Luís Silva

The Clear-PEM Electronics System

The Clear-PEM detector system is a compact positron emission mammography scanner with about 12000 channels aiming at high sensitivity and good spatial resolution. Front-end, Trigger, and Data Acquisition electronics are crucial components of this system. The on-detector front-end is implemented as a data-driven synchronous system that identifies and selects the analog signals whose energy is above a predefined threshold. The off-detector trigger logic uses digitized front-end data streams to compute pulse amplitudes and timing. Based on this information it generates a coincidence trigger signal that is used to initiate the conditioning and transfer of the relevant data to the data acquisition computer. To minimize dead-time, the data acquisition electronics makes extensive use of pipeline processing structures and derandomizer memories with multievent capacity. The system operates at 100-MHz clock frequency, and is capable of sustaining a data acquisition rate of 1 million events per second with an efficiency above 95%, at a total single photon background rate of 10 MHz. The basic component of the front-end system is a low-noise amplifier-multiplexer chip presently under development. The off-detector system is designed around a dual-bus crate backplane for fast intercommunication between the system boards. The trigger and data acquisition logic is implemented in large FPGAs with 4 million gates. Monte Carlo simulation results evaluating the trigger performance, as well as results of hardware simulations are presented, showing the correctness of the design and the implementation approach

Variation in clutch size in relation to nest size in birds

Nests are structures built to support and protect eggs and/or offspring from predators, parasites, and adverse weather conditions. Nests are mainly constructed prior to egg laying, meaning that parent birds must make decisions about nest site choice and nest building behavior before the start of egg-laying. Parent birds should be selected to choose nest sites and to build optimally sized nests, yet our current understanding of clutch size-nest size relationships is limited to small-scale studies performed over short time periods. Here, we quantified the relationship between clutch size and nest size, using an exhaustive database of 116 slope estimates based on 17,472 nests of 21 species of hole and non-hole-nesting birds. There was a significant, positive relationship between clutch size and the base area of the nest box or the nest, and this relationship did not differ significantly between open nesting and hole-nesting species. The slope of the relationship showed significant intraspecific and interspecific heterogeneity among four species of secondary hole-nesting species, but also among all 116 slope estimates. The estimated relationship between clutch size and nest box base area in study sites with more than a single size of nest box was not significantly different from the relationship using studies with only a single size of nest box. The slope of the relationship between clutch size and nest base area in different species of birds was significantly negatively related to minimum base area, and less so to maximum base area in a given study. These findings are consistent with the hypothesis that bird species have a general reaction norm reflecting the relationship between nest size and clutch size. Further, they suggest that scientists may influence the clutch size decisions of hole-nesting birds through the provisioning of nest boxes of varying sizes.

Clutch-size variation in Western Palaearctic secondary hole-nesting passerine birds in relation to nest box design

Secondary hole-nesting birds that do not construct nest holes themselves and hence regularly breed in nest boxes constitute important model systems for field studies in many biological disciplines with hundreds of scientists and amateurs involved. Those research groups are spread over wide geographic areas that experience considerable variation in environmental conditions, and researchers provide nest boxes of varying designs that may inadvertently introduce spatial and temporal variation in reproductive parameters. We quantified the relationship between mean clutch size and nest box size and material after controlling for a range of environmental variables in four of the most widely used model species in the Western Palaearctic: great tit Parus major, blue tit Cyanistes caeruleus, pied flycatcher Ficedula hypoleuca and collared flycatcher F.albicollis from 365 populations and 79610 clutches. Nest floor area and nest box material varied non-randomly across latitudes and longitudes, showing that scientists did not adopt a random box design. Clutch size increased with nest floor area in great tits, but not in blue tits and flycatchers. Clutch size of blue tits was larger in wooden than in concrete nest boxes. These findings demonstrate that the size of nest boxes and material used to construct nest boxes can differentially affect clutch size in different species. The findings also suggest that the nest box design may affect not only focal species, but also indirectly other species through the effects of nest box design on productivity and therefore potentially population density and hence interspecific competition.

The Strait of Gibraltar poses an effective barrier to host-specialised but not to host-generalised lineages of avian Haemosporidia

One of the major concerns with ongoing environmental global change is the ability of parasites to shift their distribution (both geographically and across hosts) and to increase in virulence. To understand the structure, diversity and connectivity of parasite communities across the Mediterranean Sea, we used avian haemosporidian communities associated with forest birds of northwestern Africa and northwestern Iberia as a model system. We characterised host specificity of lineages and tested whether host generalists are more likely to cross the biogeographic barrier imposed by the Strait of Gibraltar than host specialists. We sampled 321 birds of 43 species in northwestern Africa and 735 birds of 49 species in northwestern Iberia. Using a PCR-based approach to amplify Plasmodium, Haemoproteus and Leucocytozoon parasites, we retrieved 969 sequences representing 200 unique cytochrome-b lineages. Haemosporidians infected a significantly higher proportion of birds in northwestern Africa (78.5%) than in northwestern Iberia (50.5%). Relative diversity of different haemosporidian genera did not differ between our study areas, but Plasmodium was overrepresented among individual infections in northwestern Iberia. Haemoproteus and Leucocytozoon lineages were predominantly host-specialised and Plasmodium lineages were host-generalised. The number of regions occupied by lineages was significantly associated with their host specificity and abundance. These data are consistent with the positive abundance-occupancy relationship and patterns of host specificity among different haemosporidian genera observed in other studies.

Performance simulation studies of the clear-PEM DAQ/trigger system

The clear-PEM detector is a positron emission mammography scanner based on high-granularity avalanche photodiodes readout with 12 288 channels. The front-end sub-system is instrumented with low-noise 192:2 channel amplifier-multiplexer ASICs and free-running sampling ADCs. The off-detector trigger, implemented in a FPGA based architecture, computes the pulses amplitude and timing required for coincidence validation from the front-end data streams. A high-level C++ simulation tool was developed for data acquisition performance analysis and validated at bit level against FPGA VHDL testbenches. In this work, simulation studies concerning the performance of the on-line/off-line energy and time extraction algorithms and the foreseen detector energy and time resolution are presented. Time calibration, trigger efficiency and ghosting are also discussed

Interspecific variation in the relationship between clutch size, laying date and intensity of urbanization in four species of hole-nesting birds

Abstract The increase in size of human populations in urban and agricultural areas has resulted in considerable habitat conversion globally. Such anthropogenic areas have specific environmental characteristics, which influence the physiology, life history, and population dynamics of plants and animals. For example, the date of bud burst is advanced in urban compared to nearby natural areas. In some birds, breeding success is determined by synchrony between timing of breeding and peak food abundance. Pertinently, caterpillars are an important food source for the nestlings of many bird species, and their abundance is influenced by environmental factors such as temperature and date of bud burst. Higher temperatures and advanced date of bud burst in urban areas could advance peak caterpillar abundance and thus affect breeding phenology of birds. In order to test whether laying date advance and clutch sizes decrease with the intensity of urbanization, we analyzed the timing of breeding and clutch size in relation to intensity of urbanization as a measure of human impact in 199 nest box plots across Europe, North Africa, and the Middle East (i.e., the Western Palearctic) for four species of hole‐nesters: blue tits (Cyanistes caeruleus), great tits (Parus major), collared flycatchers (Ficedula albicollis), and pied flycatchers (Ficedula hypoleuca). Meanwhile, we estimated the intensity of urbanization as the density of buildings surrounding study plots measured on orthophotographs. For the four study species, the intensity of urbanization was not correlated with laying date. Clutch size in blue and great tits does not seem affected by the intensity of urbanization, while in collared and pied flycatchers it decreased with increasing intensity of urbanization. This is the first large‐scale study showing a species‐specific major correlation between intensity of urbanization and the ecology of breeding. The underlying mechanisms for the relationships between life history and urbanization remain to be determined. We propose that effects of food abundance or quality, temperature, noise, pollution, or disturbance by humans may on their own or in combination affect laying date and/or clutch size.

Implementation and analysis of traffic safety protocols based on ETSI Standard

The European Telecommunications Standards Institute (ETSI) standard has defined the Basic Set of Applications (BSA) which is composed of three main application classes road/traffic safety, traffic efficiency, and other value-added applications. Traffic safety applications strongly rely on the exchange of two types of safety messages that have been standardized by ETSI namely Cooperative Awareness Messages (CAMs) and Decentralized Environmental Notification Messages (DENMs). The ETSIs comprehensive and well documented standards present the structures and implementations guidelines of these safety messages yet there is lack of extensive work on the implementation and validation. Therefore, this paper presents a comprehensive architecture and implementation that has been developed to validate the potentials of CAM and DENM messaging capabilities. This paper evaluates the performance of CAM and DENM facilities through a custom IEEE 802.11p (ITS-G5) based prototype (IT2S) deployed in a field trial. The tests validates the CAM performance by tracking vehicles and various performance indicators such the packet error rate (PER), Received Signal strength (RSSI), connection distance between the OBUs and RSU, number of messages transmitted, GPS coordinates and successful packets received. Similarly, DENMs are validated by events such as traffic information, hazardous location and accidents. These tests motivate towards the unified solution for the implementation of a complete ITS.

The importance of lizards and small mammals as reservoirs for Borrelia lusitaniae in Portugal

Borrelia lusitaniae is a pathogen frequent in the Mediterranean area. Apart from lizards, evidence for birds and small mammals as competent reservoirs for this genospecies has been occasional. We collected questing ticks, skin biopsies and Ixodes sp. ticks feeding on lizards, birds and small mammals in a B. burgdorferi s.l. (sensu lato) enzootic area to assess their importance in the maintenance of B. lusitaniae. Borrelia lusitaniae was the most prevalent genospecies in questing ticks and was commonly found in larvae feeding on Psammodromus algirus. One biopsy infected with B. lusitaniae was collected from the tail of one Podarcis hispanica, which suggests systemic infection. Ixodes ricinus larvae feeding on Apodemus sylvaticus were infected with B. lusitaniae but with a lower prevalence. Our results reinforce the importance of lizards as reservoirs for B. lusitaniae, suggesting that P. algirus, in particular, acts as main reservoir for B. lusitaniae in Portugal.

Improved Message Forwarding for Multi-Hop HaRTES Real-Time Ethernet Networks

Nowadays, switched Ethernet networks are used in complex systems that encompass tens to hundreds of nodes and thousands of signals. Such scenarios require multi-switch architectures where communications frequently occur in multiple hops. In this paper we investigate techniques to allow efficient multi-hop communication using HaRTES switches. These are modified Ethernet switches that provide real-time traffic scheduling, dynamic bandwidth management and temporal isolation between real-time and non-real-time traffic. This paper addresses the problem of forwarding traffic in HaRTES networks. Two methods have been recently proposed, namely Distributed Global Scheduling (DGS) that buffers traffic between switches, and Reduced Buffering Scheme (RBS), that uses immediate forwarding. In this paper, we discuss the design and implementation of RBS within HaRTES and we carry out an experimental validation with a prototype implementation. Then, we carry out a comparison between RBS and DGS using worst-case response time analysis and simulation. The comparison clearly establishes the superiority of RBS concerning end-to-end response times. In fact, with sample message sets, we achieved reductions in end-to-end delay that were as high as 80 %.

eCall++: An enhanced emergency call system for improved road safety

This paper presents an enhanced emergency Call (eCall) system that combines the native eCall services with the benefits provided by vehicular communications networks. The proposed solution, named eCall++, consists of a mobile application that automatically detects an accident and disseminates the alert notification, both via eCall and vehicular communications standards (IEEE WAVE / ETSI ITS-G5). In this work, two additional services are introduced: a passenger detection algorithm that informs the emergency services about the number of people inside the car during the crash; and a video streaming mechanism that enables vehicles in the vicinity of the accident to send a live record of the accident scene. These features are developed and implemented on an Android device connected to a custom vehicular communications system (the IT2S platform). The experimentally obtained results validate the proposed system and provide viable evidence to add additional features to the conventional eCall architecture.