An embedded distributed tool for transportation systems health assessment

International audienceThis article presents an embedded distributed tool for health assessment of complex systems. The presented architecture is based on a solving method for embedded technical diagnostics and prognostics. This tool provides services enabling the evaluation of the health status of complex systems. Diagnostic services provide information for the maintenance decision support system that leads to reduce the periods of unavailability and determine if their future mission can be carried out. The diagnostic and prognostic functions are detailed and the exchanged data are specified. An example shows the feasibility of the proposed architecture and demonstrates the correctness of the developed algorithms

Addressing data integration challenges to link ecological processes across scales

Data integration is a statistical modeling approach that incorporates multiple data sources within a unified analytical framework. Macrosystems ecology – the study of ecological phenomena at broad scales, including interactions across scales – increasingly employs data integration techniques to expand the spatiotemporal scope of research and inferences, increase the precision of parameter estimates, and account for multiple sources of uncertainty in estimates of multiscale processes. We highlight four common analytical challenges to data integration in macrosystems ecology research: data scale mismatches, unbalanced data, sampling biases, and model development and assessment. We explain each problem, discuss current approaches to address the issue, and describe potential areas of research to overcome these hurdles. Use of data integration techniques has increased rapidly in recent years, and given the inferential value of such approaches, we expect continued development and wider application across ecological disciplines, especially in macrosystems ecology

Forest stand conditions after Phytophthora ramorum management in northern California: post-treatment observations inform future responses

In 2006, several isolated Phytophthora ramorum infested locations were selected just outside an 800-ha infested area in southern Humboldt County, California, for silvicultural treatments that targeted the removal and/or reduction of tanoak (Notholithocarpus densiflorus) and California bay laurel (Umbellularia californica), the main tree hosts supporting sporulation of P. ramorum. The treatments included cutting of hosts, cutting with burning, and herbicide removal. Important differences emerged between the treatment responses in shrub cover, tanoak resprouting, fuel loads, and host tree regeneration. In 2010, another isolated infestation was verified in northern Humboldt County. This infestation was 80 km away from the core infested area in southern Humboldt. Stand-level P. ramorum disease dynamic models and forest growth simulations parameterized with data collected in this northern infestation suggested that California bay laurel and tanoak thinning treatments may slow tanoak mortality, foster a greater component of mature tanoak over the next 100 years, and contribute to greater amounts of live-tree carbon. Reviewing these long-running, landscape-scale P. ramorum management projects provides a platform to inform future adaptive management of P. ramorum. This paper summarizes two presentations from the Sixth Sudden Oak Death Science Symposium held in June 2016 in San Francisco, California

Chronic wasting disease detection and mortality sources in semi-protected deer population

Surveillance for wildlife diseases is essential for assessing population dynamics of ungulates, especially in free-ranging populations where infected animals are difficult to sample. Chronic wasting disease (CWD) is an emerging infectious disease of concern because of the potential for substantial negative effects on populations of cervids. Variability in the likelihood that CWD is detected could invalidate traditional estimators for prevalence. In some instances, deer located after death cannot be tested for infectious diseases, including CWD, because of lack of availability or condition of appropriate tissues. We used various methods to detect infectious diseases that could cause mortality for deer Odocoileus spp. residing in Wind Cave National Park, South Dakota, USA, and we report survival estimates for animals in this population. We included 34 monthly encounters of deer resightings and 67 mortalities. We tested live deer by tonsillar biopsy for CWD and estimated pooled prevalence (mean ± SE) at 5.6 ± 3.0% over the three-year study. Live deer potentially had exposure to several infectious diseases, including bluetongue, epizootic hemorrhagic disease, bovine viral diarrhea, West Nile virus, and malignant catarrhal fever, but no apparent morbidity or mortality from those diseases. We tested survival and influence of covariates, including age and sex, using known-fate analysis in Program MARK. Those data best supported a model with time-invariant encounter probability and an annual survival of 72.8%. Even without direct pressure from hunting within the park, average life expectancy in this population was 3.2 years. Only 68% of mortalities contained sufficient material for CWD sampling (because of predation and scavenger activity) and \u3e42% of these were CWD-positive. These findings underscore the possible biases in postmortem surveillance estimates of disease prevalence because of potential for subclinical infected animals to be removed by predators and not tested

Outstanding challenges and future directions for biodiversity monitoring using citizen science data

1. There is increasing availability and use of unstructured and semi-structured citizen science data in biodiversity research and conservation. This expansion of a rich source of ‘big data’ has sparked numerous research directions, driving the development of analytical approaches that account for the complex observation processes in these datasets. 2. We review outstanding challenges in the analysis of citizen science data for biodiversity monitoring. For many of these challenges, the potential impact on ecological inference is unknown. Further research can document the impact and explore ways to address it. In addition to outlining research directions, describing these challenges may be useful in considering the design of future citizen science projects or additions to existing projects. 3. We outline challenges for biodiversity monitoring using citizen science data in four partially overlapping categories: challenges that arise as a result of (a) observer behaviour; (b) data structures; (c) statistical models; and (d) communication. Potential solutions for these challenges are combinations of: (a) collecting additional data or metadata; (b) analytically combining different datasets; and (c) developing or refining statistical models. 4. While there has been important progress to develop methods that tackle most of these challenges, there remain substantial gains in biodiversity monitoring and subsequent conservation actions that we believe will be possible by further research and development in these areas. The degree of challenge and opportunity that each of these presents varies substantially across different datasets, taxa and ecological questions. In some cases, a route forward to address these challenges is clear, while in other cases there is more scope for exploration and creativity

Les effets relatifs des variables caractérisants les petits étangs, et des interactions avec les prédateurs, sur l'occupation et l'abondance des espèces de trois groupes de vertébrés dans le Nord-du-Québec

Les milieux humides font partie des écosystèmes les plus menacés au monde. Dans les paysages boréaux, les milieux humides fournissent des services écologiques précieux et constituent des habitats de qualité pour plusieurs espèces. Dans le nord du Canada, les écosystèmes des milieux humides se transforment sous l’effet combiné des perturbations naturelles, du changement climatique et de l’utilisation des sols par l’humain. Ces territoires nordiques représenteront dans un avenir proche un potentiel croissant d’accès aux ressources naturelles, en particulier pour l’exploitation du bois, le développement hydroélectrique et les activités minières. Par conséquent, il peut en résulter une perte ou une réduction de l’habitat des espèces qui dépendent de certains types de milieux humides. Les milieux humides contenant de petits étangs (< 8 ha) sont particulièrement importants pour plusieurs vertébrés qui choisissent ces habitats pour se reposer, se nourrir et se reproduire, notamment les amphibiens, les oiseaux et les mammifères. Cependant, peu d’études ont porté sur la présence de vertébrés au sein des petits étangs et les connaissances sont donc encore fragmentaires. Nous manquons de connaissances sur les préférences en matière d’habitat, et sur l’influence des facteurs biotiques et abiotiques sur les espèces boréales. L’examen de ces facteurs est une première étape pour aborder la gestion des milieux humides et des espèces associées dans les milieux nordiques. L’objectif général de cette thèse était de comparer l’utilisation des étangs de tourbières et des étangs de castors, et de quantifier l’influence des facteurs qui caractérisent ces habitats, ainsi que les interactions biotiques sur trois groupes de vertébrés: les amphibiens, les oiseaux et les mammifères. La région d’étude est située dans la forêt boréale canadienne, dans la région Eeyou-Istchee Baie James, dans le nord-ouest du Québec. Nous avons échantillonné 38 étangs de tourbières et 12 étangs de castors de mai à août 2018 et de mai à juillet 2019, avec deux campagnes d’échantillonnage par an. Dans le chapitre II, nous avons examiné le rôle des facteurs propres à l’étang et au paysage sur l’occupation et l’abondance de trois espèces d’anoures à différents stades de leur cycle de vie, y compris les masses d’oeufs, les juvéniles et les mâles chanteurs. Les résultats n’indiquent pas d’effets significatifs des variables explicatives sur la probabilité d’occupation des mâles chanteurs. Les individus métamorphosés de la grenouille du Nord (Lithobates septentrionalis) étaient plus abondants dans les étangs de plus petite surface et à pH moins acides. L’effort reproducteur de la grenouille des bois (Lithobates sylvaticus) était plus élevé dans les étangs de castors que dans les étangs de tourbières. Ce chapitre renforce l’idée que les étangs de castors sont des environnements plus productifs pour les amphibiens que les étangs de tourbières. Les étangs de tourbières sont autant utilisés par les anoures juvéniles et adultes que les étangs à castors. Ce chapitre suggère aussi, étant donné que nous avons utilisé des méthodes visuelles et acoustiques complémentaires, que les amphibiens des latitudes nordiques sont des généralistes de l’habitat et ne sont pas limités à des facteurs spécifiques aux étangs et aux paysages. Dans le chapitre III, nous avons évalué comment l’occupation des oiseaux différait entre les deux types d’étangs, et comment les oiseaux répondaient aux facteurs locaux et paysagers, ainsi qu’à la présence d’un important prédateur de nids : l’écureuil roux (Tamiasciurus hudsonicus). Les enregistrements acoustiques ont permis d’identifier un total de 96 espèces d’oiseaux que nous avons regroupées en quatre guildes : espèces de début de succession, des forêts matures, généralistes et des milieux humides. Les résultats indiquent que les étangs de castors abritent une plus grande richesse d’espèces d’oiseaux de celle des étangs de tourbières, une tendance principalement due aux espèces de début de succession. La richesse des espèces était plus faible en présence d’écureuils roux. Les espèces forestières matures ont réagi positivement à la couverture forestière dans un rayon de 1000 m autour de l’étang. Ce chapitre démontre donc que les assemblages d’oiseaux profitent de la modification de l’habitat par les castors et sont affectés négativement par la présence des écureuils roux. Cela peut être dû à un effet direct de prédation ou parce que certaines espèces ne partagent pas le même habitat que ce prédateur. Le chapitre IV utilise une méthode d’échantillonnage passive différente, par pièges photographiques, pour comprendre comment les caractéristiques de l’habitat affectent les mammifères et les oiseaux qui utilisent les tourbières et les étangs de castors. Les données provenant de 150 stations de caméras ont documenté 11 espèces de mammifères de taille moyenne à grande et 45 espèces d’oiseaux. Les résultats ont montré que deux espèces de mammifères et quatre espèces d’oiseaux avaient des préférences inattendues pour les étangs de tourbières plutôt que pour les étangs de castors. La proximité des routes n’a pas affecté l’occupation des étangs. Nous avons démontré la pertinence de l’utilisation d’approches multi-espèces dans des régions où des informations de base sur la répartition des espèces ne sont généralement pas disponibles. Nous soulignons également que les pièges photographiques sont efficaces pour étudier les espèces d’oiseaux de milieu humide, en particulier les oiseaux aquatiques. Finalement, le couvert forestier n’a pas eu d’effet sur l’utilisation des étangs par les espèces, révélant ainsi une réponse différente selon les techniques d’observation utilisées dans cette thèse (visuelles et acoustiques) pour évaluer les réactions des espèces aux caractéristiques du paysage. Cette thèse de doctorat constitue une référence sur les étangs utilisés par les vertébrés dans leur aire de répartition nordique et dans une zone géographique peu explorée. Ces travaux de recherche auront permis de faire progresser la compréhension de deux types majeurs de milieux humides dans la région boréale. Les tourbières, considérées jusqu’à présent comme des environnements pauvres et hostiles, peuvent abriter une diversité remarquable de vertébrés à divers stades de leur cycle de vie. Cependant, les étangs de castors semblent être plus productifs en masse d’oeufs que les tourbières, bien que des études additionnelles soient nécessaires pour élucider la valeur différentielle des étangs de castors actifs et abandonnés. Un meilleur affinement des paramètres biologiques affectant la qualité de l’habitat pour diverses espèces et une reconnaissance plus large des interactions biotiques impliquant diverses espèces (prédation, compétition, par exemple) aideront à clarifier les modèles écologiques d’occupation des espèces. Dans un contexte de pressions anthropiques et climatiques croissantes sur les milieux humides boréaux, une meilleure compréhension des milieux humides permettra de mieux conserver ces habitats de grande qualité, ce qui profitera à un large ensemble d’espèces

Eco-epidemiological approach to management of tuberculosis in free-ranging and captive wildlife, An

2018 Summer.Includes bibliographical references.Tuberculosis (TB) is a disease of global importance affecting millions of humans, livestock, and wildlife. Control and eventual eradication of TB depends on dedicated management actions for all species. Accurately diagnosing TB can be challenging in wildlife species, for which validated tests may be unavailable or of limited sensitivity or specificity. Managing TB in wildlife poses additional difficulties, requiring considerable time and resources to implement at an appropriately broad scale. Each unique ecosystem where TB occurs requires management interventions designed to meet the area's conservation, ecological, social, and financial needs. In this dissertation, I explored the diagnosis and management of tuberculosis in wildlife in three different settings: free-ranging European badgers (Meles meles) in Ireland, working African elephants (Loxodonta africana) in Zimbabwe, and captive African and Asian elephants (Elephas maximus) in North America. Badgers are a reservoir of bovine TB in Ireland, while captive elephants around the world are at risk of TB from their human handlers. Badgers have historically been managed by culling, but there is a current transitioning to vaccination as the primary management tool. In contrast, captive elephants in high-resource settings are typically treated for TB upon diagnosis, although this option may be limited in low-income countries. The first objective of this research was to assess the impact of environmental factors in management of TB over three different studies. I explored how biotic and abiotic factors influence trapping success of badgers being managed for bovine TB in Ireland. In a second study of badgers, I estimated density of a population undergoing vaccination in relation to environmental variables and prior management history. Underlying badger density is an important driver in the TB disease dynamics between cattle and badgers, and can be used in predictions about and assessment of outcomes under vaccination. Finally, I examined potential risk factors for TB seropositive status in working African elephants in Zimbabwe, and identified unique potential exposures from the environment. The second objective of this dissertation was to study the performance of diagnostic tests in a novel setting and interpret the results in the context of exposures within the ecosystem. This study employed two serological tests, STAT-PAK and DPP, for the first time in working African elephants in a range country. I interpreted the results suggestive of exposure to mycobacteria in some elephants based on possible interactions with the complex community of humans, livestock, wildlife, and mycobacteria. The third objective of this dissertation was to develop recommendations for TB management programs based on surveys, capture data, and consideration of individual, population, and community factors. The results from our badger trapping study in Ireland formed the basis of suggested conditions under which vaccine delivery can be increased, because captures are most likely. We used mark-recapture data to estimate badger density in a vaccination area, which adds an important dimension to the Irish TB management program that includes badgers and cattle. Population density is an important factor in pathogen transmission and estimating density using these methods may be a priority for other wildlife populations being managed for TB. Our study of TB treatment in elephants provided a compilation of empirical data for elephant managers and veterinarians to inform clinical decision making. It also underscores the need for improved diagnostics to more confidently identify when animals are no longer infectious. For working African elephants, we documented other wildlife species with host potential on and around facilities, and considered these as possible sources for mycobacterial transmission. Our management guidelines for TB prevention specifically include measures to reduce direct and indirect contact with potential host species. Management of TB across humans and animal species remains a challenging prospect. A One Health approach that incorporates data and techniques across disciplines to build a complete picture of disease control is ideal for TB in wildlife. I drew from ecology and epidemiology to implement a holistic approach to diagnosing and managing TB in species of conservation concern, provide insight into the challenges of diagnosing and managing TB in free-ranging and captive wildlife, describe the benefits of a transdisciplinary approach, and expose areas in need of further research

Projecting climate-related disease burden : a guide for health departments

Climate change is expected to adversely affect public health through multiple pathways. Assessing the projected health burden is an important step for public health agencies to prepare for these impacts. This can be done qualitatively or quantitatively, but quantitative projections may provide more useful information about likely impacts.Many health departments are not particularly familiar with scenario-based, quantitative disease projections. To facilitate this process, the Climate and Health Program (CHP) at the Centers for Disease Control and Prevention (CDC) developed the Building Resilience Against Climate Effects (BRACE) framework. As part of BRACE, health agencies are encouraged to produce estimates of the future burden of disease for climate-related health outcomes. These estimates can then be used to rank the health outcomes, prioritize preventive actions, and design health adaptation plans.This guide presents a starting point for health departments interested in developing climate change health impact projections and lays out a general map of the process of establishing exposure-response relationships and developing scenario-based projections. The specifics of the process used to project future disease burden will vary greatly depending on local climate impacts, underlying vulnerabilities, the disease of interest, and other factors. While there is no \u201cgold standard\u201d for projecting the health impacts of climate change, our goal is to provide a digestible but thorough overview that will orient those interested in projecting climate change disease burden to facilitate public health preparedness for the challenges ahead.CS255978-APublication date from document properties.ProjectingClimateRelatedDiseaseBurden_508.pd

Bayesian hierarchical methods for species distribution modelling under imperfect detection

Monitoring the distribution of wildlife populations has become essential for the understanding of how species are affected by environmental changes and to provide adequate management plans and effective strategies for the conservation of biodiversity. The growing concern about biodiversity loss has led to a rapid development of sampling methods and data collection schemes that enables data of the distributions for multiple species to be obtained at different temporal and spatial scales. Nowadays, biodiversity conservation involves monitoring programs that target multiple species within a community where individual species responses vary widely. This high variability makes the task of identifying the ecological processes that drive species distributions challenging and complex. This complexity has led to the development of a wide range of species distribution models that allow the identification of the most important areas for biodiversity conservation. However, describing such processes is no easy task due to the sources of uncertainty that occur at different spatial and temporal scales and that are induced by imperfect detectability. Thus, modern methods in statistics are increasingly being used to analyse the distribution and abundance of wildlife populations while accounting for the multiple sources of error associated with both, the ecological process of interest and the data collection process. The present work extends some of the well-established species distribution modelling techniques that address imperfect detection and propose new methods to describe different attributes of biological communities (e.g. species rarity) and their relationship with the environment. Computer simulations were used to assess models performance. Then, the proposed methods were applied to a data set of Odonata occurrence records in water bodies across the UK that were partially observed due to imperfect detection. The data for this research were provided by the Hydroscape project (www.hydroscapeblog.wordpress.com), a project that aim to determine how different connectivity metrics interact with environmental stressors to affect species diversity in UK freshwaters. Chapter 1 gives a background of the ecological concepts and statistical principles that are commonly used in species distribution modelling, introduces the questions of interest and the aims of this research. It also shows an overview of the data and presents an exploratory analysis that will be necessary to take into account for the analysis in subsequent chapters. Chapter 2 reviews some of the existing models that have been developed to investigate species distributions under imperfect detection and apply such methods to the Odonata case study, discusses the importance of accounting for imperfect species detection through a simulation study, and compares different software and approaches that have been developed to fit such models. Chapter 3 proposes a new method to quantify species rarity in a community when species are detected imperfectly. Then, a two-step modeling framework is proposed as an approach that enables for a complex hierarchical model to be analyzed in different stages to provide a pragmatic computationally efficient method for choosing the most relevant predictors affecting an ecological response of interest while propagating the uncertainty associated with the estimation of this quantity on a second analysis. In chapter 4, a new method that accounts for non-linear relationships between species distribution and environmental conditions is developed. A simulation study is presented to assess the model performance under different scenarios and different methodological consideration practices are discussed. Chapter 5 provides an application of the model developed in chapter 4 to investigate Odonata species distribution temporal patterns and discusses how these results can be used for biodiversity conservation and management. Finally, chapter 6 summarizes the main outcomes of this research and discusses the methodological innovations and challenges of the proposed methods with a final discussion on possible future work