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Upon a recent rapid increase of the finfish aquaculture industry in the Coast of Bays, an area of the South Coast of Newfoundland (9 fold production growth from 2003 to 2013), Fisheries and Oceans Canada (DFO) carried out a research project to better understand the physical oceanography of the area. This report is the second of a series aiming to provide an oceanographic knowledge baseline of the Coast of Bays (i.e., data and analyses) to help manage and ensure the sustainable growth of the aquaculture industry. This report presents the analysis of 790 water profiles of temperature, salinity and dissolved oxygen concentration sampled at 276 stations over the course of a 5-year oceanographic program (2009-13). The profiles were analyzed using along-channel vertical sections plots (i.e., transects), surface property maps and water masses statistics. The results of this study highlight the hydrographic structure of three distinct geographical regions: a very stratified fjord subject to large freshwater runoff (Bay d'Espoir), a large stratified bay subject to important freshwater runoff (Belle Bay) and a peninsula producing limited amount of freshwater discharge and consisting of two open bays and one narrow inlet (Connaigre Peninsula). As a result of the geographical variation of freshwater inputs, the surface layer characteristics (temperature, salinity, dissolved oxygen and pycnocline depth) vary significantly among the bays studied. Bellow the seasonal surface layer, two main water masses were identified and are unevenly distributed across the area; due mainly to topographic features which impede or limit water exchanges (i.e., sills). Short-term (i.e., order of hours to days), seasonal and inter-annual variations are also discussed but their assessment, and understanding, is limited by the spatial and temporal resolution. Similarly, the physical processes responsible for those variations are poorly understood. Further research would be needed to address those important knowledge gaps. Based on these geographical differences across regions and within each of the bay studied, hydrographic zones are defined and may be used, in conjunction with other relevant factors, for aquaculture management purposes. Data used and presented in this report are available at the Government of Canada's Open Data website. [ABSTRACT FROM AUTHOR]

Upon a recent rapid increase of the finfish aquaculture industry in the Coast of Bays, an area of the South Coast of Newfoundland (nine-fold production growth from 2003 to 2013), Fisheries and Oceans Canada (DFO) carried out a research project to better understand the physical oceanography of the area. This report is the first of a series aiming to provide an oceanographic knowledge baseline of the Coast of Bays (i.e., data and analyses) to help manage and ensure the sustainable growth of the aquaculture industry. Bathymetric, topographic and hydrologic data as well as sea water temperature, tides and wind data were used to determine the geographic, hydrologic and oceanographic characteristics of the area. The area includes five major bays where the aquaculture activities are currently occurring or planned. The results of these analyses indicate that the Coast of Bays area can be divided in three regions of distinct geographic, hydrologic and oceanographic characteristics: a deep, long and narrow fjord subject to large runoff (Bay d'Espoir), a deep and wide bay subject to less but still significant runoff (Belle Bay) and a shallower region, more exposed to the open ocean and subject to very small runoff (Connaigre Peninsula). The annual average freshwater discharge was found to be about 252 m3/s in Bay d'Espoir, about 71 m3/s in Belle Bay and about 10 m3/s in the Connaigre Peninsula and characterised by a strong seasonal cycle with a large spring freshet (April-May), a low in summer (July-August) and smaller peak in late-fall/early-winter (November-December). Tides are semi-diurnal and small, with a range of about 2 m (large tides). Thus, and due to the large volumes of the bays considered, flushing times due to tides only are large and unequal, varying from about 30 days in the Connaigre Peninsula to about 70 days in Bay d'Espoir and Belle Bay. The study area is also characterized, as a whole, by a strong heating and cooling seasonal cycle with sea-surface (0-20 m) water temperature amplitude of about 7°C.Differences among the three regions in terms of seasonal cycle amplitudes and phases as well as monthly statistics and vertical mixing estimates were found and suggest a potential effect of the freshwater input on thermal stratification. The wind climate of the area is also strongly seasonal with prevailing and strong winds from the westnorthwest/ northeast in winter/spring (about 35-45 km/h median speed) and prevailing and much weaker winds from the southwest in summer (about 20-30 km/h median speed). Finally, bathymetric characteristics were used to delineate the area in basins which can be used, in conjunction with other relevant factors, for aquaculture zoning management purposes. [ABSTRACT FROM AUTHOR]

Within communities, species are wrapped in a set of feedbacks with each other and with their environment. When such feedbacks are strong enough they can generate alternative stable states. So far, research on alternative stable states has mostly focused on systems with a small number of species and a limited diversity of interaction types. Here, we analyze a spatial model of plant community dynamics in stressed ecosystems such as drylands, where each species is characterized by a strategy, and the different species interact through facilitation and competition for space and resources, such as water. We identify three different types of multistability emerging from the interplay of competition and facilitation. Under low-stress levels, plant communities organize in small groups of coexisting species, maintained by space, competition and facilitation ("cliques"). Under higher stress levels, positive feedback from facilitation lead to the dominance of a single facilitating species ("mutual exclusion states"). At the highest stress levels, the single facilitating species left in the system coexists with the desert state. By linking community ecology and alternative stable states theory using a spatial plant community model for stressed ecosystems, our study contributes to highlight the importance of positive feedback loops for the stability of ecological communities., (© 2024 The Author(s). Ecology published by Wiley Periodicals LLC on behalf of The Ecological Society of America.)

Interspecific interactions can influence species' activity and movement patterns. In particular, species may avoid or attract each other through reactive responses in space and/or time. However, data and methods to study such reactive interactions have remained scarce and were generally limited to two interacting species. At this time, the deployment of camera traps opens new opportunities but adapted statistical techniques are still required to analyze interaction patterns with such data. We present the multivariate Hawkes process (MHP) and show how it can be used to analyze interactions between several species using camera trap data. Hawkes processes use flexible pairwise interaction functions, allowing us to consider asymmetries and variations over time when depicting reactive temporal interactions. After describing the theoretical foundations of the MHP, we outline how its framework can be used to study interspecific interactions with camera trap data. We design a simulation study to evaluate the performance of the MHP and of another existing method to infer interactions from camera trap-like data. We also use the MHP to infer reactive interactions from real camera trap data for five species from South African savannas (impala Aepyceros melampus, greater kudu Tragelaphus strepsiceros, lion Panthera leo, blue wildebeest Connochaetes taurinus and Burchell's zebra Equus quagga burchelli). The simulation study shows that the MHP can be used as a tool to benchmark other methods of interspecific interaction inference and that this model can reliably infer interactions when enough data are considered. The analysis of real data highlights evidence of predator avoidance by prey and herbivore-herbivore attraction. Lastly, we present the advantages and limits of the MHP and discuss how it can be improved to infer attraction/avoidance patterns more reliably. As camera traps are increasingly used, the multivariate Hawkes process provides a promising framework to decipher the complexity of interactions structuring ecological communities., (© 2024 The Ecological Society of America.)

We used 4 years of publicly available data (2016-2019) on chemical usage at salmon sites with information on production, stocking, locations and environmental conditions to explore patterns of anti-sea lice treatments in a Canadian province. Results show that sequential chemical treatments are prevalent, emamectin benzoate (EMB) with azamethiphos being the most used combination with a decrease in ivermectin usage. Relatively high rates of usage of EMB per fish biomass may point to potential lice resistance patterns with information needed on mechanisms and local populations. Lower or no chemical usage at some sites indicate less sea lice infestations likely influenced by localized site conditions (coves), and a lessened need for medication due to the usage of cleaner fish and possibly other non-chemical methods (not documented in this report). The year/climate influenced chemical input only in sites with higher treatment levels likely due to effects on sea lice growth and reproduction. Observed differences between years are warmer surface temperature in the fall, a higher freshwater input in spring, and stronger wind conditions for 2017 and 2018 with more medication usage for these two years. The lack of significant effect of site distances calculated in zones of influence based on 24 h potential connectivity patterns highlight the need to refine the resolution of hydrodynamic processes., (© 2022. The Author(s).)

Effects of finfish aquaculture on benthic communities at hard bottom sites can be assessed using visual indicators of organic enrichment, namely bacterial mats, opportunistic polychaetes, and/or barren substrates (i.e., with no visible epifauna). Under some regulatory frameworks, the presence of visual indicators beyond a certain threshold proportion (e.g., > 70%) of mandatory sampling stations at a site signals an unacceptable degree of benthic organic loading. However, relationships between visual indicator presence and other biological characters such as epibenthic taxon richness are unclear, and should be examined to advise on the validity of existing legislative frameworks. Here, we used video data collected for regulatory purposes before and after aquaculture production to document (1) change in epibenthic taxon richness (TR) and its discriminatory power in determining aquaculture impact and (2) the association between TR change and the presence of visual indicators. Despite low richness values overall, our results show a significant post-production decrease in TR in the near-cage area, which was predicted to be affected by aquaculture. Decreases in TR were associated with visual indicator presence, validating the use of a suite of visual indicators to detect organic deposition. Importantly, visual indicators should be considered together in the context of regulation, given that relationships between TR and indicators were not linear when the latter are considered individually.

Finfish aquaculture can be installed over hard and patchy substrates where grab sampling is challenging and use of video can be an appropriate tool to document benthic changes. Video monitoring can show visual indicators of enrichment, namely flocculent matter, Beggiatoa-like mats, and opportunistic polychaete complexes (OPC). We examined factors influencing presence of indicators using 52 video monitoring reports collected in Newfoundland, Canada. The main driving factor was distance to cage, with indicators showing a higher probability of occurrence within 10m from cages due to low current velocities. Indicators were less prevalent on sites dominated by hard substrates while OPC in particular were restricted to depths >35m. Beggiatoa-like bacteria covered a larger surface than the two other indicators; however, our results suggest the necessity of amalgamating information related to all the indicators (including bare stations that could indicate anoxia) to establish a more accurate evaluation of aquaculture impact., (Crown Copyright © 2016. Published by Elsevier Ltd. All rights reserved.)

A critical question in tapping behavior is to understand whether the temporal control is exerted on the duration and trajectory of the downward-upward hand movement or on the pause between hand movements. In the present study, we determined the duration of both the movement execution and pauses of monkeys performing a synchronization-continuation task (SCT), using the speed profile of their tapping behavior. We found a linear increase in the variance of pause-duration as a function of interval, while the variance of the motor implementation was relatively constant across intervals. In fact, 96% of the variability of the duration of a complete tapping cycle (pause + movement) was due to the variability of the pause duration. In addition, we performed a Bayesian model selection to determine the effect of interval duration (450-1,000 ms), serial-order (1-6 produced intervals), task phase (sensory cued or internally driven), and marker modality (auditory or visual) on the duration of the movement-pause and tapping movement. The results showed that the most important parameter used to successfully perform the SCT was the control of the pause duration. We also found that the kinematics of the tapping movements was concordant with a stereotyped ballistic control of the hand pressing the push-button. The present findings support the idea that monkeys used an explicit timing strategy to perform the SCT, where a dedicated timing mechanism controlled the duration of the pauses of movement, while also triggered the execution of fixed movements across each interval of the rhythmic sequence., (Copyright © 2014 the American Physiological Society.)

This paper is a survey of existing estimation methods for pharmacokinetic/pharmacodynamic (PK/PD) models based on stochastic differential equations (SDEs). Most parametric estimation methods proposed for SDEs require high frequency data and are often poorly suited for PK/PD data which are usually sparse. Moreover, PK/PD experiments generally include not a single individual but a group of subjects, leading to a population estimation approach. This review concentrates on estimation methods which have been applied to PK/PD data, for SDEs observed with and without measurement noise, with a standard or a population approach. Besides, the adopted methodologies highly differ depending on the existence or not of an explicit transition density of the SDE solution., (Copyright © 2013 Elsevier B.V. All rights reserved.)

Growth curve data consist of repeated measurements of a continuous growth process over time in a population of individuals. These data are classically analyzed by nonlinear mixed models. However, the standard growth functions used in this context prescribe monotone increasing growth and can fail to model unexpected changes in growth rates. We propose to model these variations using stochastic differential equations (SDEs) that are deduced from the standard deterministic growth function by adding random variations to the growth dynamics. A Bayesian inference of the parameters of these SDE mixed models is developed. In the case when the SDE has an explicit solution, we describe an easily implemented Gibbs algorithm. When the conditional distribution of the diffusion process has no explicit form, we propose to approximate it using the Euler-Maruyama scheme. Finally, we suggest validating the SDE approach via criteria based on the predictive posterior distribution. We illustrate the efficiency of our method using the Gompertz function to model data on chicken growth, the modeling being improved by the SDE approach., (© 2009 INRA, Government of France.)

An accurate estimation of the hemodynamic response function (HRF) in functional magnetic resonance imaging (fMRI) is crucial for a precise spatial and temporal estimate of the underlying neuronal processes. Recent works have proposed non-parametric estimation of the HRF under the hypotheses of linearity and stationarity in time. Biological literature suggests, however, that response magnitude may vary with attention or ongoing activity. We therefore test a more flexible model that allows for the variation of the magnitude of the HRF with time in a maximum likelihood framework. Under this model, the magnitude of the HRF evoked by a single event may vary across occurrences of the same type of event. This model is tested against a simpler model with a fixed magnitude using information theory. We develop a standard EM algorithm to identify the event magnitudes and the HRF. We test this hypothesis on a series of 32 regions (4 ROIS on eight subjects) of interest and find that the more flexible model is better than the usual model in most cases. The important implications for the analysis of fMRI time series for event-related neuroimaging experiments are discussed.