Ligand-Induced structural changes in TEM‑1 probed by molecular dynamics and relative binding free energy calculations

The TEM family of enzymes has had a crucial impact on the pharmaceutical industry due to their important role in antibiotic resistance. Even with the latest technologies in structural biology and genomics, no 3D structure of a TEM- 1/antibiotic complex is known previous to acylation. Therefore, the comprehension of their capability in acylate antibiotics is based on the protein macromolecular structure uncomplexed. In this work, molecular docking, molecular dynamic simulations, and relative free energy calculations were applied in order to get a comprehensive and thorough analysis of TEM-1/ampicillin and TEM-1/amoxicillin complexes. We described the complexes and analyzed the effect of ligand binding on the overall structure. We clearly demonstrate that the key residues involved in the stability of the ligand (hot-spots) vary with the nature of the ligand. Structural effects such as (i) the distances between interfacial residues (Ser70−Oγ and Lys73−Nζ, Lys73−Nζ and Ser130−Oγ, and Ser70−Oγ−Ser130−Oγ), (ii) side chain rotamer variation (Tyr105 and Glu240), and (iii) the presence of conserved waters can be also influenced by ligand binding. This study supports the hypothesis that TEM-1 suffers structural modifications upon ligand binding.

A survey in Portuguese X-ray fluoroscopy equipment: dose rates and image quality

X-ray fluoroscopy is essential in both diagnosis and medical intervention, although it may contribute to significant radiation doses to patients that have to be optimised and justified. Therefore, it is crucial to the patient to be exposed to the lowest achievable dose without compromising the image quality. The purpose of this study was to perform an analysis of the quality control measurements, particularly dose rates, contrast and spatial resolution of Portuguese fluoroscopy equipment and also to provide a contribution to the establishment of reference levels for the equipment performance parameters. Measurements carried out between 2007 and 2013 on 143 fluoroscopy equipment distributed by 34 nationwide health units were analysed. The measurements suggest that image quality and dose rates of Portuguese equipment are congruent with other studies, and in general, they are as per the Portuguese law. However, there is still a possibility of improvements intending optimisation at a national level.

Modelação do viaduto do Corgo durante o ensaio de carga estático

Trabalho Final de Mestrado elaborado no Laboratório Nacional de Engenharia Civil (LNEC) para a obtenção do grau de Mestre em Engenharia Civil pelo Instituto Superior de Engenharia de Lisboa no âmbito do protocolo de cooperação entre o ISEL e o LNEC

Avaliação e a Qualidade das Práticas de Inclusão para Alunos com PEA: Escala LAQI (Louisiana Autism Quality Indicators)

Dissertação apresentada à Escola Superior de Educação de Lisboa para obtenção de grau de mestre em Educação Especial, domínio Cognição e Multideficiência

RadiaLE: A framework for designing and assessing link quality estimators in wireless sensor networks

Stringent cost and energy constraints impose the use of low-cost and low-power radio transceivers in large-scale wireless sensor networks (WSNs). This fact, together with the harsh characteristics of the physical environment, requires a rigorous WSN design. Mechanisms for WSN deployment and topology control, MAC and routing, resource and mobility management, greatly depend on reliable link quality estimators (LQEs). This paper describes the RadiaLE framework, which enables the experimental assessment, design and optimization of LQEs. RadiaLE comprises (i) the hardware components of the WSN testbed and (ii) a software tool for setting-up and controlling the experiments, automating link measurements gathering through packets-statistics collection, and analyzing the collected data, allowing for LQEs evaluation. We also propose a methodology that allows (i) to properly set different types of links and different types of traffic, (ii) to collect rich link measurements, and (iii) to validate LQEs using a holistic and unified approach. To demonstrate the validity and usefulness of RadiaLE, we present two case studies: the characterization of low-power links and a comparison between six representative LQEs. We also extend the second study for evaluating the accuracy of the TOSSIM 2 channel model.

Radio link quality estimation in wireless sensor networks: a survey

Radio link quality estimation in Wireless Sensor Networks (WSNs) has a fundamental impact on the network performance and also affects the design of higher-layer protocols. Therefore, for about a decade, it has been attracting a vast array of research works. Reported works on link quality estimation are typically based on different assumptions, consider different scenarios, and provide radically different (and sometimes contradictory) results. This article provides a comprehensive survey on related literature, covering the characteristics of low-power links, the fundamental concepts of link quality estimation in WSNs, a taxonomy of existing link quality estimators, and their performance analysis. To the best of our knowledge, this is the first survey tackling in detail link quality estimation in WSNs. We believe our efforts will serve as a reference to orient researchers and system designers in this area.

Quantifying the channel quality for interference-aware wireless sensor networks

Reliability of communications is key to expand application domains for sensor networks. SinceWireless Sensor Networks (WSN) operate in the license-free Industrial Scientific and Medical (ISM) bands and hence share the spectrum with other wireless technologies, addressing interference is an important challenge. In order to minimize its effect, nodes can dynamically adapt radio resources provided information about current spectrum usage is available. We present a new channel quality metric, based on availability of the channel over time, which meaningfully quantifies spectrum usage. We discuss the optimum scanning time for capturing the channel condition while maintaining energy-efficiency. Using data collected from a number of Wi-Fi networks operating in a library building, we show that our metric has strong correlation with the Packet Reception Rate (PRR). This suggests that quantifying interference in the channel can help in adapting resources for better reliability. We present a discussion of the usage of our metric for various resource allocation and adaptation strategies.

OPTIMAX 2014 - Radiation dose and image quality optimisation in medical imaging

Medical imaging is a powerful diagnostic tool. Consequently, the number of medical images taken has increased vastly over the past few decades. The most common medical imaging techniques use X-radiation as the primary investigative tool. The main limitation of using X-radiation is associated with the risk of developing cancers. Alongside this, technology has advanced and more centres now use CT scanners; these can incur significant radiation burdens compared with traditional X-ray imaging systems. The net effect is that the population radiation burden is rising steadily. Risk arising from X-radiation for diagnostic medical purposes needs minimising and one way to achieve this is through reducing radiation dose whilst optimising image quality. All ages are affected by risk from X-radiation however the increasing population age highlights the elderly as a new group that may require consideration. Of greatest concern are paediatric patients: firstly they are more sensitive to radiation; secondly their younger age means that the potential detriment to this group is greater. Containment of radiation exposure falls to a number of professionals within medical fields, from those who request imaging to those who produce the image. These staff are supported in their radiation protection role by engineers, physicists and technicians. It is important to realise that radiation protection is currently a major European focus of interest and minimum competence levels in radiation protection for radiographers have been defined through the integrated activities of the EU consortium called MEDRAPET. The outcomes of this project have been used by the European Federation of Radiographer Societies to describe the European Qualifications Framework levels for radiographers in radiation protection. Though variations exist between European countries radiographers and nuclear medicine technologists are normally the professional groups who are responsible for exposing screening populations and patients to X-radiation. As part of their training they learn fundamental principles of radiation protection and theoretical and practical approaches to dose minimisation. However dose minimisation is complex – it is not simply about reducing X-radiation without taking into account major contextual factors. These factors relate to the real world of clinical imaging and include the need to measure clinical image quality and lesion visibility when applying X-radiation dose reduction strategies. This requires the use of validated psychological and physics techniques to measure clinical image quality and lesion perceptibility.

Structural stability of adenylate kinase from the sulfate-reducing bacteria Desulfovibrio gigas

Biophysical Chemistry 110 (2004) 83–92

Improving quality-of-service in wireless sensor networks by mitigating “Hidden-Node Collisions”

Wireless sensor networks (WSNs) emerge as underlying infrastructures for new classes of large-scale networked embedded systems. However, WSNs system designers must fulfill the quality-of-service (QoS) requirements imposed by the applications (and users). Very harsh and dynamic physical environments and extremely limited energy/computing/memory/communication node resources are major obstacles for satisfying QoS metrics such as reliability, timeliness, and system lifetime. The limited communication range of WSN nodes, link asymmetry, and the characteristics of the physical environment lead to a major source of QoS degradation in WSNs-the ldquohidden node problem.rdquo In wireless contention-based medium access control (MAC) protocols, when two nodes that are not visible to each other transmit to a third node that is visible to the former, there will be a collision-called hidden-node or blind collision. This problem greatly impacts network throughput, energy-efficiency and message transfer delays, and the problem dramatically increases with the number of nodes. This paper proposes H-NAMe, a very simple yet extremely efficient hidden-node avoidance mechanism for WSNs. H-NAMe relies on a grouping strategy that splits each cluster of a WSN into disjoint groups of non-hidden nodes that scales to multiple clusters via a cluster grouping strategy that guarantees no interference between overlapping clusters. Importantly, H-NAMe is instantiated in IEEE 802.15.4/ZigBee, which currently are the most widespread communication technologies for WSNs, with only minor add-ons and ensuring backward compatibility with their protocols standards. H-NAMe was implemented and exhaustively tested using an experimental test-bed based on ldquooff-the-shelfrdquo technology, showing that it increases network throughput and transmission success probability up to twice the values obtained without H-NAMe. H-NAMe effectiveness was also demonstrated in a target tracking application with mobile robots - over a WSN deployment.

An approach for reliability-based robust design optimisation of angle-ply composites

Variations of manufacturing process parameters and environmental aspects may affect the quality and performance of composite materials, which consequently affects their structural behaviour. Reliability-based design optimisation (RBDO) and robust design optimisation (RDO) searches for safe structural systems with minimal variability of response when subjected to uncertainties in material design parameters. An approach that simultaneously considers reliability and robustness is proposed in this paper. Depending on a given reliability index imposed on composite structures, a trade-off is established between the performance targets and robustness. Robustness is expressed in terms of the coefficient of variation of the constrained structural response weighted by its nominal value. The Pareto normed front is built and the nearest point to the origin is estimated as the best solution of the bi-objective optimisation problem.

Quality-of-service in wireless sensor networks: state-of-the-art and future directions

Wireless sensor networks (WSNs) are one of today’s most prominent instantiations of the ubiquituous computing paradigm. In order to achieve high levels of integration, WSNs need to be conceived considering requirements beyond the mere system’s functionality. While Quality-of-Service (QoS) is traditionally associated with bit/data rate, network throughput, message delay and bit/packet error rate, we believe that this concept is too strict, in the sense that these properties alone do not reflect the overall quality-ofservice provided to the user/application. Other non-functional properties such as scalability, security or energy sustainability must also be considered in the system design. This paper identifies the most important non-functional properties that affect the overall quality of the service provided to the users, outlining their relevance, state-of-the-art and future research directions.

Synechocystis ferredoxin/ferredoxin-NADP+-reductase/NADP+ complex: Structural model obtained by NMR-restrained docking

FEBS Letters 579 (2005) 4585–4590

F-LQE: a Fuzzy Link Quality Estimator for wireless sensor networks

Radio Link Quality Estimation (LQE) is a fundamental building block for Wireless Sensor Networks, namely for a reliable deployment, resource management and routing. Existing LQEs (e.g. PRR, ETX, Fourbit, and LQI ) are based on a single link property, thus leading to inaccurate estimation. In this paper, we propose F-LQE, that estimates link quality on the basis of four link quality properties: packet delivery, asymmetry, stability, and channel quality. Each of these properties is defined in linguistic terms, the natural language of Fuzzy Logic. The overall quality of the link is specified as a fuzzy rule whose evaluation returns the membership of the link in the fuzzy subset of good links. Values of the membership function are smoothed using EWMA filter to improve stability. An extensive experimental analysis shows that F-LQE outperforms existing estimators.

Demo abstract: RadiaLE: a framework for benchmarking link quality estimators

Link quality estimation is a fundamental building block for the design of several different mechanisms and protocols in wireless sensor networks (WSN). A thorough experimental evaluation of link quality estimators (LQEs) is thus mandatory. Several WSN experimental testbeds have been designed ([1–4]) but only [3] and [2] targeted link quality measurements. However, these were exploited for analyzing low-power links characteristics rather than the performance of LQEs. Despite its importance, the experimental performance evaluation of LQEs remains an open problem, mainly due to the difficulty to provide a quantitative evaluation of their accuracy. This motivated us to build a benchmarking testbed for LQE - RadiaLE, which we present here as a demo. It includes (i.) hardware components that represent the WSN under test and (ii.) a software tool for the set up and control of the experiments and also for analyzing the collected data, allowing for LQEs evaluation.