Dose response severity functions for acoustic disturbance in cetaceans using recurrent event survival analysis

This work was financially supported by the U. S. Office of Naval Research grant N00014‐12‐1‐0204, under the project “Multi‐study Ocean acoustics Human effects Analysis” (MOCHA). . L. Tyack received funding from the MASTS pooling initiative (The Marine Alliance for Science and Technology for Scotland) and their support is gratefully acknowledged. MASTS is funded by the Scottish Funding Council (grant reference HR09011) and contributing institutions. The case study data were provided by the 3S project, which was funded by the U.S. Office of Naval Research, the Norwegian Ministry of Defense, the Netherlands Ministry of Defense, and WWF Norway.Behavioral response studies (BRSs) aim to enhance our understanding of the behavior changes made by animals in response to specific exposure levels of different stimuli, often presented in an increasing dosage. Here, we focus on BRSs that aim to understand behavioral responses of free-ranging whales and dolphins to manmade acoustic signals (although the methods are applicable more generally). One desired outcome of these studies is dose-response functions relevant to different species, signals and contexts. We adapted and applied recurrent event survival analysis (Cox proportional hazard models) to data from the 3S BRS project, where multiple behavioral responses of different severities had been observed per experimental exposure and per individual based upon expert scoring. We included species, signal type, exposure number and behavioral state prior to exposure as potential covariates. The best model included all main effect terms, with the exception of exposure number, as well as two interaction terms. The interactions between signal and behavioral state, and between species and behavioral state highlighted that the sensitivity of animals to different signal types (a 6–7 kHz upsweep sonar signal [MFAS] or a 1–2 kHz upsweep sonar signal [LFAS]) depended on their behavioral state (feeding or nonfeeding), and this differed across species. Of the three species included in this analysis (sperm whale [Physeter macrocephalus], killer whale [Orcinus orca] and long-finned pilot whale [Globicephala melas]), killer whales were consistently the most likely to exhibit behavioral responses to naval sonar exposure. We conclude that recurrent event survival analysis provides an effective framework for fitting dose-response severity functions to data from behavioral response studies. It can provide outputs that can help government and industry to evaluate the potential impacts of anthropogenic sound production in the ocean.Publisher PDFPeer reviewe

Hypsometric and geometric controls on hydrodynamics, tidal asymmetry, and sediment connectivity in shallow estuarine systems.

Estuaries and tidal basins are highly dynamic coastal systems that serve as a transition zone between the river and the ocean. The morphological evolution of these diverse environments is modulated by non-linear feedbacks between tides, meteorological forcing, and sediment transport processes. This thesis focuses on the fundamental links between these physical processes, and the geomorphologic characteristics of shallow estuarine systems, specifically: (i) how shallow basin geometries and hypsometries affect hydrodynamics and tidal asymmetry, (ii) how wind-induced currents modify velocity asymmetry in shallow basins, and (iii) defining the relationships between geometry, hypsometry, and sediment connectivity inside shallow estuarine systems. Linking geomorphological characteristics and tidal processes in shallow tidal basins The links between tidal basin geometry and hypsometry, bed shear stress patterns, tidal velocity- and slack water asymmetry, and hypsometric profile shapes were explored for six shallow microtidal basins of Tauranga Harbour, New Zealand. Model results, obtained from a depth-averaged numerical model developed in Delft3D for the full estuarine system, indicated that tidal distortion increases with distance from basin entrance. A simple ratio between tidal basin width and entrance width was defined to describe the planform shape of the basin. This metric, termed the ‘basin dilation factor’ indicates whether a basin can be designated as a divergent or convergent geometry. Shallow basins with a constricted geometry and relatively deep entrance channels were found to be associated with small bed shear stress values and high rates of flood-directed tidal velocity asymmetry in the sheltered basin centres. These results suggest substantial potential for sediment deposition of larger particles. Moreover, slack water asymmetry within these basins was weakly ebb-directed, indicating a small potential for export of fine sediments. These divergent, depositional basins were found to be characterized by convex hypsometric profiles with elevated intertidal regions. Conversely, unconstricted, convergent basins were associated with larger bed shear stress values and more ebb-directed tidal velocity asymmetry within basin centres. Consequently, there was limited potential for overall sediment deposition inside these basins. The slack water asymmetry was weakly flood-dominant, suggesting limited potential for fine sediment input. The comparatively high-energy conditions within these exposed tidal basins were associated with a less convex hypsometric intertidal profile. This study highlights the impacts of specific geomorphologic basin characteristics on tidal processes in shallow estuarine systems. The ability to predict the links between tidal asymmetry and morphological changes in tide-dominated systems is beneficial for coastal management, as the morphological evolution of estuarine systems affects coastal ecosystem functioning, port and estuary navigability, and potential for coastal protection. Understanding the effects of wind-driven currents on velocity asymmetry in shallow tidal basins Numerical modelling experiments were conducted for a series of idealized basins in which planform shape and bathymetry were varied. The model results were used to examine how wind-generated currents modulate horizontal velocity asymmetry patterns in shallow tidal basins. This study revealed that wind-driven currents primarily influence mean and peak flow velocities inside the basins, with a limited effect on tidal harmonics. Faster wind speeds led to more extreme horizontal velocity asymmetry (larger velocity asymmetry values), without substantially modifying overall spatial patterns of velocity asymmetry. The velocity asymmetry was found to be strongly depth-dependent, with changes to asymmetry patterns being most evident for wind speeds of 6 m/s and greater, and for wind directions parallel to the main axes of the tidal channels in the basins. Shallow intertidal regions inside the basins were characterized by a downwind-directed increase in velocity asymmetry, whereas deeper subtidal channels experienced asymmetry changes in the opposite direction. Wind event duration and timing were also found to influence the velocity asymmetry patterns. The differences between the relative size of the peak flood- and ebb directed currents were most evident for wind events with a duration of 6 hours or less that coincide with flooding tides. The results of this study highlight that hydrodynamics, sediment transport, and morphological evolution in shallow estuaries are modulated by tidal processes as well as meteorological forcing. Since anthropogenically induced climate change is expected to increase the intensity of extreme meteorological events, the ability to predict future pathways of morphological change in shallow estuarine systems, based on specific meteorological conditions as well as well-defined local tidal regimes, is vital for the management of these dynamic systems. An examination of sediment connectivity in a shallow estuarine system The sediment connectivity framework was used to examine links between hydrodynamics, sediment transport pathways, and local hypsometry inside a shallow estuarine system (Tauranga Harbour, New Zealand). The estuary was divided into twenty geomorphic cells, representing tidal channels, intertidal flats, and shallow sub-basins. Depth-averaged numerical modelling simulations were carried out to quantify tide-driven sediment connectivity between the cells for five sediment grainsize classes. Connectivity matrices were developed for the different grainsize classes, based on modelled sediment mass loads. Sediment connectivity inside the estuary was found to be modulated by tidal energy, estuarine morphology (depth), sub-basin hypsometry and geometry (planform shape), and sediment characteristics. The connectivity matrices, combined with metrics such as link density and cell strength, illustrated that sediment mass loads, and hence connectivity, were largest in the high-energy environments of the deep tidal channels located in the main estuary. In the more sheltered upper estuary, and inside the shallow sub-basins, connectivity was reduced. For fine sediments ( 275 μm) was found to be ~20%, with transport pathways primarily confined to the deeper regions of the estuary. An in-depth analysis of sediment transport pathways between the shallow sub-basins emphasized that flood-dominant, divergent basins with a convex-shaped hypsometric profile mainly function as sediment sinks, whereas ebb-dominant convergent basins act as sediment sources. This thesis highlights the substantial dependence of tidal asymmetry, morphology, sediment transport and connectivity on hypsometry, geometry, and grainsize characteristics inside shallow estuaries. Additionally, the effects of wind-driven currents on the non-linear physical processes inside these highly dynamic environments are described. Overall, this work provides a novel elucidation of some of the relationships between geometric parameters and forcing mechanisms applicable to many shallow coastal systems

Neural Correlates of Intentional Communication

We know a great deal about the neurophysiological mechanisms supporting instrumental actions, i.e., actions designed to alter the physical state of the environment. In contrast, little is known about our ability to select communicative actions, i.e., actions directly designed to modify the mental state of another agent. We have recently provided novel empirical evidence for a mechanism in which a communicator selects his actions on the basis of a prediction of the communicative intentions that an addressee is most likely to attribute to those actions. The main novelty of those findings was that this prediction of intention recognition is cerebrally implemented within the intention recognition system of the communicator, is modulated by the ambiguity in meaning of the communicative acts, and not by their sensorimotor complexity. The characteristics of this predictive mechanism support the notion that human communicative abilities are distinct from both sensorimotor and linguistic processes

Brain Mechanisms Underlying Human Communication

Human communication has been described as involving the coding-decoding of a conventional symbol system, which could be supported by parts of the human motor system (i.e. the “mirror neurons system”). However, this view does not explain how these conventions could develop in the first place. Here we target the neglected but crucial issue of how people organize their non-verbal behavior to communicate a given intention without pre-established conventions. We have measured behavioral and brain responses in pairs of subjects during communicative exchanges occurring in a real, interactive, on-line social context. In two fMRI studies, we found robust evidence that planning new communicative actions (by a sender) and recognizing the communicative intention of the same actions (by a receiver) relied on spatially overlapping portions of their brains (the right posterior superior temporal sulcus). The response of this region was lateralized to the right hemisphere, modulated by the ambiguity in meaning of the communicative acts, but not by their sensorimotor complexity. These results indicate that the sender of a communicative signal uses his own intention recognition system to make a prediction of the intention recognition performed by the receiver. This finding supports the notion that our communicative abilities are distinct from both sensorimotor processes and language abilities

Modulation of Litter Decomposition by the Soil Microbial Food Web Under Influence of Land Use Change

Soil microbial communities modulate soil organic matter (SOM) dynamics by catalyzing litter decomposition. However, our understanding of how litter-derived carbon (C) flows through the microbial portion of the soil food web is far from comprehensive. This information is necessary to facilitate reliable predictions of soil C cycling and sequestration in response to a changing environment such as land use change in the form of agricultural abandonment. To examine the flow of litter-derived C through the soil microbial food web and it’s response to land use change, we carried out an incubation experiment with soils from six fields; three recently abandoned and three long term abandoned fields. In these soils, the fate of 13C-labeled plant litter was followed by analyzing phospholipid fatty acids (PLFA) over a period of 56 days. The litter-amended soils were sampled over time to measure 13CO2 and mineral N dynamics. Microbial 13C-incorporation patterns revealed a clear succession of microbial groups during litter decomposition. Fungi were first to incorporate 13C-label, followed by G− bacteria, G+ bacteria, actinomycetes and micro-fauna. The order in which various microbial groups responded to litter decomposition was similar across all the fields examined, with no clear distinction between recent and long-term abandoned soils. Although the microbial biomass was initially higher in long-term abandoned soils, the net amount of 13C-labeled litter that was incorporated by the soil microbial community was ultimately comparable between recent and long-term abandoned fields. In relative terms, this means there was a higher efficiency of litter-derived 13C-incorporation in recent abandoned soil microbial communities compared to long-term abandoned soils, most likely due to a net shift from SOM-derived C toward root-derived C input in the soil microbial food web following land-abandonment

Optimal stride frequencies in running at different speeds

During running at a constant speed, the optimal stride frequency (SF) can be derived from the u-shaped relationship between SF and heart rate (HR). Changing SF towards the optimum of this relationship is beneficial for energy expenditure and may positively change biomechanics of running. In the current study, the effects of speed on the optimal SF and the nature of the u-shaped relation were empirically tested using Generalized Estimating Equations. To this end, HR was recorded from twelve healthy (4 males, 8 females) inexperienced runners, who completed runs at three speeds. The three speeds were 90%, 100% and 110% of self-selected speed. A self-selected SF (SFself) was determined for each of the speeds prior to the speed series. The speed series started with a free-chosen SF condition, followed by five imposed SF conditions (SFself, 70, 80, 90, 100 strides·min-1) assigned in random order. The conditions lasted 3 minutes with 2.5 minutes of walking in between. SFself increased significantly (p<0.05) with speed with averages of 77, 79, 80 strides·min-1 at 2.4, 2.6, 2.9 m·s-1, respectively). As expected, the relation between SF and HR could be described by a parabolic curve for all speeds. Speed did not significantly affect the curvature, nor did it affect optimal SF. We conclude that over the speed range tested, inexperienced runners may not need to adapt their SF to running speed. However, since SFself were lower than the SFopt of 83 strides·min-1, the runners could reduce HR by increasing their SFself