Algorithmique et complexité des systèmes à compteurs

Réalisé en cotutelle avec l'École normale supérieure de Cachan – Université Paris-Saclay

Desenvolvimento de um sistema eletronico com registro simultaneo de amplitude e instante de ocorrencias dos pulsos, aplicado ao metodo de coincidencias 4'pi''beta''gama'

Dissertacao (Mestrado)

Movement patterns and habitat use of the silver tip shark ("Carcharhinus albimarginatus") at the Revillagigedo Archipelago

[EN]The Revillegigedo Archipelago Biosphere Reserve is home to several shark species that spend at least part of their life history associated with oceanic islands associated with hotspots of pelagic biodiversity and in particular with apex predators. Silvertip sharks (Carcharhinus albimarginatus) are is commonly found in all the islands of the archipelago. However, very little is known about the spatial and temporal scales of their habitat use and associated ecological role. In this study, we employed passive acoustic telemetry to investigate the residency patterns and migration dynamics of 35 silvertip sharks tagged in three islands of the archipelago (San Benedicto, Socorro and Roca Partida) and monitored for a period of between 7 and 1165 (mean ± SD: 553.7± 354.2) days.

Migration and Residence Patterns of Salmonids in Puget Sound, Washington

Thesis (Ph.D.)--University of Washington, 2016-08

Navigating uncertain waters: a critical review of inferring foraging behaviour from location and dive data in pinnipeds

In the last thirty years, the emergence and progression of biologging technology has led to great advances in marine predator ecology. Large databases of location and dive observations from biologging devices have been compiled for an increasing number of diving predator species (such as pinnipeds, sea turtles, seabirds and cetaceans), enabling complex questions about animal activity budgets and habitat use to be addressed. Central to answering these questions is our ability to correctly identify and quantify the frequency of essential behaviours, such as foraging. Despite technological advances that have increased the quality and resolution of location and dive data, accurately interpreting behaviour from such data remains a challenge, and analytical methods are only beginning to unlock the full potential of existing datasets. This review evaluates both traditional and emerging methods and presents a starting platform of options for future studies of marine predator foraging ecology, particularly from location and two-dimensional (time-depth) dive data. We outline the different devices and data types available, discuss the limitations and advantages of commonly-used analytical techniques, and highlight key areas for future research. We focus our review on pinnipeds - one of the most studied taxa of marine predators - but offer insights that will be applicable to other air-breathing marine predator tracking studies. We highlight that traditionally-used methods for inferring foraging from location and dive data, such as first-passage time and dive shape analysis, have important caveats and limitations depending on the nature of the data and the research question. We suggest that more holistic statistical techniques, such as state-space models, which can synthesise multiple track, dive and environmental metrics whilst simultaneously accounting for measurement error, offer more robust alternatives. Finally, we identify a need for more research to elucidate the role of physical oceanography, device effects, study animal selection, and developmental stages in predator behaviour and data interpretation.

Avaliação de sensores de baixo custo e de métodos de referência para a monitorização da qualidade do ar

A crescente urbanização global tem como consequência o aumento dos níveis de poluentes na atmosfera e a respetiva deterioração da qualidade do ar. O controlo da poluição atmosférica e monitorização da qualidade do ar são passos fundamentais para implementar estratégias de redução e estimular a consciência ambiental dos cidadãos. Com este intuito, existem várias técnicas e tecnologias que podem ser usadas para monitorizar a qualidade do ar. A utilização de microsensores surge como uma ferramenta inovadora para a monitorização da qualidade do ar. E, apesar dos desempenhos dos microsensores permitirem uma nova estratégia, resultando em respostas rápidas, baixos custos operacionais e eficiências elevadas, que não podem ser alcançados apenas com abordagens convencionais, ainda é necessário aprofundar o conhecimento a fim de integrar estas novas tecnologias, particularmente quanto à verificação do desempenho dos sensores comparativamente aos métodos de referência em campanhas experimentais. Esta dissertação, desenvolvida no Instituto do Ambidente e Desenvolvimento em forma de estágio, teve como objetivo a avaliação do desempenho de sensores de baixo custo comparativamente com os métodos de referência, tendo como base uma campanha de monitorização da qualidade do ar realizada no centro de Aveiro durante 2 semanas de outubro de 2014. De forma mais específica pretende-se perceber até que ponto se podem utilizar sensores de baixo custo que cumpram os requisitos especificados na legislação e as especificidades das normas, estabelecendo assim um protocolo de avaliação de microsensores. O trabalho realizado passou ainda pela caracterização da qualidade do ar no centro de Aveiro para o período da campanha de monitorização. A aplicação de microsensores eletroquímicos, MOS e OPC em paralelo com equipamento de referência neste estudo de campo permitiu avaliar a fiabilidade e a incerteza destas novas tecnologias de monitorização. Com este trabalho verificou-se que os microsensores eletroquímicos são mais precisos comparativamente aos microsensores baseados em óxidos metálicos, apresentando correlações fortes com os métodos de referência para diversos poluentes. Por sua vez, os resultados obtidos pelos contadores óticos de partículas foram satisfatórios, contudo poderiam ser melhorados quer pelo modo de amostragem, quer pelo método de tratamento de dados aplicado. Idealmente, os microsensores deveriam apresentar fortes correlações com o método de referência e elevada eficiência de recolha de dados. No entanto, foram identificados alguns problemas na eficiência de recolha de dados dos sensores que podem estar relacionados com a humidade relativa e temperaturas elevadas durante a campanha, falhas de comunicação intermitentes e, também, a instabilidade e reatividade causada por gases interferentes. Quando as limitações das tecnologias de sensores forem superadas e os procedimentos adequados de garantia e controlo de qualidade possam ser cumpridos, os sensores de baixo custo têm um grande potencial para permitir a monitorização da qualidade do ar com uma elevada cobertura espacial, sendo principalmente benéfico em áreas urbanas.

Avaliação de sensores de baixo custo e de métodos de referência para a monitorização da qualidade do ar

A crescente urbanização global tem como consequência o aumento dos níveis de poluentes na atmosfera e a respetiva deterioração da qualidade do ar. O controlo da poluição atmosférica e monitorização da qualidade do ar são passos fundamentais para implementar estratégias de redução e estimular a consciência ambiental dos cidadãos. Com este intuito, existem várias técnicas e tecnologias que podem ser usadas para monitorizar a qualidade do ar. A utilização de microsensores surge como uma ferramenta inovadora para a monitorização da qualidade do ar. E, apesar dos desempenhos dos microsensores permitirem uma nova estratégia, resultando em respostas rápidas, baixos custos operacionais e eficiências elevadas, que não podem ser alcançados apenas com abordagens convencionais, ainda é necessário aprofundar o conhecimento a fim de integrar estas novas tecnologias, particularmente quanto à verificação do desempenho dos sensores comparativamente aos métodos de referência em campanhas experimentais. Esta dissertação, desenvolvida no Instituto do Ambidente e Desenvolvimento em forma de estágio, teve como objetivo a avaliação do desempenho de sensores de baixo custo comparativamente com os métodos de referência, tendo como base uma campanha de monitorização da qualidade do ar realizada no centro de Aveiro durante 2 semanas de outubro de 2014. De forma mais específica pretende-se perceber até que ponto se podem utilizar sensores de baixo custo que cumpram os requisitos especificados na legislação e as especificidades das normas, estabelecendo assim um protocolo de avaliação de microsensores. O trabalho realizado passou ainda pela caracterização da qualidade do ar no centro de Aveiro para o período da campanha de monitorização. A aplicação de microsensores eletroquímicos, MOS e OPC em paralelo com equipamento de referência neste estudo de campo permitiu avaliar a fiabilidade e a incerteza destas novas tecnologias de monitorização. Com este trabalho verificou-se que os microsensores eletroquímicos são mais precisos comparativamente aos microsensores baseados em óxidos metálicos, apresentando correlações fortes com os métodos de referência para diversos poluentes. Por sua vez, os resultados obtidos pelos contadores óticos de partículas foram satisfatórios, contudo poderiam ser melhorados quer pelo modo de amostragem, quer pelo método de tratamento de dados aplicado. Idealmente, os microsensores deveriam apresentar fortes correlações com o método de referência e elevada eficiência de recolha de dados. No entanto, foram identificados alguns problemas na eficiência de recolha de dados dos sensores que podem estar relacionados com a humidade relativa e temperaturas elevadas durante a campanha, falhas de comunicação intermitentes e, também, a instabilidade e reatividade causada por gases interferentes. Quando as limitações das tecnologias de sensores forem superadas e os procedimentos adequados de garantia e controlo de qualidade possam ser cumpridos, os sensores de baixo custo têm um grande potencial para permitir a monitorização da qualidade do ar com uma elevada cobertura espacial, sendo principalmente benéfico em áreas urbanas.

Early post-fledgling survival in a fragmented population of a tropical cooperative breeding passerine

During the last years tropical forest has been a target of intense study especially due to its recent big scale destruction. Although a lot still needs to be explored, we start realizing how negative can the impact of our actions be for the ecosystem. Subsequently, the living community have been developing strategies to overcome this problem avoiding bottlenecks or even extinctions. Cooperative breeding (CB) has been recently pointed out as one of those strategies. CB is a breeding system where more than two individuals raise one brood. In most of the cases, extra individuals are offspring that delay their dispersal and independent breeding what allows them to help their parents raising their siblings in the subsequent breeding season. Such behavior is believed to be due, per example, to the lack of mates or breeding territories (ecological constraints hypothesis), a consequence of habitat fragmentation and/or disturbance. From this point, CB is easily promoted by a higher reproductive success of group vs pairs or single individuals. Accordingly, during this thesis I explore the early post-fledging survival of a cooperative breeding passerine, namely the impact of individual/habitat quality in its survival probability during the dependence period of the chicks. Our study species is the Cabanis’s greenbul (Phyllastrephus cabanisi), a medium-sized, brownish passerine, classified within the Pycnonotidae family. It is found over part of Central Africa in countries such as Angola, Democratic Republic of the Congo, Mozambique and Kenya, inhabiting primary and secondary forests, as well as woodland of various types up to 2700m of altitude. Previous studies have concluded that PC is a facultative cooperative breeder. This study was conducted in Taita Hills (TH) at the Eastern Arc Mountains (EAM), a chain of mountains running from Southeast Kenya to the South of Tanzania. TH comprises an area of 430 ha and has been suffering intense deforestation reflecting 98% forest reduction over the last 200 years. Nowadays its forest is divided in fragments and our study was based in 5of those fragments. We access the post-fledging survival through radio-telemetry. The juvenile survey was done through the breeding females in which transmitters were placed with a leg-loop technique. Ptilochronology is consider to be the study of feather growth bars and has been used to study the nutritional state of a bird. This technique considers that the feather growth rate is positively proportional to the individual capability of ingesting food and to the food availability. This technique is therefore used to infer for individual/habitat quality. Survival was lowest during the first 5 days post-fledging representing 53.3%. During the next 15 days, risk of predation decreased with only 14.3% more deceased individuals. This represents a total of only 33% survived individuals in the end of the 50 days. Our results showed yet a significant positive relationship between flock size and post-fledging survival as well as between ptilochronology values and post-fledgling survival. In practice, these imply that on this population, as bigger the flock, as greater the post fledging survival and that good habitat quality or good BF quality, will lead to a higher juvenile survival rate. We believe that CB is therefore an adaptive behaviour to the lack of mates/breeding territory originated from the mass forest destruction and disturbance. Such results confirms the critical importance of habitat quality in the post-fledging survival and, for the first time, demonstrates how flock size influences the living probability of the juveniles and therefore how it impacts the (local) population dynamics of this species. In my opinion, future research should be focus in disentangle individual and habitat quality from each other and verify which relationship exist between them. Such study will allow us to understand which factor has a stronger influence in the post-fledging survival and therefore redirect our studies in that direction. In order to confirm the negative impact of human disturbance and forest fragmentation, it would be of major relevance to compare the reproductive strategies and reproductive success of populations living in intact forests and disturbed patches.

Spatial behavior of two coral reef fishes within a Caribbean Marine Protected Area

A better understanding of the key ecological processes of marine organisms is fundamental to improving design and effective implementation of marine protected areas (MPAs) and marine biodiversity. The movement behavior of coral reef fish is a complex mechanism that is highly linked to species life-history traits, predation risk and food resources. We used passive acoustic telemetry to study monthly, daily and hourly movement patterns and space use in two species, Schoolmaster snapper (Lutjanus apodus) and Stoplight parrotfish (Sparisoma viride). We investigated the spatial overlap between the two species and compared intra-specific spatial overlap between day and night. Presence-absence models showed different diel presence and habitat use patterns between the two species. We constructed a spatial network of the movement patterns, which showed that for both species when fish were detected by the array of receivers most movements were made around the coral reef habitat while occasionally moving to silt habitats. Our results show that most individuals made predictable daily crepuscular migrations between different locations and habitat types, although individual behavioral changes were observed for some individuals across time. Our study also highlights the necessity to consider multiple species during MPA implementation and to take into account the specific biological and ecological traits of each species. The low number of fish detected within the receiver array, as well as the intraspecific variability observed in this study, highlight the need to compare results across species and individuals to be used for MPA management.

The pre-reproductive period in a tropical bird: parental care, dispersal, survival, and avian life histories

The period between offspring birth and recruitment into the breeding population is considered one of the least understood components of animal life histories. Yet, examining this period is essential for studies of parental care, dispersal, demography, and life histories. Studies of the pre-reproductive period are particularly few in tropical regions, where the organization of life histories are predicted to differ compared to northern hemisphere species. For my dissertation I used radio-telemetry, mark-resighting, and field observations to study the pre-reproductive period in a Neotropical bird, the western slaty-antshrike (Thamnophilus atrinucha), in Panama. First, I found that parental care after offspring left the nest (the post-fledging period) was greater than care during the nestling period. Prolonged care resulted in a clear trade-off for parents as they did not nest again until fledglings from the first brood were independent. Parents fed offspring for a prolonged duration during the post-fledging period and higher post-fledging survival was observed compared to many northern hemisphere species. Second, I observed that offspring that remained with parents for longer periods on the natal territory had higher survival both while on the natal territory and after dispersal compared to those dispersing earlier. Parental aggression towards offspring increased with offspring age and offspring dispersed earlier when parents renested. Contrary to other family living species, only a small proportion of antshrike offspring remained on the natal territory until the following year and all dispersed to float. Floating is when juveniles wander within other breeding pairs’ territories. These results suggest that the benefits of delayed dispersal declined with offspring age and with renesting by parents. Third, I observed that survival during the dependent period and first year was greater in slaty antshrikes compared to that of northern hemisphere species. Pre-reproductive survival relative to adult survival was equal or greater than that observed in northern hemisphere species. The date offspring left the nest, mass, and age at dispersal influenced offspring survival, whereas offspring sex and year did not. Relatively high survival during the pre-reproductive period coupled with comparatively low annual productivity clarifies how many tropical species achieve replacement. High juvenile survival appears to obtain from extended post-fledging parental care, delayed dispersal, low costs of dispersal, and a less seasonal environment. Lastly, I experimentally manipulated begging at the nest to examine changes in parental behavior. Under elevated begging, parents increased provisioning rates and reduced the time between arrival to the nest and feeding of nestlings, potentially to reduce begging sounds. Furthermore, parents switched to preferentially feed the closest offspring during the begging treatment. This suggests parents either allowed sibling competition to influence feeding decisions, or feeding the closer nestling increased the efficiency of provisioning. In summary, I found that slaty antshrikes have delayed age at reproduction, higher post-fledging and first year survival, extended post-fledging parental care, equal or greater pre-reproductive survival relative to adult survival, and delayed dispersal compared to many northern hemisphere passerines. These results suggest that this tropical species has a strategy of high investment into few offspring. Furthermore, reproductive effort is equal or greater at least in slaty antshrikes compared to northern hemisphere species, suggesting that the latitudinal gradient in clutch size is not explained by a gradient in reproductive effort.

Thermal analysis during bone drilling using rigid polyurethane foams: numerical and experimental methodologies

Osteotomy or bone cutting is a common procedure in orthopaedic surgery, mainly in the treatment of fractures and reconstructive surgery. However, the excessive heat produced during the bone drilling process is a problem that counters the benefits of this type of surgery, because it can result in thermal osteonecrosis, bone reabsorption and damage the osseointegration of implants. The analysis of different drilling parameters and materials can allow to decrease the temperature during the bone drilling process and contribute to a greater success of this kind of surgical interventions. The main goal of this study was to build a numerical three-dimensional model to simulate the drilling process considering the type of bone, the influence of cooling and the bone density of the different composite materials with similar mechanical properties to the human bone and generally used in experimental biomechanics. The numerical methodology was coupled with an experimental methodology. The use of cooling proved to be essential to decrease the material damage during the drilling process. It was concluded that the materials with less porosity and density present less damage in drilling process. The developed numerical model proved to be a great tool in this kind of analysis. © 2016, The Brazilian Society of Mechanical Sciences and Engineering.