Hydrogen peroxide sensing, signaling and regulation of transcription factors

The regulatory mechanisms by which hydrogen peroxide (H2O2) modulates the activity of transcription factors in bacteria (OxyR and PerR), lower eukaryotes (Yap1, Maf1, Hsf1 and Msn2/4) and mammalian cells (AP-1, NRF2, CREB, HSF1, HIF-1, TP53, NF-κB, NOTCH, SP1 and SCREB-1) are reviewed. The complexity of regulatory networks increases throughout the phylogenetic tree, reaching a high level of complexity in mammalians. Multiple H2O2 sensors and pathways are triggered converging in the regulation of transcription factors at several levels: (1) synthesis of the transcription factor by upregulating transcription or increasing both mRNA stability and translation; (ii) stability of the transcription factor by decreasing its association with the ubiquitin E3 ligase complex or by inhibiting this complex; (iii) cytoplasm-nuclear traffic by exposing/masking nuclear localization signals, or by releasing the transcription factor from partners or from membrane anchors; and, (iv) DNA binding and nuclear transactivation by modulating transcription factor affinity towards DNA, co-activators or repressors, and by targeting specific regions of chromatin to activate individual genes. We also discuss how H2O2 biological specificity results from diverse thiol protein sensors, with different reactivity of their sulfhydryl groups towards H2O2, being activated by different concentrations and times of exposure to H2O2. The specific regulation of local H2O2 concentrations is also crucial and results from H2O2 localized production and removal controlled by signals. Finally, we formulate equations to extract from typical experiments quantitative data concerning H2O2 reactivity with sensor molecules. Rate constants of 140 M-1s−1 and ≥ 1.3 × 103 M-1s−1 were estimated, respectively, for the reaction of H2O2 with KEAP1 and with an unknown target that mediates NRF2 protein synthesis. In conclusion, the multitude of H2O2 targets and mechanisms provides an opportunity for highly specific effects on gene regulation that depend on the cell type and on signals received from the cellular microenvironment.

An Evaluation of Local Feature Combiners for Robot Visual Localization

In the last decade, local image features have been widely used in robot visual localization. To assess image similarity, a strategy exploiting these features compares raw descriptors extracted from the current image to those in the models of places. This paper addresses the ensuing step in this process, where a combining function must be used to aggregate results and assign each place a score. Casting the problem in the multiple classifier systems framework, we compare several candidate combiners with respect to their performance in the visual localization task. A deeper insight into the potential of the sum and product combiners is provided by testing two extensions of these algebraic rules: threshold and weighted modifications. In addition, a voting method, previously used in robot visual localization, is assessed. All combiners are tested on a visual localization task, carried out on a public dataset. It is experimentally demonstrated that the sum rule extensions globally achieve the best performance. The voting method, whilst competitive to the algebraic rules in their standard form, is shown to be outperformed by both their modified versions.

Use of negative information in positioning and tracking algorithms

To avoid additional hardware deployment, indoor localization systems have to be designed in such a way that they rely on existing infrastructure only. Besides the processing of measurements between nodes, localization procedure can include the information of all available environment information. In order to enhance the performance of Wi-Fi based localization systems, the innovative solution presented in this paper considers also the negative information. An indoor tracking method inspired by Kalman filtering is also proposed.

How a cyber-physical system can efficiently obtain a snapshot of physical information even in the presence of sensor faults

We present a distributed algorithm for cyber-physical systems to obtain a snapshot of sensor data. The snapshot is an approximate representation of sensor data; it is an interpolation as a function of space coordinates. The new algorithm exploits a prioritized medium access control (MAC) protocol to efficiently transmit information of the sensor data. It scales to a very large number of sensors and it is able to operate in the presence of sensor faults.

Molybdenum-containing proteins from Sulphate Reducing Bacteria: studying proteins with novel cofactors and revealing new features of old enzymes

Dissertação apresentada para a obtenção do Grau de Doutor em Bioquímica, especialidade de Bioquímica-Física pela Universidade Nova de Lisboa, Faculdade de Ciências e Tecnologia

An experimental study to compare the interface pressure and experience of healthy participants when lying still for 20 minutes in a supine position on two different imaging surfaces

Introduction: Pressure ulcers are a high cost, high volume issue for health and medical care providers, affecting patients’ recovery and psychological wellbeing. The current research of support surfaces on pressure as a risk factor in the development of pressure ulcers is not relevant to the specialised, controlled environment of the radiological setting. Method: 38 healthy participants aged 19-51 were placed supine on two different imaging surfaces. The XSENSOR pressure mapping system was used to measure the interface pressure. Data was acquired over a time of 20 minutes preceded by 6 minutes settling time to reduce measurement error. Qualitative information regarding participants’ opinion on pain and comfort was recorded using a questionnaire. Data analysis was performed using SPSS 22. Results: Data was collected from 30 participants aged 19 to 51 (mean 25.77, SD 7.72), BMI from 18.7 to 33.6 (mean 24.12, SD 3.29), for two surfaces, following eight participant exclusions due to technical faults. Total average pressure, average pressure for jeopardy areas (head, sacrum & heels) and peak pressure for jeopardy areas were calculated as interface pressure in mmHg. Qualitative data showed that a significant difference in experiences of comfort and pain was found in the jeopardy areas (P<0.05) between the two surfaces. Conclusion: A significant difference is seen in average pressure between the two surfaces. Pain and comfort data also show a significant difference between the surfaces, both findings support the proposal for further investigation into the effects of radiological surfaces as a risk factor for the formation of pressure ulcers.

Localization studies of the FemXAB protein family in Staphylococcus aureus

Dissertação apresentada para a obtenção do Grau de Mestre em Genética Molecular e Biomedicina, pela Universidade Nova de Lisboa, Faculdade de Ciências e Tecnologia

Reconstructing the architectural evolution of volcanic islands from combined K/AR, morphologic, tectonic, and magnetic data. The Faial Island exemple (Azores)

The morpho-structural evolution of oceanic islands results from competition between volcano growth and partial destruction by mass-wasting processes. We present here a multi-disciplinary study of the successive stages of development of Faial (Azores) during the last 1 Myr. Using high-resolution digital elevation model (DEM), and new K/Ar, tectonic, and magnetic data, we reconstruct the rapidly evolving topography at successive stages, in response to complex interactions between volcanic construction and mass wasting, including the development of a graben. We show that: (1) sub-aerial evolution of the island first involved the rapid growth of a large elongated volcano at ca. 0.85 Ma, followed by its partial destruction over half a million years; (2) beginning about 360 ka a new small edifice grew on the NE of the island, and was subsequently cut by normal faults responsible for initiation of the graben; (3) after an apparent pause of ca. 250 kyr, the large Central Volcano (CV) developed on the western side of the island at ca 120 ka, accumulating a thick pile of lava flows in less than 20 kyr, which were partly channelized within the graben; (4) the period between 120 ka and 40 ka is marked by widespread deformation at the island scale, including westward propagation of faulting and associated erosion of the graben walls, which produced sedimentary deposits; subsequent growth of the CV at 40 ka was then constrained within the graben, with lava flowing onto the sediments up to the eastern shore; (5) the island evolution during the Holocene involves basaltic volcanic activity along the main southern faults and pyroclastic eruptions associated with the formation of a caldera volcano-tectonic depression. We conclude that the whole evolution of Faial Island has been characterized by successive short volcanic pulses probably controlled by brief episodes of regional deformation. Each pulse has been separated by considerable periods of volcanic inactivity during which the Faial graben gradually developed. We propose that the volume loss associated with sudden magma extraction from a shallow reservoir in different episodes triggered incremental downward graben movement, as observed historically, when immediate vertical collapse of up to 2 m was observed along the western segments of the graben at the end of the Capelinhos eruptive crises (1957-58).

Global localization with non-quantized local image features

In the field of appearance-based robot localization, the mainstream approach uses a quantized representation of local image features. An alternative strategy is the exploitation of raw feature descriptors, thus avoiding approximations due to quantization. In this work, the quantized and non-quantized representations are compared with respect to their discriminativity, in the context of the robot global localization problem. Having demonstrated the advantages of the non-quantized representation, the paper proposes mechanisms to reduce the computational burden this approach would carry, when applied in its simplest form. This reduction is achieved through a hierarchical strategy which gradually discards candidate locations and by exploring two simplifying assumptions about the training data. The potential of the non-quantized representation is exploited by resorting to the entropy-discriminativity relation. The idea behind this approach is that the non-quantized representation facilitates the assessment of the distinctiveness of features, through the entropy measure. Building on this finding, the robustness of the localization system is enhanced by modulating the importance of features according to the entropy measure. Experimental results support the effectiveness of this approach, as well as the validity of the proposed computation reduction methods.

Pentagonal parch-excited sectorized antenna for localization systems

A pentagonal patch-excited sectorized antenna (SA) suitable for 2.4-2.5 GHz localization systems was studied and developed. The integration of six patch-excited structures converges into a sectorized antenna called Hive5 that provides gain improvement compared to a patch antenna, maximum variation of 3 dB beam width over the radiation pattern and circular polarization (CP). This antenna is presented and analyzed taking into account the tap length and the flare angle. The proposed antenna in combination with a RF-Switch provides a cost effective solution for localization based on Wireless Sensor Networks (WSN) and will be used for implementing angle of arrival (AoA) techniques combined with RF fingerprinting techniques.

Mechanical behavior and localized failure modes in a porous basalt from the Azores

Basaltic rocks are the main component of the oceanic upper crust, thus of potential interest for water and geothermal resources, storage of CO2 and volcanic edifice stability. In this work, we investigated experimentally the mechanical behavior and the failure modes of a porous basalt, with an initial connected porosity of 18%. Results were acquired under triaxial compression experiments at confining pressure in the range of 25-200 MPa on water saturated samples. In addition, a purely hydrostatic test was also performed to reach the pore collapse critical pressure P*. During hydrostatic loading, our results show that the permeability is highly pressure dependent, which suggests that the permeability is mainly controlled by pre-existing cracks. When the sample is deformed at pressure higher than the pore collapse pressure P*, some very small dilatancy develops due to microcracking, and an increase in permeability is observed. Under triaxial loading, two modes of deformation can be highlighted. At low confining pressure (Pc < 50 MPa), the samples are brittle and shear localization occurs. For confining pressure > 50 MPa, the stress-strain curves are characterized by strain hardening and volumetric compaction. Stress drops are also observed, suggesting that compaction may be localized. The presence of compaction bands is confirmed by our microstructure analysis. In addition, the mechanical data allows us to plot the full yield surface for this porous basalt, which follows an elliptic cap as previously observed in high porosity sandstones and limestones.

Low-cost vibration sensors: tendencies and applications in condition monitoring of machines and structures

Trabalho Final de Mestrado para obtenção do grau de Mestre em Engenharia Mecânica

Terminology and knowledge engineering conference. New frontiers in the constructive symbiosis of terminology and knowledge engineering

To meet the increasing demands of the complex inter-organizational processes and the demand for continuous innovation and internationalization, it is evident that new forms of organisation are being adopted, fostering more intensive collaboration processes and sharing of resources, in what can be called collaborative networks (Camarinha-Matos, 2006:03). Information and knowledge are crucial resources in collaborative networks, being their management fundamental processes to optimize. Knowledge organisation and collaboration systems are thus important instruments for the success of collaborative networks of organisations having been researched in the last decade in the areas of computer science, information science, management sciences, terminology and linguistics. Nevertheless, research in this area didn’t give much attention to multilingual contexts of collaboration, which pose specific and challenging problems. It is then clear that access to and representation of knowledge will happen more and more on a multilingual setting which implies the overcoming of difficulties inherent to the presence of multiple languages, through the use of processes like localization of ontologies. Although localization, like other processes that involve multilingualism, is a rather well-developed practice and its methodologies and tools fruitfully employed by the language industry in the development and adaptation of multilingual content, it has not yet been sufficiently explored as an element of support to the development of knowledge representations - in particular ontologies - expressed in more than one language. Multilingual knowledge representation is then an open research area calling for cross-contributions from knowledge engineering, terminology, ontology engineering, cognitive sciences, computational linguistics, natural language processing, and management sciences. This workshop joined researchers interested in multilingual knowledge representation, in a multidisciplinary environment to debate the possibilities of cross-fertilization between knowledge engineering, terminology, ontology engineering, cognitive sciences, computational linguistics, natural language processing, and management sciences applied to contexts where multilingualism continuously creates new and demanding challenges to current knowledge representation methods and techniques. In this workshop six papers dealing with different approaches to multilingual knowledge representation are presented, most of them describing tools, approaches and results obtained in the development of ongoing projects. In the first case, Andrés Domínguez Burgos, Koen Kerremansa and Rita Temmerman present a software module that is part of a workbench for terminological and ontological mining, Termontospider, a wiki crawler that aims at optimally traverse Wikipedia in search of domainspecific texts for extracting terminological and ontological information. The crawler is part of a tool suite for automatically developing multilingual termontological databases, i.e. ontologicallyunderpinned multilingual terminological databases. In this paper the authors describe the basic principles behind the crawler and summarized the research setting in which the tool is currently tested. In the second paper, Fumiko Kano presents a work comparing four feature-based similarity measures derived from cognitive sciences. The purpose of the comparative analysis presented by the author is to verify the potentially most effective model that can be applied for mapping independent ontologies in a culturally influenced domain. For that, datasets based on standardized pre-defined feature dimensions and values, which are obtainable from the UNESCO Institute for Statistics (UIS) have been used for the comparative analysis of the similarity measures. The purpose of the comparison is to verify the similarity measures based on the objectively developed datasets. According to the author the results demonstrate that the Bayesian Model of Generalization provides for the most effective cognitive model for identifying the most similar corresponding concepts existing for a targeted socio-cultural community. In another presentation, Thierry Declerck, Hans-Ulrich Krieger and Dagmar Gromann present an ongoing work and propose an approach to automatic extraction of information from multilingual financial Web resources, to provide candidate terms for building ontology elements or instances of ontology concepts. The authors present a complementary approach to the direct localization/translation of ontology labels, by acquiring terminologies through the access and harvesting of multilingual Web presences of structured information providers in the field of finance, leading to both the detection of candidate terms in various multilingual sources in the financial domain that can be used not only as labels of ontology classes and properties but also for the possible generation of (multilingual) domain ontologies themselves. In the next paper, Manuel Silva, António Lucas Soares and Rute Costa claim that despite the availability of tools, resources and techniques aimed at the construction of ontological artifacts, developing a shared conceptualization of a given reality still raises questions about the principles and methods that support the initial phases of conceptualization. These questions become, according to the authors, more complex when the conceptualization occurs in a multilingual setting. To tackle these issues the authors present a collaborative platform – conceptME - where terminological and knowledge representation processes support domain experts throughout a conceptualization framework, allowing the inclusion of multilingual data as a way to promote knowledge sharing and enhance conceptualization and support a multilingual ontology specification. In another presentation Frieda Steurs and Hendrik J. Kockaert present us TermWise, a large project dealing with legal terminology and phraseology for the Belgian public services, i.e. the translation office of the ministry of justice, a project which aims at developing an advanced tool including expert knowledge in the algorithms that extract specialized language from textual data (legal documents) and whose outcome is a knowledge database including Dutch/French equivalents for legal concepts, enriched with the phraseology related to the terms under discussion. Finally, Deborah Grbac, Luca Losito, Andrea Sada and Paolo Sirito report on the preliminary results of a pilot project currently ongoing at UCSC Central Library, where they propose to adapt to subject librarians, employed in large and multilingual Academic Institutions, the model used by translators working within European Union Institutions. The authors are using User Experience (UX) Analysis in order to provide subject librarians with a visual support, by means of “ontology tables” depicting conceptual linking and connections of words with concepts presented according to their semantic and linguistic meaning. The organizers hope that the selection of papers presented here will be of interest to a broad audience, and will be a starting point for further discussion and cooperation.

Enhanced PCA-based localization using depth maps with missing data

In this paper a new method for self-localization of mobile robots, based on a PCA positioning sensor to operate in unstructured environments, is proposed and experimentally validated. The proposed PCA extension is able to perform the eigenvectors computation from a set of signals corrupted by missing data. The sensor package considered in this work contains a 2D depth sensor pointed upwards to the ceiling, providing depth images with missing data. The positioning sensor obtained is then integrated in a Linear Parameter Varying mobile robot model to obtain a self-localization system, based on linear Kalman filters, with globally stable position error estimates. A study consisting in adding synthetic random corrupted data to the captured depth images revealed that this extended PCA technique is able to reconstruct the signals, with improved accuracy. The self-localization system obtained is assessed in unstructured environments and the methodologies are validated even in the case of varying illumination conditions.

On the hydrogeology of the Lower Tagus Basin and its Cenozoic geologic evolution

The chemical features of the ground water in the Lower Tagus Cenozoic deposits are strongly influenced by lithology, by the velocity and direction of the water movement as well as by the localization of the recharge and discharge zones. The mineralization varies between 80 and 900 mg/l. It is minimal in the recharge zones and in the Pliocene sand and maximum in the Miocene carbonated and along the alluvial valley. Mineralization always reflects the time of permanence, the temperature and the pressure. The natural process of water mineralization is disturbed in agricultural areas because the saline concentration of the infiltration water exceeds that of the infiltrated rainwater. In the discharge zones, the rise of the more mineralized, some times thermal deep waters related to tectonic accidents give rise to anomalies in the distribution of the aquiferous system mineralization model. The diversity of the hydrochemical facies of the ground water may be related to several factors whose identification is some times difficult.