational methods for reproducing crystallographic fragment screening results with submissions performing relatively weakly. Chapter 4 demonstrates the advantages of X-ray crystallographic screening of crude reaction mixtures generated robotically, showcasing reduced time, solvent, and hardware requirements. Soaking crude reaction mixtures maintains crystal integrity which led to the identification of 22 binders, 3 with an alternate pose caused by a single methyl addition to the core fragment and 1 hit in assays. It demonstrates how affordable methods can generate large amounts of crystallographic data of fragment elaborations. Chapter 5 develops an algorithmic approach to extract features associated with crystallographic binding, deriving simple binding scores using data from Chapter 4. The method identifies 26 false negatives with binding scores enriching binders over non-binders. Employing these scores prospectively in a virtual screening demonstrated how binding features can be exploited to select further follow-up compounds leading to low micromolar potencies. Chapter 6 attempts to integrate more computationally intensive methods to identify fragment follow-up compounds with increased potency through virtual screening enhanced with free energy calculations. Only two out of six synthesised follow-up compounds showed weak binding in assays, and none were resolved in crystal structures. This thesis tackles critical challenges in follow-up design, synthesis, and dataset analysis, underlining the limitations of existing methods in advancing fragment-based drug discovery. It emphasises the necessity of integrative approaches for an optimised “design, make, test” cycle in fragment-based drug discovery

How often should dead-reckoned animal movement paths be corrected for drift?

Abstract: Background: Understanding what animals do in time and space is important for a range of ecological questions, however accurate estimates of how animals use space is challenging. Within the use of animal-attached tags, radio telemetry (including the Global Positioning System, ‘GPS’) is typically used to verify an animal’s location periodically. Straight lines are typically drawn between these ‘Verified Positions’ (‘VPs’) so the interpolation of space-use is limited by the temporal and spatial resolution of the system’s measurement. As such, parameters such as route-taken and distance travelled can be poorly represented when using VP systems alone. Dead-reckoning has been suggested as a technique to improve the accuracy and resolution of reconstructed movement paths, whilst maximising battery life of VP systems. This typically involves deriving travel vectors from motion sensor systems and periodically correcting path dimensions for drift with simultaneously deployed VP systems. How often paths should be corrected for drift, however, has remained unclear. Methods and results: Here, we review the utility of dead-reckoning across four contrasting model species using different forms of locomotion (the African lion Panthera leo, the red-tailed tropicbird Phaethon rubricauda, the Magellanic penguin Spheniscus magellanicus, and the imperial cormorant Leucocarbo atriceps). Simulations were performed to examine the extent of dead-reckoning error, relative to VPs, as a function of Verified Position correction (VP correction) rate and the effect of this on estimates of distance moved. Dead-reckoning error was greatest for animals travelling within air and water. We demonstrate how sources of measurement error can arise within VP-corrected dead-reckoned tracks and propose advancements to this procedure to maximise dead-reckoning accuracy. Conclusions: We review the utility of VP-corrected dead-reckoning according to movement type and consider a range of ecological questions that would benefit from dead-reckoning, primarily concerning animal–barrier interactions and foraging strategies

Contextualized Monitoring in the Marine Environment

Marine mammal monitoring has seen improvements in the last few decades with advances made to both the monitoring hardware and post-processing computation methods. The addition of tag-based hydrophones, Fastloc GPS units, and an ever-increasing array of IMU sensors, coupled with the use of energetics proxies such as Overall Dynamic Body Acceleration (ODBA), has led to new insights into marine mammal swimming behavior that would not be possible using traditional secondary-observer methods. However, these advances have primarily been focused on and implemented in wild animal tracking, with less attention paid to the managed environment. This is a particularly important gap, as the cooperative nature of managed animals allows for research on swimming kinematics and energetics behavior with an intricacy that is difficult to achieve in the wild. While proxy-based methods are useful for relative inter-or-intra-animal comparisons, they are not robust enough for absolute energetics estimates for the animals, which can limit our understanding of their metabolic patterns. Proxies such as ODBA are based on filtered on-animal IMU data, and measure the aggregate high-pass acceleration as an estimate for the magnitude of the animal’s activity level at a given point in time. Depending on its body structure and locomotive gait, tag placement on the animal and the specific filtering techniques used can significantly impact the results. Any relation made to energetics is then strictly a mapping: a relation that may apply well to an individual or group under specific experimental conditions, but is not generalizable. To address this gap, this dissertation presents new tag-based hardware and data processing methods for persistently estimating cetacean swimming kinematics and energetics, which are functional in both managed and wild settings. Unfortunately, localization techniques for managed environments have not been thoroughly explored, so a new animal tracking method is required to spatially contextualize information on swimming behavior. State-of-the-art wild cetacean localization operates via sparse GPS updates upon animal surfacings, and can be paired with biologging-tag-based odometry for a continuous track. Such an approach is hindered by the structure and scale of managed environments: GPS suffers from increased error near and within buildings, and current odometry methods are insufficiently precise for habitat scales where locations of interest might be separated by meters, rather than kilometers (such as in the wild). There is then a need for a tracking method that uses an alternate source of absolute animal locations that can achieve the high precision necessary for meaningful results given the spatial scale. To this end, this dissertation presents a novel animal localization framework, based on tracking and sensor filtering techniques from the field of robotics that have been tailored for use in this setting. Overall, this research targets two main gaps: 1) the lack of persistent, absolute estimates of animal swimming energetics and kinematics, and 2) the lack of a robust, precise localization method for managed cetaceans. To address these gaps, the hardware and animal tracking methods developed to enable the rest of the dissertation are first defined. Next, a physics-based approach to directly monitor cetacean swimming energetics is both presented and implemented to study animal propulsion patterns under varying effort conditions. Finally, a high-fidelity 3D monitoring framework is introduced for tracking institutionally-managed cetaceans, and is applied alongside the energetics estimation method to provide a first look at the potential of spatially-contextualized animal monitoring.PHDRoboticsUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/169756/1/gabaldon_1.pd

Oceanus.

v. 36, no. 3 (1993