Analysis of the Organic Hydroperoxide Response of Chromobacterium violaceum Reveals That OhrR Is a Cys-Based Redox Sensor Regulated by Thioredoxin

Organic hydroperoxides are oxidants generated during bacterial-host interactions. Here, we demonstrate that the peroxidase OhrA and its negative regulator OhrR comprise a major pathway for sensing and detoxifying organic hydroperoxides in the opportunistic pathogen Chromobacterium violaceum. Initially, we found that an ohrA mutant was hypersensitive to organic hydroperoxides and that it displayed a low efficiency for decomposing these molecules. Expression of ohrA and ohrR was specifically induced by organic hydroperoxides. These genes were expressed as monocistronic transcripts and also as a bicistronic ohrR-ohrA mRNA, generating the abundantly detected ohrA mRNA and the barely detected ohrR transcript. The bicistronic transcript appears to be processed. OhrR repressed both the ohrA and ohrR genes by binding directly to inverted repeat sequences within their promoters in a redox-dependent manner. Site-directed mutagenesis of each of the four OhrR cysteine residues indicated that the conserved Cys21 is critical to organic hydroperoxide sensing, whereas Cys126 is required for disulfide bond formation. Taken together, these phenotypic, genetic and biochemical data indicate that the response of C. violaceum to organic hydroperoxides is mediated by OhrA and OhrR. Finally, we demonstrated that oxidized OhrR, inactivated by intermolecular disulfide bond formation, is specifically regenerated via thiol-disulfide exchange by thioredoxin (but not other thiol reducing agents such as glutaredoxin, glutathione and lipoamide), providing a physiological reducing system for this thiol-based redox switch.

Management and routing algorithms for ad-hoc and sensor networks

Large scale wireless adhoc networks of computers, sensors, PDAs etc. (i.e. nodes) are revolutionizing connectivity and leading to a paradigm shift from centralized systems to highly distributed and dynamic environments. An example of adhoc networks are sensor networks, which are usually composed by small units able to sense and transmit to a sink elementary data which are successively processed by an external machine. Recent improvements in the memory and computational power of sensors, together with the reduction of energy consumptions, are rapidly changing the potential of such systems, moving the attention towards datacentric sensor networks. A plethora of routing and data management algorithms have been proposed for the network path discovery ranging from broadcasting/floodingbased approaches to those using global positioning systems (GPS). We studied WGrid, a novel decentralized infrastructure that organizes wireless devices in an adhoc manner, where each node has one or more virtual coordinates through which both message routing and data management occur without reliance on either flooding/broadcasting operations or GPS. The resulting adhoc network does not suffer from the deadend problem, which happens in geographicbased routing when a node is unable to locate a neighbor closer to the destination than itself. WGrid allow multidimensional data management capability since nodes' virtual coordinates can act as a distributed database without needing neither special implementation or reorganization. Any kind of data (both single and multidimensional) can be distributed, stored and managed. We will show how a location service can be easily implemented so that any search is reduced to a simple query, like for any other data type. WGrid has then been extended by adopting a replication methodology. We called the resulting algorithm WRGrid. Just like WGrid, WRGrid acts as a distributed database without needing neither special implementation nor reorganization and any kind of data can be distributed, stored and managed. We have evaluated the benefits of replication on data management, finding out, from experimental results, that it can halve the average number of hops in the network. The direct consequence of this fact are a significant improvement on energy consumption and a workload balancing among sensors (number of messages routed by each node). Finally, thanks to the replications, whose number can be arbitrarily chosen, the resulting sensor network can face sensors disconnections/connections, due to failures of sensors, without data loss. Another extension to {WGrid} is {W*Grid} which extends it by strongly improving network recovery performance from link and/or device failures that may happen due to crashes or battery exhaustion of devices or to temporary obstacles. W*Grid guarantees, by construction, at least two disjoint paths between each couple of nodes. This implies that the recovery in W*Grid occurs without broadcasting transmissions and guaranteeing robustness while drastically reducing the energy consumption. An extensive number of simulations shows the efficiency, robustness and traffic road of resulting networks under several scenarios of device density and of number of coordinates. Performance analysis have been compared to existent algorithms in order to validate the results.

Design of wireless sensor networks for fluid dynamic applications

In fluid dynamics research, pressure measurements are of great importance to define the flow field acting on aerodynamic surfaces. In fact the experimental approach is fundamental to avoid the complexity of the mathematical models for predicting the fluid phenomena. It’s important to note that, using in-situ sensor to monitor pressure on large domains with highly unsteady flows, several problems are encountered working with the classical techniques due to the transducer cost, the intrusiveness, the time response and the operating range. An interesting approach for satisfying the previously reported sensor requirements is to implement a sensor network capable of acquiring pressure data on aerodynamic surface using a wireless communication system able to collect the pressure data with the lowest environmental–invasion level possible. In this thesis a wireless sensor network for fluid fields pressure has been designed, built and tested. To develop the system, a capacitive pressure sensor, based on polymeric membrane, and read out circuitry, based on microcontroller, have been designed, built and tested. The wireless communication has been performed using the Zensys Z-WAVE platform, and network and data management have been implemented. Finally, the full embedded system with antenna has been created. As a proof of concept, the monitoring of pressure on the top of the mainsail in a sailboat has been chosen as working example.

Cooperative communication and distributed detection in wireless sensor networks

Recent progress in microelectronic and wireless communications have enabled the development of low cost, low power, multifunctional sensors, which has allowed the birth of new type of networks named wireless sensor networks (WSNs). The main features of such networks are: the nodes can be positioned randomly over a given field with a high density; each node operates both like sensor (for collection of environmental data) as well as transceiver (for transmission of information to the data retrieval); the nodes have limited energy resources. The use of wireless communications and the small size of nodes, make this type of networks suitable for a large number of applications. For example, sensor nodes can be used to monitor a high risk region, as near a volcano; in a hospital they could be used to monitor physical conditions of patients. For each of these possible application scenarios, it is necessary to guarantee a trade-off between energy consumptions and communication reliability. The thesis investigates the use of WSNs in two possible scenarios and for each of them suggests a solution that permits to solve relating problems considering the trade-off introduced. The first scenario considers a network with a high number of nodes deployed in a given geographical area without detailed planning that have to transmit data toward a coordinator node, named sink, that we assume to be located onboard an unmanned aerial vehicle (UAV). This is a practical example of reachback communication, characterized by the high density of nodes that have to transmit data reliably and efficiently towards a far receiver. It is considered that each node transmits a common shared message directly to the receiver onboard the UAV whenever it receives a broadcast message (triggered for example by the vehicle). We assume that the communication channels between the local nodes and the receiver are subject to fading and noise. The receiver onboard the UAV must be able to fuse the weak and noisy signals in a coherent way to receive the data reliably. It is proposed a cooperative diversity concept as an effective solution to the reachback problem. In particular, it is considered a spread spectrum (SS) transmission scheme in conjunction with a fusion center that can exploit cooperative diversity, without requiring stringent synchronization between nodes. The idea consists of simultaneous transmission of the common message among the nodes and a Rake reception at the fusion center. The proposed solution is mainly motivated by two goals: the necessity to have simple nodes (to this aim we move the computational complexity to the receiver onboard the UAV), and the importance to guarantee high levels of energy efficiency of the network, thus increasing the network lifetime. The proposed scheme is analyzed in order to better understand the effectiveness of the approach presented. The performance metrics considered are both the theoretical limit on the maximum amount of data that can be collected by the receiver, as well as the error probability with a given modulation scheme. Since we deal with a WSN, both of these performance are evaluated taking into consideration the energy efficiency of the network. The second scenario considers the use of a chain network for the detection of fires by using nodes that have a double function of sensors and routers. The first one is relative to the monitoring of a temperature parameter that allows to take a local binary decision of target (fire) absent/present. The second one considers that each node receives a decision made by the previous node of the chain, compares this with that deriving by the observation of the phenomenon, and transmits the final result to the next node. The chain ends at the sink node that transmits the received decision to the user. In this network the goals are to limit throughput in each sensor-to-sensor link and minimize probability of error at the last stage of the chain. This is a typical scenario of distributed detection. To obtain good performance it is necessary to define some fusion rules for each node to summarize local observations and decisions of the previous nodes, to get a final decision that it is transmitted to the next node. WSNs have been studied also under a practical point of view, describing both the main characteristics of IEEE802:15:4 standard and two commercial WSN platforms. By using a commercial WSN platform it is realized an agricultural application that has been tested in a six months on-field experimentation.

Wireless Sensor Networks for Monitoring Applications

Wireless Sensor Networks (WSNs) are getting wide-spread attention since they became easily accessible with their low costs. One of the key elements of WSNs is distributed sensing. When the precise location of a signal of interest is unknown across the monitored region, distributing many sensors randomly/uniformly may yield with a better representation of the monitored random process than a traditional sensor deployment. In a typical WSN application the data sensed by nodes is usually sent to one (or more) central device, denoted as sink, which collects the information and can either act as a gateway towards other networks (e.g. Internet), where data can be stored, or be processed in order to command the actuators to perform special tasks. In such a scenario, a dense sensor deployment may create bottlenecks when many nodes competing to access the channel. Even though there are mitigation methods on the channel access, concurrent (parallel) transmissions may occur. In this study, always on the scope of monitoring applications, the involved development progress of two industrial projects with dense sensor deployments (eDIANA Project funded by European Commission and Centrale Adritica Project funded by Coop Italy) and the measurement results coming from several different test-beds evoked the necessity of a mathematical analysis on concurrent transmissions. To the best of our knowledge, in the literature there is no mathematical analysis of concurrent transmission in 2.4 GHz PHY of IEEE 802.15.4. In the thesis, experience stories of eDIANA and Centrale Adriatica Projects and a mathematical analysis of concurrent transmissions starting from O-QPSK chip demodulation to the packet reception rate with several different types of theoretical demodulators, are presented. There is a very good agreement between the measurements so far in the literature and the mathematical analysis.

Technologies for Ambient intelligence: from Smart Objects to Sensor Networks

n the last few years, the vision of our connected and intelligent information society has evolved to embrace novel technological and research trends. The diffusion of ubiquitous mobile connectivity and advanced handheld portable devices, amplified the importance of the Internet as the communication backbone for the fruition of services and data. The diffusion of mobile and pervasive computing devices, featuring advanced sensing technologies and processing capabilities, triggered the adoption of innovative interaction paradigms: touch responsive surfaces, tangible interfaces and gesture or voice recognition are finally entering our homes and workplaces. We are experiencing the proliferation of smart objects and sensor networks, embedded in our daily living and interconnected through the Internet. This ubiquitous network of always available interconnected devices is enabling new applications and services, ranging from enhancements to home and office environments, to remote healthcare assistance and the birth of a smart environment. This work will present some evolutions in the hardware and software development of embedded systems and sensor networks. Different hardware solutions will be introduced, ranging from smart objects for interaction to advanced inertial sensor nodes for motion tracking, focusing on system-level design. They will be accompanied by the study of innovative data processing algorithms developed and optimized to run on-board of the embedded devices. Gesture recognition, orientation estimation and data reconstruction techniques for sensor networks will be introduced and implemented, with the goal to maximize the tradeoff between performance and energy efficiency. Experimental results will provide an evaluation of the accuracy of the presented methods and validate the efficiency of the proposed embedded systems.

The APSEL4D Monolithic Active Pixel Sensor and its Usage in a Single Electron Interference Experiment

We have realized a Data Acquisition chain for the use and characterization of APSEL4D, a 32 x 128 Monolithic Active Pixel Sensor, developed as a prototype for frontier experiments in high energy particle physics. In particular a transition board was realized for the conversion between the chip and the FPGA voltage levels and for the signal quality enhancing. A Xilinx Spartan-3 FPGA was used for real time data processing, for the chip control and the communication with a Personal Computer through a 2.0 USB port. For this purpose a firmware code, developed in VHDL language, was written. Finally a Graphical User Interface for the online system monitoring, hit display and chip control, based on windows and widgets, was realized developing a C++ code and using Qt and Qwt dedicated libraries. APSEL4D and the full acquisition chain were characterized for the first time with the electron beam of the transmission electron microscope and with 55Fe and 90Sr radioactive sources. In addition, a beam test was performed at the T9 station of the CERN PS, where hadrons of momentum of 12 GeV/c are available. The very high time resolution of APSEL4D (up to 2.5 Mfps, but used at 6 kfps) was fundamental in realizing a single electron Young experiment using nanometric double slits obtained by a FIB technique. On high statistical samples, it was possible to observe the interference and diffractions of single isolated electrons traveling inside a transmission electron microscope. For the first time, the information on the distribution of the arrival time of the single electrons has been extracted.

The NreABC system of Staphylococcus carnosus combines nitrate and oxygen sensing by an NreA,NreB sensor complex

Staphylococcus carnosus is a facultative anaerobic bacterium which features the cytoplasmic NreABC system. It is necessary for regulation of nitrate respiration and the nitrate reductase gene narG in response to oxygen and nitrate availability. NreB is a sensor kinase of a two-component system and represents the oxygen sensor of the system. It binds an oxygen labile [4Fe-4S]2+ cluster under anaerobic conditions. NreB autophosphorylates and phosphoryl transfer activates the response regulator NreC which induces narG expression. The third component of the Nre system is the nitrate receptor NreA. In this study the role of the nitrate receptor protein NreA in nitrate regulation and its functional and physiological effect on oxygen regulation and interaction with the NreBC two-component system were detected. In vivo, a reporter gene assay for measuring expression of the NreABC regulated nitrate reductase gene narG was used for quantitative evaluation of NreA function. Maximal narG expression in wild type S. carnosus required anaerobic conditions and the presence of nitrate. Deletion of nreA allowed expression of narG under aerobic conditions, and under anaerobic conditions nitrate was no longer required for maximal induction. This indicates that NreA is a nitrate regulated inhibitor of narG expression. Purified NreA and variant NreA(Y95A) inhibited the autophosphorylation of anaerobic NreB in part and completely, respectively. Neither NreA nor NreA(Y95A) stimulated dephosphorylation of NreB-phosphate, however. Inhibition of phosphorylation was relieved completely when NreA with bound nitrate (NreA•[NO3-]) was used. The same effects of NreA were monitored with aerobically isolated Fe-S-less NreB, which indicates that NreA does not have an influence on the iron-sulfur cluster of NreB. In summary, the data of this study show that NreA interacts with the oxygen sensor NreB and controls its phosphorylation level in a nitrate dependent manner. This modulation of NreB-function by NreA and nitrate results in nitrate/oxygen co-sensing by an NreA/NreB sensory unit. It transmits the regulatory signal from oxygen and nitrate in a joint signal to target promoters. Therefore, nitrate and oxygen regulation of nitrate dissimilation follows a new mode of regulation not present in other facultative anaerobic bacteria.

Implementation of a VLSI amplifier interfaced with biomedical sensors for ultra wide band data transmission

This thesis presents a CMOS Amplifier with High Common Mode rejection designed in UMC 130nm technology. The goal is to achieve a high amplification factor for a wide range of biological signals (with frequencies in the range of 10Hz-1KHz) and to reject the common-mode noise signal. It is here presented a Data Acquisition System, composed of a Delta-Sigma-like Modulator and an antenna, that is the core of a portable low-complexity radio system; the amplifier is designed in order to interface the data acquisition system with a sensor that acquires the electrical signal. The Modulator asynchronously acquires and samples human muscle activity, by sending a Quasi-Digital pattern that encodes the acquired signal. There is only a minor loss of information translating the muscle activity using this pattern, compared to an encoding technique which uses astandard digital signal via Impulse-Radio Ultra-Wide Band (IR-UWB). The biological signals, needed for Electromyographic analysis, have an amplitude of 10-100μV and need to be highly amplified and separated from the overwhelming 50mV common mode noise signal. Various tests of the firmness of the concept are presented, as well the proof that the design works even with different sensors, such as Radiation measurement for Dosimetry studies.

Mac protocols for linear wireless (sensor) networks

Wireless sensor networks (WSNs) consist of a large number of sensor nodes, characterized by low power constraint, limited transmission range and limited computational capabilities [1][2].The cost of these devices is constantly decreasing, making it possible to use a large number of sensor devices in a wide array of commercial, environmental, military, and healthcare fields. Some of these applications involve placing the sensors evenly spaced on a straight line for example in roads, bridges, tunnels, water catchments and water pipelines, city drainages, oil and gas pipelines etc., making a special class of these networks which we define as a Linear Wireless Network (LWN). In LWNs, data transmission happens hop by hop from the source to the destination, through a route composed of multiple relays. The peculiarity of the topology of LWNs, motivates the design of specialized protocols, taking advantage of the linearity of such networks, in order to increase reliability, communication efficiency, energy savings, network lifetime and to minimize the end-to-end delay [3]. In this thesis a novel contention based Medium Access Control (MAC) protocol called L-CSMA, specifically devised for LWNs is presented. The basic idea of L-CSMA is to assign different priorities to nodes based on their position along the line. The priority is assigned in terms of sensing duration, whereby nodes closer to the destination are assigned shorter sensing time compared to the rest of the nodes and hence higher priority. This mechanism speeds up the transmission of packets which are already in the path, making transmission flow more efficient. Using NS-3 simulator, the performance of L-CSMA in terms of packets success rate, that is, the percentage of packets that reach destination, and throughput are compared with that of IEEE 802.15.4 MAC protocol, de-facto standard for wireless sensor networks. In general, L-CSMA outperforms the IEEE 802.15.4 MAC protocol.

Visualization and validation of (Q)SAR models

Analyzing and modeling relationships between the structure of chemical compounds, their physico-chemical properties, and biological or toxic effects in chemical datasets is a challenging task for scientific researchers in the field of cheminformatics. Therefore, (Q)SAR model validation is essential to ensure future model predictivity on unseen compounds. Proper validation is also one of the requirements of regulatory authorities in order to approve its use in real-world scenarios as an alternative testing method. However, at the same time, the question of how to validate a (Q)SAR model is still under discussion. In this work, we empirically compare a k-fold cross-validation with external test set validation. The introduced workflow allows to apply the built and validated models to large amounts of unseen data, and to compare the performance of the different validation approaches. Our experimental results indicate that cross-validation produces (Q)SAR models with higher predictivity than external test set validation and reduces the variance of the results. Statistical validation is important to evaluate the performance of (Q)SAR models, but does not support the user in better understanding the properties of the model or the underlying correlations. We present the 3D molecular viewer CheS-Mapper (Chemical Space Mapper) that arranges compounds in 3D space, such that their spatial proximity reflects their similarity. The user can indirectly determine similarity, by selecting which features to employ in the process. The tool can use and calculate different kinds of features, like structural fragments as well as quantitative chemical descriptors. Comprehensive functionalities including clustering, alignment of compounds according to their 3D structure, and feature highlighting aid the chemist to better understand patterns and regularities and relate the observations to established scientific knowledge. Even though visualization tools for analyzing (Q)SAR information in small molecule datasets exist, integrated visualization methods that allows for the investigation of model validation results are still lacking. We propose visual validation, as an approach for the graphical inspection of (Q)SAR model validation results. New functionalities in CheS-Mapper 2.0 facilitate the analysis of (Q)SAR information and allow the visual validation of (Q)SAR models. The tool enables the comparison of model predictions to the actual activity in feature space. Our approach reveals if the endpoint is modeled too specific or too generic and highlights common properties of misclassified compounds. Moreover, the researcher can use CheS-Mapper to inspect how the (Q)SAR model predicts activity cliffs. The CheS-Mapper software is freely available at http://ches-mapper.org.

Tecnologie per la fruizione e rappresentazione di open data

La presente tesi è uno studio sugli strumenti e le tecnologie che caratterizzano l'utilizzo degli open data, in particolare, nello sviluppo di applicazioni web moderne che fanno uso di questo tipo di dati.

Toward optimal display of physiologic status in critical care: I. Recreating bedside displays from archived physiologic data

BACKGROUND: Physiologic data display is essential to decision making in critical care. Current displays echo first-generation hemodynamic monitors dating to the 1970s and have not kept pace with new insights into physiology or the needs of clinicians who must make progressively more complex decisions about their patients. The effectiveness of any redesign must be tested before deployment. Tools that compare current displays with novel presentations of processed physiologic data are required. Regenerating conventional physiologic displays from archived physiologic data is an essential first step. OBJECTIVES: The purposes of the study were to (1) describe the SSSI (single sensor single indicator) paradigm that is currently used for physiologic signal displays, (2) identify and discuss possible extensions and enhancements of the SSSI paradigm, and (3) develop a general approach and a software prototype to construct such "extended SSSI displays" from raw data. RESULTS: We present Multi Wave Animator (MWA) framework-a set of open source MATLAB (MathWorks, Inc., Natick, MA, USA) scripts aimed to create dynamic visualizations (eg, video files in AVI format) of patient vital signs recorded from bedside (intensive care unit or operating room) monitors. Multi Wave Animator creates animations in which vital signs are displayed to mimic their appearance on current bedside monitors. The source code of MWA is freely available online together with a detailed tutorial and sample data sets.

Three-dimensional portable document format: a simple way to present 3-dimensional data in an electronic publication

Three-dimensional (3D) models of teeth and soft and hard tissues are tessellated surfaces used for diagnosis, treatment planning, appliance fabrication, outcome evaluation, and research. In scientific publications or communications with colleagues, these 3D data are often reduced to 2-dimensional pictures or need special software for visualization. The portable document format (PDF) offers a simple way to interactively display 3D surface data without additional software other than a recent version of Adobe Reader (Adobe, San Jose, Calif). The purposes of this article were to give an example of how 3D data and their analyses can be interactively displayed in 3 dimensions in electronic publications, and to show how they can be exported from any software for diagnostic reports and communications among colleagues.

MaxMAC: a Maximally Traffic-Adaptive MAC Protocol for Wireless Sensor Networks

Energy efficiency is a major concern in the design of Wireless Sensor Networks (WSNs) and their communication protocols. As the radio transceiver typically accounts for a major portion of a WSN node’s power consumption, researchers have proposed Energy-Efficient Medium Access (E2-MAC) protocols that switch the radio transceiver off for a major part of the time. Such protocols typically trade off energy-efficiency versus classical quality of service parameters (throughput, latency, reliability). Today’s E2-MAC protocols are able to deliver little amounts of data with a low energy footprint, but introduce severe restrictions with respect to throughput and latency. Regrettably, they yet fail to adapt to varying traffic load at run-time. This paper presents MaxMAC, an E2-MAC protocol that targets at achieving maximal adaptivity with respect to throughput and latency. By adaptively tuning essential parameters at run-time, the protocol reaches the throughput and latency of energy-unconstrained CSMA in high-traffic phases, while still exhibiting a high energy-efficiency in periods of sparse traffic. The paper compares the protocol against a selection of today’s E2-MAC protocols and evaluates its advantages and drawbacks.