The New Era of Physio-Logging and Their Grand Challenges

In-water electrical impedance tomography: EIT and the sea

Objective.Electrical impedance tomography (EIT) has shown the ability to provide clinically useful functional information on ventilation in humans and other land mammals. We are motivated to use EIT with sea mammals and human divers, since EIT could provide unique information on lung ventilation that can help address diver performance and safety, and veterinary and behavioral questions. However, in-water use of EIT is challenging, primarily because sea water is more conductive than the body.Approach.We first address this issue by modeling the in-water component and evaluating image reconstruction algorithms.Main results.EIT is able to produce reasonable images if an outer insulating layer allows a water layer thickness <2% of the body radius. We next describe the design of custom EIT belts with an outer neoprene insulator to minimize current leakage. We show example underwater EIT recordings in human and dolphin subjects.Significance.We demonstrate in-water EIT is feasible with appropriate techniques.

Surfacing and diving behavior associated with thermal physiology in oceanic habitats of skipjack tuna (Katsuwonus pelamis) in the western north Pacific Ocean

Introduction

Thermal physiology is a pivotal biotic factor for the ecophysiology of commercially valuable tuna, influencing not only horizontal but also vertical behaviors. We aimed to examine how the thermal physiology of skipjack tuna (Katsuwonus pelamis, SKJ) can explain the differences in their vertical behavior, focusing on surfacing and diving, among various thermal environments during their northward migration in the western North Pacific.

Methods

We analyzed archival tag data collected during 2012-2015, with individual time series (Fork length: 38-49 cm, N = 38) of swimming depth, water temperature, and peritoneal body temperature during northward migration from subtropical areas to temperate regions around Japan. We quantified surfacing and diving behavior as an index of vertical behavior and estimated the whole-body heat transfer coefficient (λ) during the cooling and warming phases associated with diving using body and water temperature records as indicators of thermal physiology.

Results

In the southern mixed layer areas, SKJ were widely distributed at a depth layer <200 m, whereas they were restricted to the surface in the strong thermocline areas in the north. The dive duration was significantly shortened with a strong thermal gradient during northward migration. We observed minor to no differences in λ values between the cooling and warming phases in the southern areas, whereas the λ values in temperate areas differed by a factor of 2-3 between the phases.

Discussion

Our findings of changes in λ values between the cooling and warming phases represent the first evidence of thermoregulation in SKJ. Surfacing preference behavior and short dive duration in temperate areas may be an avoidance of prolonged exposure to cold temperatures, a behavior commonly exhibited in other tuna. Moreover, we discussed how the changes in vertical behavior driven by thermal physiology can explain spatial heterogeneity in SKJ fishery grounds in the western Pacific Ocean.

Closing the air gap: the use of drones for studying wildlife ecophysiology

Techniques for non-invasive sampling of ecophysiological data in wild animals have been developed in response to challenges associated with studying captive animals or using invasive methods. Of these, drones, also known as Unoccupied Aerial Vehicles (UAVs), and their associated sensors, have emerged as a promising tool in the ecophysiology toolkit. In this review, we synthesise research in a scoping review on the use of drones for studying wildlife ecophysiology using the PRISMA-SCr checklist and identify where efforts have been focused and where knowledge gaps remain. We use these results to explore current best practices and challenges and provide recommendations for future use. In 136 studies published since 2010, drones aided studies on wild animal body condition and morphometrics, kinematics and biomechanics, bioenergetics, and wildlife health (e.g. microbiomes, endocrinology, and disease) in both aquatic and terrestrial environments. Focal taxa are biased towards marine mammals, particularly cetaceans. While conducted globally, research is primarily led by institutions based in North America, Oceania, and Europe. The use of drones to obtain body condition and morphometric data through standard colour sensors and single camera photogrammetry predominates. Techniques such as video tracking and thermal imaging have also allowed insights into other aspects of wildlife ecophysiology, particularly when combined with external sampling techniques such as biologgers. While most studies have used commercially available multirotor platforms and standard colour sensors, the modification of drones to collect samples, and integration with external sampling techniques, have allowed multidisciplinary studies to integrate a suite of remote sensing methods more fully. We outline how technological advances for drones will play a key role in the delivery of both novel and improved wildlife ecophysiological data. We recommend that researchers prepare for the influx of drone-assisted advancements in wildlife ecophysiology through multidisciplinary and cross-institutional collaborations. We describe best practices to diversify across species and environments and use current data sources and technologies for more comprehensive results.

Cardiorespiratory adaptations in small cetaceans and marine mammals

The dive response, or the 'master switch of life', is probably the most studied physiological trait in marine mammals and is thought to conserve the available O2 for the heart and brain. Although generally thought to be an autonomic reflex, several studies indicate that the cardiovascular changes during diving are anticipatory and can be conditioned. The respiratory adaptations, where the aquatic breathing pattern resembles intermittent breathing in land mammals, with expiratory flow exceeding 160 litres s-1 has been measured in cetaceans, and where exposure to extreme pressures results in alveolar collapse (atelectasis) and recruitment upon ascent. Cardiorespiratory coupling, where breathing results in changes in heart rate, has been proposed to improve gas exchange. Cardiorespiratory coupling has also been reported in marine mammals, and in the bottlenose dolphin, where it alters both heart rate and stroke volume. When accounting for this respiratory dependence on cardiac function, several studies have reported an absence of a diving-related bradycardia except during dives that exceed the duration that is fuelled by aerobic metabolism. This review summarizes what is known about the respiratory physiology in marine mammals, with a special focus on cetaceans. The cardiorespiratory coupling is reviewed, and the selective gas exchange hypothesis is summarized, which provides a testable mechanism for how breath-hold diving vertebrates may actively prevent uptake of N2 during routine dives, and how stress results in failure of this mechanism, which results in diving-related gas emboli.

How Reproducibility Will Accelerate Discovery Through Collaboration in Physio-Logging

What new questions could ecophysiologists answer if physio-logging research was fully reproducible? We argue that technical debt (computational hurdles resulting from prioritizing short-term goals over long-term sustainability) stemming from insufficient cyberinfrastructure (field-wide tools, standards, and norms for analyzing and sharing data) trapped physio-logging in a scientific silo. This debt stifles comparative biological analyses and impedes interdisciplinary research. Although physio-loggers (e.g., heart rate monitors and accelerometers) opened new avenues of research, the explosion of complex datasets exceeded ecophysiology’s informatics capacity. Like many other scientific fields facing a deluge of complex data, ecophysiologists now struggle to share their data and tools. Adapting to this new era requires a change in mindset, from “data as a noun” (e.g., traits, counts) to “data as a sentence”, where measurements (nouns) are associate with transformations (verbs), parameters (adverbs), and metadata (adjectives). Computational reproducibility provides a framework for capturing the entire sentence. Though usually framed in terms of scientific integrity, reproducibility offers immediate benefits by promoting collaboration between individuals, groups, and entire fields. Rather than a tax on our productivity that benefits some nebulous greater good, reproducibility can accelerate the pace of discovery by removing obstacles and inviting a greater diversity of perspectives to advance science and society. In this article, we 1) describe the computational challenges facing physio-logging scientists and connect them to the concepts of technical debt and cyberinfrastructure, 2) demonstrate how other scientific fields overcame similar challenges by embracing computational reproducibility, and 3) present a framework to promote computational reproducibility in physio-logging, and bio-logging more generally.

An accelerometer-derived ballistocardiogram method for detecting heartrates in free-ranging marine mammals

Physio-logging methods, which use animal-borne devices to record physiological variables, are entering a new era driven by advances in sensor development. However, existing datasets collected with traditional bio-loggers, such as accelerometers, still contain untapped eco-physiological information. Here, we present a computational method for extracting heart rate from high-resolution accelerometer data using a ballistocardiogram. We validated our method with simultaneous accelerometer–electrocardiogram tag deployments in a controlled setting on a killer whale (Orcinus orca) and demonstrate the predictions correspond with previously observed cardiovascular patterns in a blue whale (Balaenoptera musculus), including the magnitude of apneic bradycardia and increase in heart rate prior to and during ascent. Our ballistocardiogram method may be applied to mine heart rates from previously collected accelerometery data and expand our understanding of comparative cardiovascular physiology.

Highlighted Article: Validation of a computational method for extracting heart rate in free-ranging cetaceans from high-resolution accelerometer data using a ballistocardiogram.

Near-Infrared Spectroscopy as a Tool for Marine Mammal Research and Care

Developments in wearable human medical and sports health trackers has offered new solutions to challenges encountered by eco-physiologists attempting to measure physiological attributes in freely moving animals. Near-infrared spectroscopy (NIRS) is one such solution that has potential as a powerful physio-logging tool to assess physiology in freely moving animals. NIRS is a non-invasive optics-based technology, that uses non-ionizing radiation to illuminate biological tissue and measures changes in oxygenated and deoxygenated hemoglobin concentrations inside tissues such as skin, muscle, and the brain. The overall footprint of the device is small enough to be deployed in wearable physio-logging devices. We show that changes in hemoglobin concentration can be recorded from bottlenose dolphins and gray seals with signal quality comparable to that achieved in human recordings. We further discuss functionality, benefits, and limitations of NIRS as a standard tool for animal care and wildlife tracking for the marine mammal research community.

Advances in thermal physiology of diving marine mammals: The dual role of peripheral perfusion

The ability to maintain a high core body temperature is a defining characteristic of all mammals, yet their diverse habitats present disparate thermal challenges that have led to specialized adaptations. Marine mammals inhabit a highly conductive environment. Their thermoregulatory capabilities far exceed our own despite having limited avenues of heat transfer. Additionally, marine mammals must balance their thermoregulatory demands with those associated with diving (i.e. oxygen conservation), both of which rely on cardiovascular adjustments. This review presents the progress and novel efforts in investigating marine mammal thermoregulation, with a particular focus on the role of peripheral perfusion. Early studies in marine mammal thermal physiology were primarily performed in the laboratory and provided foundational knowledge through in vivo experiments and ex vivo measurements. However, the ecological relevance of these findings remains unknown because comparable efforts on free-ranging animals have been limited. We demonstrate the utility of biologgers for studying their thermal adaptations in the context in which they evolved. Our preliminary results from freely diving northern elephant seals (Mirounga angustirostris) reveal blubber's dynamic nature and the complex interaction between thermoregulation and the dive response due to the dual role of peripheral perfusion. Further exploring the potential use of biologgers for measuring physiological variables relevant to thermal physiology in other marine mammal species will enhance our understanding of the relative importance of morphology, physiology, and behavior for thermoregulation and overall homeostasis.

Moving average and standard deviation thresholding (MAST): a novel algorithm for accurate R-wave detection in the murine electrocardiogram

Advances in implantable radio-telemetry or diverse biologging devices capable of acquiring high-resolution ambulatory electrocardiogram (ECG) or heart rate recordings facilitate comparative physiological investigations by enabling detailed analysis of cardiopulmonary phenotypes and responses in vivo. Two priorities guiding the meaningful adoption of such technologies are: (1) automation, to streamline and standardize large dataset analysis, and (2) flexibility in quality-control. The latter is especially relevant when considering the tendency of some fully automated software solutions to significantly underestimate heart rate when raw signals contain high-amplitude noise. We present herein moving average and standard deviation thresholding (MAST), a novel, open-access algorithm developed to perform automated, accurate, and noise-robust single-channel R-wave detection from ECG obtained in chronically instrumented mice. MAST additionally and automatically excludes and annotates segments where R-wave detection is not possible due to artefact levels exceeding signal levels. Customizable settings (e.g. window width of moving average) allow for MAST to be scaled for use in non-murine species. Two expert reviewers compared MAST's performance (true/false positive and false negative detections) with that of a commercial ECG analysis program. Both approaches were applied blindly to the same random selection of 270 3-min ECG recordings from a dataset containing varying amounts of signal artefact. MAST exhibited roughly one quarter the error rate of the commercial software and accurately detected R-waves with greater consistency and virtually no false positives (sensitivity, Se: 98.48% ± 4.32% vs. 94.59% ± 17.52%, positive predictivity, +P: 99.99% ± 0.06% vs. 99.57% ± 3.91%, P < 0.001 and P = 0.0274 respectively, Wilcoxon signed rank; values are mean ± SD). Our novel, open-access approach for automated single-channel R-wave detection enables investigators to study murine heart rate indices with greater accuracy and less effort. It also provides a foundational code for translation to other mammals, ectothermic vertebrates, and birds.

What is physiologging? Introduction to the theme issue, part 2

The physiological mechanisms by which animals regulate energy expenditure, respond to stimuli and stressors, and maintain homeostasis at the tissue, organ and whole organism levels can be described by 'physiologging'-that is, the use of onboard miniature electronic devices to record physiological metrics of animals in captivity or free-living in the wild. Despite its origins in the 1960s, physiologging has evolved more slowly than its umbrella field of biologging. However, the recording of physiological metrics in free-living animals will be key to solving some of the greatest challenges in biodiversity conservation, issues pertaining to animal health and welfare, and for inspiring future therapeutic strategies for human health. Current physiologging technologies encompass the measurement of physiological variables such as heart rate, brain activity, body temperature, muscle stimulation and dynamic movement, yet future developments will allow for onboard logging of metrics relating to organelle, molecular and genetic function. This article is part of the theme issue 'Measuring physiology in free-living animals (Part II)'.

The early life of king penguins: ontogeny of dive capacity and foraging behaviour in an expert diver

The period of emancipation in seabirds, when juveniles change from a terrestrial existence to a life at sea, is associated with many challenges. Apart from finding favourable foraging sites, they have to develop effective prey search patterns and physiological capacities that enable them to capture sufficient prey to meet their energetic needs. Animals that dive to forage, such as king penguins (Aptenodytes patagonicus), need to acquire an adequate breath-hold capacity, allowing them to locate and capture prey at depth. To investigate the ontogeny of their dive capacity and foraging performance, we implanted juvenile king penguins before their first departure to sea and also adult breeders with a data-logger recording pressure and temperature. We found that juvenile king penguins possess a remarkable dive capacity when leaving their natal colony, enabling them to conduct dives in excess of 100 m within their first week at sea. Despite this, juvenile dive/foraging performance, investigated in relation to dive depth, remained below the adult level throughout their first year at sea, probably reflecting physiological limitations as a result of incomplete maturation. A significantly shallower foraging depth of juveniles, particularly during their first 5 months at sea, could also indicate differences in foraging strategy and targeted prey. The initially greater wiggle rate suggests that juveniles fed opportunistically and also targeted different prey from adults and/or that many of the wiggles of juveniles reflect unsuccessful prey-capture attempts, indicating a lower foraging proficiency. After 5 months, this difference disappeared, suggesting sufficient physical maturation and improvement of juvenile foraging skills.