Individual Variation Affects Outbreak Magnitude and Predictability in an Extended Multi-Pathogen SIR Model of Pigeons Vising Dairy Farms

Zoonotic disease transmission between animals and humans is a growing risk and the agricultural context acts as a likely point of transition, with individual heterogeneity acting as an important contributor. Thus, understanding the dynamics of disease spread in the wildlife-livestock interface is crucial for mitigating these risks of transmission. Specifically, the interactions between pigeons and in-door cows at dairy farms can lead to significant disease transmission and economic losses for farmers; putting livestock, adjacent human populations, and other wildlife species at risk. In this paper, we propose a novel spatio-temporal multi-pathogen model with continuous spatial movement. The model expands on the Susceptible-Exposed-Infected-Recovered-Dead (SEIRD) framework and accounts for both within-species and cross-species transmission of pathogens, as well as the exploration-exploitation movement dynamics of pigeons, which play a critical role in the spread of infection agents. In addition to model formulation, we also implement it as an agent-based simulation approach and use empirical field data to investigate different biologically realistic scenarios, evaluating the effect of various parameters on the epidemic spread. Namely, in agreement with theoretical expectations, the model predicts that the heterogeneity of the pigeons' movement dynamics can drastically affect both the magnitude and stability of outbreaks. In addition, joint infection by multiple pathogens can have an interactive effect unobservable in single-pathogen SIR models, reflecting a non-intuitive inhibition of the outbreak. Our findings highlight the impact of heterogeneity in host behavior on their pathogens and allow realistic predictions of outbreak dynamics in the multi-pathogen wildlife-livestock interface with consequences to zoonotic diseases in various systems

Linear Current-Mode Active Pixel Sensor

A current mode CMOS active pixel sensor (APS) providing linear light-to-current conversion with inherently low fixed pattern noise (FPN) is presented. The pixel features adjustable-gain current output using a pMOS readout transistor in the linear region of operation. This paper discusses the pixel’s design and operation, and presents an analysis of the pixel’s temporal noise and FPN. Results for zero and first-order pixel mismatch are presented. The pixel was implemented in a both a 3.3 V 0.35 µm and a 1.8 V 0.18 µm CMOS process. The 0.35 µm process pixel had an uncorrected FPN of 1.4%/0.7% with/without column readout mismatch. The 0.18 µm process pixel had 0.4% FPN after delta-reset sampling (DRS). The pixel size in both processes was 10 X 10 µm2, with fill factors of 26% and 66%, respectively

A guide to pre-processing high-throughput animal tracking data

1. Modern, high-throughput animal tracking studies collect increasingly large volumes of data at very fine temporal scales. At these scales, location error can exceed the animal’s step size, leading to mis-estimation of key movement metrics such as speed. ‘Cleaning’ the data to reduce location errors prior to analyses is one of the main ways movement ecologists deal with noisy data, and has the advantage of being more scalable to massive datasets than more complex methods. Though data cleaning is widely recommended, and ecologists routinely consider cleaned data to be the ground-truth, inclusive uniform guidance on this crucial step, and on how to organise the cleaning of massive datasets, is still rather scarce. 2. A pipeline for cleaning massive high-throughput datasets must balance ease of use and computationally efficient signal vs. noise screening, in which location errors are rejected without discarding valid animal movements. Another useful feature of a pre-processing pipeline is efficiently segmenting and clustering location data for statistical methods, while also being scalable to large datasets and robust to imperfect sampling. Manual methods being prohibitively time consuming, and to boost reproducibility, a robust pre-processing pipeline must be automated. 3. In this article we provide guidance on building pipelines for pre-processing high-throughput animal tracking data in order to prepare it for subsequent analysis. Our recommended pipeline, consisting of removing outliers, smoothing the filtered result, and thinning it to a uniform sampling interval, is applicable to many massive tracking datasets. We apply this pipeline to simulated movement data with location errors, and also show a case study of how large volumes of cleaned data can be transformed into biologically meaningful ‘residence patches’, for quick biological inference on animal space use. We use calibration data to illustrate how pre-processing improves its quality, and to verify that the residence patch synthesis accurately captures animal space use. Finally, turning to tracking data from Egyptian fruit bats (Rousettus aegyptiacus), we demonstrate the pre-processing pipeline and residence patch method in a fully worked out example. 4. To help with fast implementation of standardised methods, we developed the R package atlastools, which we also introduce here. Our pre-processing pipeline and atlastools can be used with any high-throughput animal movement data in which the high data-volume combined with knowledge of the tracked individuals’ movement capacity can be used to reduce location errors. The atlastools function is easy to use for beginners, while providing a template for further development. The use of common pre-processing steps that are simple yet robust promotes standardised methods in the field of movement ecology and leads to better inferences from data

Social interactions in striped hyena inferred from camera trap data: is it more social than previously thought?

Understanding the drivers promoting sociality over solitariness in animal species is imperative for predicting future population trends and informing conservation and management. In this study we investigate the social structure of a desert dwelling population of striped hyena Hyaena hyaena. This species is historically regarded as strictly solitary albeit being the least studied of the extant Hyaenids. Accumulating evidence regarding the frequency of social interactions suggests a revision of striped hyena social structure is required. We hypothesized that striped hyena has a social structure that is more complex than expected for a strictly solitary species. For that end, we deployed an array of camera-traps in a remote desert region in Israel, and compared observed frequencies of striped hyena co-occurrence against null models to test whether hyena co-occurred more than expected by chance. Seven adults were (re)captured by our camera-traps in 49 different instances over 83 tracking days. Of these, 6 exhibited shared space-use around a scarce, isolated perennial water source. Five of them, co-occurred with other hyena (in 3 instances) significantly more frequent than expected by chance (and that timing suggests reproduction is unlikely to be the driving factor). Our findings substantiate evidence of complex social structure in striped hyena, highlight the importance of a scarce resource in space-use and sociality, and provide a baseline for future research of striped hyena social structure. We suggest that similar methods be employed to evaluate social structure in other “solitary species” to better understand their social dynamics

Behavioural ecology at the spatial–social interface

Spatial and social behaviour are fundamental aspects of an animal's biology, and their social and spatial environments are indelibly linked through mutual causes and shared consequences. We define the 'spatial-social interface' as intersection of social and spatial aspects of individuals' phenotypes and environments. Behavioural variation at the spatial-social interface has implications for ecological and evolutionary processes including pathogen transmission, population dynamics, and the evolution of social systems. We link spatial and social processes through a foundation of shared theory, vocabulary, and methods. We provide examples and future directions for the integration of spatial and social behaviour and environments. We introduce key concepts and approaches that either implicitly or explicitly integrate social and spatial processes, for example, graph theory, density-dependent habitat selection, and niche specialization. Finally, we discuss how movement ecology helps link the spatial-social interface. Our review integrates social and spatial behavioural ecology and identifies testable hypotheses at the spatial-social interface

Estimating encounter location distributions from animal tracking data

1. Ecologists have long been interested in linking individual behaviour with higher level processes. For motile species, this ‘upscaling’ is governed by how well any given movement strategy maximizes encounters with positive factors and minimizes encounters with negative factors. Despite the importance of encounter events for a broad range of ecological processes, encounter theory has not kept pace with developments in animal tracking or movement modelling. Furthermore, existing work has focused primarily on the relationship between animal movement and encounter rates while the relationship between individual movement and the spatial locations of encounter events in the environment has remained conspicuously understudied. 2. Here, we bridge this gap by introducing a method for describing the long-term encounter location probabilities for movement within home ranges, termed the conditional distribution of encounters (CDE). We then derive this distribution, as well as confidence intervals, implement its statistical estimator into open-source software and demonstrate the broad ecological relevance of this distribution. 3. We first use simulated data to show how our estimator provides asymptotically consistent estimates. We then demonstrate the general utility of this method for three simulation-based scenarios that occur routinely in biological systems: (a) a population of individuals with home ranges that overlap with neighbours; (b) a pair of individuals with a hard territorial border between their home ranges; and (c) a predator with a large home range that encompassed the home ranges of multiple prey individuals. Using GPS data from white-faced capuchins Cebus capucinus, tracked on Barro Colorado Island, Panama, and sleepy lizards Tiliqua rugosa, tracked in Bundey, South Australia, we then show how the CDE can be used to estimate the locations of territorial borders, identify key resources, quantify the potential for competitive or predatory interactions and/or identify any changes in behaviour that directly result from location-specific encounter probability. 4. The CDE enables researchers to better understand the dynamics of populations of interacting individuals. Notably, the general estimation framework developed in this work builds straightforwardly off of home range estimation and requires no specialized data collection protocols. This method is now openly available via the ctmm R package

On the stratorotational instability in the quasi-hydrostatic semi-geostrophic limit

The linear normal-mode stratorotational instability (SRI) is analytically reexamined in the inviscid limit where the length scales of horizontal disturbances are large compared their vertical and radial counterparts. Boundary conditions different than channel walls are also considered. This quasi-hydrostatic, semi-geostrophic (QHSG) approximation allows one to examine the effect of a vertically varying Brunt-Vaisaila frequency, $N^2$. It is found that the normal-mode instability persists when $N^2$ increases quadratically with respect to the disc vertical coordinate. However we also find that the SRI seems to exist in this inviscid QHSG extreme only for channel wall conditions: when one or both of the reflecting walls are removed there is no instability in the asymptotic limit explored here. It is also found that only exponential-type SRI modes (as defined by Dubrulle et al. 2005) exist under these conditions. These equations also admit non-normal mode behaviour. Fixed Lagrangian pressure conditions on both radial boundaries predicts there to be no normal mode behaviour in the QHSG limit. The mathematical relationship between the results obtained here and that of the classic Eady (1949) problem for baroclinic instability is drawn. We conjecture as to the mathematical/physical nature of the SRI. The general linear problem, analyzed without approximation in the context of the Boussinesq equations, admits a potential vorticity-like quantity that is advectively conserved by the shear. Its existence means that a continuous spectrum \emph{is a generic feature of this system}. It also implies that in places where the Brunt-Vaisaila frequency becomes dominant the linearized flow may two-dimensionalize by advectively conserving its vertical vorticity.Comment: 16 pages. Accepted in MNRAS (09/05). New sections added and abstract change

Presumed killers? Vultures, stakeholders, misperceptions, and fake news

Vultures and condors are among the most threatened avian species in the world due to the impacts of human activities. Negative perceptions can contribute to these threats as some vulture species have been historically blamed for killing livestock. This perception of conflict has increased in recent years, associated with a viral spread of partial and biased information through social media and despite limited empirical support for these assertions. Here, we highlight that magnifying infrequent events of livestock being injured by vultures through publically shared videos or biased news items negatively impact efforts to conserve threatened populations of avian scavengers. We encourage environmental agencies, researchers, and practitioners to evaluate the reliability, frequency, and context of reports of vulture predation, weighing those results against the diverse and valuable contributions of vultures to environmental health and human well-being. We also encourage the development of awareness campaigns and improved livestock management practices, including commonly available nonlethal deterrence strategies, if needed. These actions are urgently required to allow the development of a more effective conservation strategy for vultures worldwide.Peer reviewe

Sphingomyelin synthase-related protein SMSr controls ceramide homeostasis in the ER

Ceramides are central intermediates of sphingolipid metabolism with critical functions in cell organization and survival. They are synthesized on the cytosolic surface of the endoplasmic reticulum (ER) and transported by ceramide transfer protein to the Golgi for conversion to sphingomyelin (SM) by SM synthase SMS1. In this study, we report the identification of an SMS1-related (SMSr) enzyme, which catalyses the synthesis of the SM analogue ceramide phosphoethanolamine (CPE) in the ER lumen. Strikingly, SMSr produces only trace amounts of CPE, i.e., 300-fold less than SMS1-derived SM. Nevertheless, blocking its catalytic activity causes a substantial rise in ER ceramide levels and a structural collapse of the early secretory pathway. We find that the latter phenotype is not caused by depletion of CPE but rather a consequence of ceramide accumulation in the ER. Our results establish SMSr as a key regulator of ceramide homeostasis that seems to operate as a sensor rather than a converter of ceramides in the ER

Understanding continent-wide variation in vulture ranging behavior to assess feasibility of Vulture Safe Zones in Africa: Challenges and possibilities

Protected areas are intended as tools in reducing threats to wildlife and preserving habitat for their long-term population persistence. Studies on ranging behavior provide insight into the utility of protected areas. Vultures are one of the fastest declining groups of birds globally and are popular subjects for telemetry studies, but continent-wide studies are lacking. To address how vultures use space and identify the areas and location of possible vulture safe zones, we assess home range size and their overlap with protected areas by species, age, breeding status, season, and region using a large continent-wide telemetry datasets that includes 163 individuals of three species of threatened Gyps vulture. Immature vultures of all three species had larger home ranges and used a greater area outside of protected areas than breeding and non-breeding adults. Cape vultures had the smallest home range sizes and the lowest level of overlap with protected areas. Rüppell\u27s vultures had larger home range sizes in the wet season, when poisoning may increase due to human-carnivore conflict. Overall, our study suggests challenges for the creation of Vulture Safe Zones to protect African vultures. At a minimum, areas of 24,000 km2 would be needed to protect the entire range of an adult African White-backed vulture and areas of more than 75,000 km2 for wider-ranging Rüppell\u27s vultures. Vulture Safe Zones in Africa would generally need to be larger than existing protected areas, which would require widespread conservation activities outside of protected areas to be successful