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.

How patchy can one get and still condense? The role of dissimilar patches in the interactions of colloidal particles

We investigate the influence of strong directional, or bonding, interactions on the phase diagram of complex fluids, and in particular on the liquid-vapour critical point. To this end we revisit a simple model and theory for associating fluids which consist of spherical particles having a hard-core repulsion, complemented by three short-ranged attractive sites on the surface (sticky spots). Two of the spots are of type A and one is of type B; the interactions between each pair of spots have strengths [image omitted], [image omitted] and [image omitted]. The theory is applied over the whole range of bonding strengths and results are interpreted in terms of the equilibrium cluster structures of the coexisting phases. In systems where unlike sites do not interact (i.e. where [image omitted]), the critical point exists all the way to [image omitted]. By contrast, when [image omitted], there is no critical point below a certain finite value of [image omitted]. These somewhat surprising results are rationalised in terms of the different network structures of the two systems: two long AA chains are linked by one BB bond (X-junction) in the former case, and by one AB bond (Y-junction) in the latter. The vapour-liquid transition may then be viewed as the condensation of these junctions and we find that X-junctions condense for any attractive [image omitted] (i.e. for any fraction of BB bonds), whereas condensation of the Y-junctions requires that [image omitted] be above a finite threshold (i.e. there must be a finite fraction of AB bonds).

Weaving encounters: towards an art of participation

In the early 21st Century, with the phenomenon of digital convergence, the consecration of Web 2.0, the decrease of the cost of cameras and video recorders, the proliferation of mobile phones, laptops and wireless technologies, we witness the arising of a new wave of media, of an informal, personal and at times “minority” nature, facilitating social networks, a culture of fans, of sharing and remix. As digital networks become fully and deeply intricate in our experience, the idea of “participation” arises as one of the most complex and controversial themes of the contemporary critical discourse, namely in what concerns contemporary art and new media art. However, the idea of “participation” as a practice or postulate traverses the 20th century art playing an essential role in its auto-critic, in questioning the concept of author, and in the dilution of the frontiers between art, “life” and society, emphasizing the process, the everyday and a community sense. As such, questioning the new media art in light of a “participatory art” (Frieling, 2008) invokes a double gaze simultaneously attentive to the emerging figures of a “participatory aesthetics” in digital arts and of the genealogy in which it is included. In fact, relating the new media art with the complex and paradoxical phenomenon of “participation” allows us to, on the one hand, avoid “digital formalism” (Lovink, 2008) and analyse the relations between digital art and contemporary social movements; on the other hand, this angle of analysis contributes to reinforce the dialogue and the links between digital art and contemporary art, questioning the alleged frontiers that separate them.

James W. Carey as critical theorist of the information age

This paper suggests that the thought of the North-American critical theorist James W. Carey provides a relevant perspective on communication and technology. Having as background American social pragmatism and progressive thinkers of the beginning of the 20th century (as Dewey, Mead, Cooley, and Park), Carey built a perspective that brought together the political economy of Harold A. Innis, the social criticism of David Riesman and Charles W. Mills and incorporated Marxist topics such as commodification and sociocultural domination. The main goal of this paper is to explore the connection established by Carey between modern technological communication and what he called the “transmissive model”, a model which not only reduces the symbolic process of communication to instrumentalization and to information delivery, but also politically converges with capitalism as well as power, control and expansionist goals. Conceiving communication as a process that creates symbolic and cultural systems, in which and through which social life takes place, Carey gives equal emphasis to the incorporation processes of communication.If symbolic forms and culture are ways of conditioning action, they are also influenced by technological and economic materializations of symbolic systems, and by other conditioning structures. In Carey’s view, communication is never a disembodied force; rather, it is a set of practices in which co-exist conceptions, techniques and social relations. These practices configure reality or, alternatively, can refute, transform and celebrate it. Exhibiting sensitiveness favourable to the historical understanding of communication, media and information technologies, one of the issues Carey explored most was the history of the telegraph as an harbinger of the Internet, of its problems and contradictions. For Carey, Internet was seen as the contemporary heir of the communications revolution triggered by the prototype of transmission technologies, namely the telegraph in the 19th century. In the telegraph Carey saw the prototype of many subsequent commercial empires based on science and technology, a pioneer model for complex business management; an example of conflict of interest for the control over patents; an inducer of changes both in language and in structures of knowledge; and a promoter of a futurist and utopian thought of information technologies. After a brief approach to Carey’s communication theory, this paper focuses on his seminal essay "Technology and ideology. The case of the telegraph", bearing in mind the prospect of the communication revolution introduced by Internet. We maintain that this essay has seminal relevance for critically studying the information society. Our reading of it highlights the reach, as well as the problems, of an approach which conceives the innovation of the telegraph as a metaphor for all innovations, announcing the modern stage of history and determining to this day the major lines of development in modern communication systems.

PAH air pollution at a Portuguese urban area: carcinogenic risks and sources identification

This study aimed to characterize air pollution and the associated carcinogenic risks of polycyclic aromatic hydrocarbon (PAHs) at an urban site, to identify possible emission sources of PAHs using several statistical methodologies, and to analyze the influence of other air pollutants and meteorological variables on PAH concentrations.The air quality and meteorological data were collected in Oporto, the second largest city of Portugal. Eighteen PAHs (the 16 PAHs considered by United States Environment Protection Agency (USEPA) as priority pollutants, dibenzo[a,l]pyrene, and benzo[j]fluoranthene) were collected daily for 24 h in air (gas phase and in particles) during 40 consecutive days in November and December 2008 by constant low-flow samplers and using polytetrafluoroethylene (PTFE) membrane filters for particulate (PM10 and PM2.5 bound) PAHs and pre-cleaned polyurethane foam plugs for gaseous compounds. The other monitored air pollutants were SO2, PM10, NO2, CO, and O3; the meteorological variables were temperature, relative humidity, wind speed, total precipitation, and solar radiation. Benzo[a]pyrene reached a mean concentration of 2.02 ngm−3, surpassing the EU annual limit value. The target carcinogenic risks were equal than the health-based guideline level set by USEPA (10−6) at the studied site, with the cancer risks of eight PAHs reaching senior levels of 9.98×10−7 in PM10 and 1.06×10−6 in air. The applied statistical methods, correlation matrix, cluster analysis, and principal component analysis, were in agreement in the grouping of the PAHs. The groups were formed according to their chemical structure (number of rings), phase distribution, and emission sources. PAH diagnostic ratios were also calculated to evaluate the main emission sources. Diesel vehicular emissions were the major source of PAHs at the studied site. Besides that source, emissions from residential heating and oil refinery were identified to contribute to PAH levels at the respective area. Additionally, principal component regression indicated that SO2, NO2, PM10, CO, and solar radiation had positive correlation with PAHs concentrations, while O3, temperature, relative humidity, and wind speed were negatively correlated.

Engineering hybrid wired/wireless fieldbus networks - a case study

Advances in networking and information technologies are transforming factory-floor communication systems into a mainstream activity within industrial automation. It is now recognized that future industrial computer systems will be intimately tied to real-time computing and to communication technologies. For this vision to succeed, complex heterogeneous factory-floor communication networks (including mobile/wireless components) need to function in a predictable, flawless, efficient and interoperable way. In this paper we re-visit the issue of supporting real-time communications in hybrid wired/wireless fieldbus-based networks, bringing into it some experimental results obtained in the framework of the RFieldbus ISEP pilot.

On the adaptation of broadcast transactions in token-passing fieldbus networks with heterogeneous transmission media

Broadcast networks that are characterised by having different physical layers (PhL) demand some kind of traffic adaptation between segments, in order to avoid traffic congestion in linking devices. In many LANs, this problem is solved by the actual linking devices, which use some kind of flow control mechanism that either tell transmitting stations to pause (the transmission) or just discard frames. In this paper, we address the case of token-passing fieldbus networks operating in a broadcast fashion and involving message transactions over heterogeneous (wired or wireless) physical layers. For the addressed case, real-time and reliability requirements demand a different solution to the traffic adaptation problem. Our approach relies on the insertion of an appropriate idle time before a station issuing a request frame. In this way, we guarantee that the linking devices’ queues do not increase in a way that the timeliness properties of the overall system turn out to be unsuitable for the targeted applications.

Designing real-time systems based on mono-master Profibus-DP networks

Profibus networks are widely used as the communication infrastructure for supporting distributed computer-controlled applications. Most of the times, these applications impose strict real-time requirements. Profibus-DP has gradually become the preferred Profibus application profile. It is usually implemented as a mono-master Profibus network, and is optimised for speed and efficiency. The aim of this paper is to analyse the real-time behaviour of this class of Profibus networks. Importantly, we develop a new methodology for evaluating the worst-case message response time in systems where high-priority and cyclic low-priority Profibus traffic coexist. The proposed analysis constitutes a powerful tool to guarantee prior to runtime the real-time behaviour of a distributed computer-controlled system based on a Profibus network, where the realtime traffic is supported either by high-priority or by cyclic poll Profibus messages.

Supporting real-time distributed computer-controlled systems with multi-hop P-NET networks

Fieldbus communication networks aim to interconnect sensors, actuators and controllers within process control applications. Therefore, they constitute the foundation upon which real-time distributed computer-controlled systems can be implemented. P-NET is a fieldbus communication standard, which uses a virtual token-passing medium-access-control mechanism. In this paper pre-run-time schedulability conditions for supporting real-time traffic with P-NET networks are established. Essentially, formulae to evaluate the upper bound of the end-to-end communication delay in P-NET messages are provided. Using this upper bound, a feasibility test is then provided to check the timing requirements for accessing remote process variables. This paper also shows how P-NET network segmentation can significantly reduce the end-to-end communication delays for messages with stringent timing requirements.

Communication response time in P-NET networks: worst-case analysis considering the actual token utilisation

Fieldbus networks aim at the interconnection of field devices such as sensors, actuators and small controllers. Therefore, they are an effective technology upon which Distributed Computer Controlled Systems (DCCS) can be built. DCCS impose strict timeliness requirements to the communication network. In essence, by timeliness requirements we mean that traffic must be sent and received within a bounded interval, otherwise a timing fault is said to occur. P-NET is a multi-master fieldbus standard based on a virtual token passing scheme. In P-NET each master is allowed to transmit only one message per token visit, which means that in the worst-case the communication response time could be derived considering that the token is fully utilised by all stations. However, such analysis can be proved to be quite pessimistic. In this paper we propose a more sophisticated P-NET timing analysis model, which considers the actual token utilisation by different masters. The major contribution of this model is to provide a less pessimistic, and thus more accurate, analysis for the evaluation of the worst-case communication response time in P-NET fieldbus networks.

Enabling inter-domain transactions in bridge-based hybrid wired/wireless PROFIBUS networks

The marriage of emerging information technologies with control technologies is a major driving force that, in the context of the factory-floor, is creating an enormous eagerness for extending the capabilities of currently available fieldbus networks to cover functionalities not considered up to a recent past. Providing wireless capabilities to such type of communication networks is a big share of that effort. The RFieldbus European project is just one example, where PROFIBUS was provided with suitable extensions for implementing hybrid wired/wireless communication systems. In RFieldbus, interoperability between wired and wireless components is achieved by the use specific intermediate networking systems operating as repeaters, thus creating a single logical ring (SLR) network. The main advantage of the SLR approach is that the effort for protocol extensions is not significant. However, a multiple logical ring (MLR) approach provides traffic and error isolation between different network segments. This concept was introduced in, where an approach for a bridge-based architecture was briefly outlined. This paper will focus on the details of the inter-Domain Protocol (IDP), which is responsible for handling transactions between different network domains (wired or wireless) running the PROFIBUS protocol.

Reliable real-time communication in CAN networks

Controller area network (CAN) is a fieldbus network suitable for small-scale distributed computer controlled systems (DCCS), being appropriate for sending and receiving short real-time messages at speeds up to 1 Mbit/sec. Several studies are available on how to guarantee the real-time requirements of CAN messages, providing preruntime schedulability conditions to guarantee the real-time communication requirements of DCCS traffic. Usually, it is considered that CAN guarantees atomic multicast properties by means of its extensive error detection/signaling mechanisms. However, there are some error situations where messages can be delivered in duplicate or delivered only by a subset of the receivers, leading to inconsistencies in the supported applications. In order to prevent such inconsistencies, a middleware for reliable communication in CAN is proposed, taking advantage of CAN synchronous properties to minimize the runtime overhead. Such middleware comprises a set of atomic multicast and consolidation protocols, upon which the reliable communication properties are guaranteed. The related timing analysis demonstrates that, in spite of the extra stack of protocols, the real-time properties of CAN are preserved since the predictability of message transfer is guaranteed.

Taxonomy of fundamental concepts of localization in cyber-physical and sensor networks

Localization is a fundamental task in Cyber-Physical Systems (CPS), where data is tightly coupled with the environment and the location where it is generated. The research literature on localization has reached a critical mass, and several surveys have also emerged. This review paper contributes on the state-of-the-art with the proposal of a new and holistic taxonomy of the fundamental concepts of localization in CPS, based on a comprehensive analysis of previous research works and surveys. The main objective is to pave the way towards a deep understanding of the main localization techniques, and unify their descriptions. Furthermore, this review paper provides a complete overview on the most relevant localization and geolocation techniques. Also, we present the most important metrics for measuring the accuracy of localization approaches, which is meant to be the gap between the real location and its estimate. Finally, we present open issues and research challenges pertaining to localization. We believe that this review paper will represent an important and complete reference of localization techniques in CPS for researchers and practitioners and will provide them with an added value as compared to previous surveys.

Distributed computing for the factory-floor: a real-time approach using WorldFIP networks

Field communication systems (fieldbuses) are widely used as the communication support for distributed computer-controlled systems (DCCS) within all sort of process control and manufacturing applications. There are several advantages in the use of fieldbuses as a replacement for the traditional point-to-point links between sensors/actuators and computer-based control systems, within which the most relevant is the decentralisation and distribution of the processing power over the field. A widely used fieldbus is the WorldFIP, which is normalised as European standard EN 50170. Using WorldFIP to support DCCS, an important issue is “how to guarantee the timing requirements of the real-time traffic?” WorldFIP has very interesting mechanisms to schedule data transfers, since it explicitly distinguishes periodic and aperiodic traffic. In this paper, we describe how WorldFIP handles these two types of traffic, and more importantly, we provide a comprehensive analysis on how to guarantee the timing requirements of the real-time traffic.

Fieldbus networks: real-time from the perspective of the application tasks

Fieldbus communication networks aim to interconnect sensors, actuators and controllers within distributed computer-controlled systems. Therefore they constitute the foundation upon which real-time applications are to be implemented. A potential leap towards the use of fieldbus in such time-critical applications lies in the evaluation of its temporal behaviour. In the past few years several research works have been performed on a number of fieldbuses. However, these have mostly focused on the message passing mechanisms, without taking into account the communicating application tasks running in those distributed systems. The main contribution of this paper is to provide an approach for engineering real-time fieldbus systems where the schedulability analysis of the distributed system integrates both the characteristics of the application tasks and the characteristics of the message transactions performed by these tasks. In particular, we address the case of system where the Process-Pascal multitasking language is used to develop P-NET based distributed applications