PILZ Protein Structure and Interactions with PILB and the FIMX EAL Domain: Implications for Control of Type IV Pilus Biogenesis

The PilZ protein was originally identified as necessary for type IV pilus (T4P) biogenesis. Since then, a large and diverse family of bacterial PilZ homology domains have been identified, some of which have been implicated in signaling pathways that control important processes, including motility, virulence and biofilm formation. Furthermore, many PilZ homology domains, though not PilZ itself, have been shown to bind the important bacterial second messenger bis(3`-> 5`)cyclic diGMP (c-diGMP). The crystal structures of the PilZ orthologs from Xanthomonas axonopodis pv Citri (PilZ(XAC1133), this work) and from Xanthomonas campestris pv campestris (XC1028) present significant structural differences to other PilZ homologs that explain its failure to bind c-diGMP. NMR analysis of PilZ(XAC1133) shows that these structural differences are maintained in solution. In spite of their emerging importance in bacterial signaling, the means by which NZ proteins regulate specific processes is not clear. In this study, we show that PilZ(XAC1133) binds to PilB, an ATPase required for TV polymerization, and to the EAL domain of FiMX(XAC2398), which regulates TV biogenesis and localization in other bacterial species. These interactions were confirmed in NMR, two-hybrid and far-Western blot assays and are the first interactions observed between any PilZ domain and a target protein. While we were unable to detect phosphodiesterase activity for FimXX(AC2398) in vitro, we show that it binds c-diGMP both in the presence and in the absence of PilZ(XAC1133). Site-directed mutagenesis studies for conserved and exposed residues suggest that PilZ(XAC1133) interactions with FimX(XAC2398) and PilB(XAC3239) are mediated through a hydrophobic surface and an unstructured C-terminal extension conserved only in PilZ orthologs. The FimX-PilZ-PilB interactions involve a full set of ""degenerate"" GGDEF, EAL and PilZ domains and provide the first evidence of the means by which PilZ orthologs and FimX interact directly with the TP4 machinery. (C) 2009 Elsevier Ltd. All rights reserved.

Monitoring and Explanation of Contract Execution: A Case Study in the Aerospace Domain

In the domain of aerospace aftermarkets, which often has long supply chains that feed into the maintenance of aircraft, contracts are used to establish agreements between aircraft operators and maintenance suppliers. However, violations at the bottom of the supply chain (part suppliers) can easily cascade to the top (aircraft operators), making it difficult to determine the source of the violation, and seek to address it. In this context, we have developed a global monitoring architecture that ensures the detection of norm violations and generates explanations for the origin of violations. In this paper, we describe the implementation and deployment of a global monitor in the aerospace domain of [8] and show how it generates explanations for violations within the maintenance supply chain. We show how these explanations can be used not only to detect violations at runtime, but also to uncover potential problems in contracts before their deployment, thus improving them.

Volunteered Geographic Information For Water Management: A Prototype Architecture

Driven by Web 2.0 technology and the almost ubiquitous presence of mobile devices, Volunteered Geographic Information (VGI) is knowing an unprecedented growth. These notable technological advancements have opened fruitful perspectives also in the field of water management and protection, raising the demand for a reconsideration of policies which also takes into account the emerging trend of VGI. This research investigates the opportunity of leveraging such technology to involve citizens equipped with common mobile devices (e.g. tablets and smartphones) in a campaign of report of water-related phenomena. The work is carried out in collaboration with ADBPO - Autorità di bacino del fiume Po (Po river basin Authority), i.e. the entity responsible for the environmental planning and protection of the basin of river Po. This is the longest Italian river, spreading over eight among the twenty Italian Regions and characterized by complex environmental issues. To enrich ADBPO official database with user-generated contents, a FOSS (Free and Open Source Software) architecture was designed which allows not only user field-data collection, but also data Web publication through standard protocols. Open Data Kit suite allows users to collect georeferenced multimedia information using mobile devices equipped with location sensors (e.g. the GPS). Users can report a number of environmental emergencies, problems or simple points of interest related to the Po river basin, taking pictures of them and providing other contextual information. Field-registered data is sent to a server and stored into a PostgreSQL database with PostGIS spatial extension. GeoServer provides then data dissemination on the Web, while specific OpenLayers-based viewers were built to optimize data access on both desktop computers and mobile devices. Besides proving the suitability of FOSS in the frame of VGI, the system represents a successful prototype for the exploitation of user local, real-time information aimed at managing and protecting water resources.

Multilayer optimization in radio resource allocation for the packet transmission in wireless networks

In the last decade mobile wireless communications have witnessed an explosive growth in the user’s penetration rate and their widespread deployment around the globe. It is expected that this tendency will continue to increase with the convergence of fixed Internet wired networks with mobile ones and with the evolution to the full IP architecture paradigm. Therefore mobile wireless communications will be of paramount importance on the development of the information society of the near future. In particular a research topic of particular relevance in telecommunications nowadays is related to the design and implementation of mobile communication systems of 4th generation. 4G networks will be characterized by the support of multiple radio access technologies in a core network fully compliant with the Internet Protocol (all IP paradigm). Such networks will sustain the stringent quality of service (QoS) requirements and the expected high data rates from the type of multimedia applications to be available in the near future. The approach followed in the design and implementation of the mobile wireless networks of current generation (2G and 3G) has been the stratification of the architecture into a communication protocol model composed by a set of layers, in which each one encompasses some set of functionalities. In such protocol layered model, communications is only allowed between adjacent layers and through specific interface service points. This modular concept eases the implementation of new functionalities as the behaviour of each layer in the protocol stack is not affected by the others. However, the fact that lower layers in the protocol stack model do not utilize information available from upper layers, and vice versa, downgrades the performance achieved. This is particularly relevant if multiple antenna systems, in a MIMO (Multiple Input Multiple Output) configuration, are implemented. MIMO schemes introduce another degree of freedom for radio resource allocation: the space domain. Contrary to the time and frequency domains, radio resources mapped into the spatial domain cannot be assumed as completely orthogonal, due to the amount of interference resulting from users transmitting in the same frequency sub-channel and/or time slots but in different spatial beams. Therefore, the availability of information regarding the state of radio resources, from lower to upper layers, is of fundamental importance in the prosecution of the levels of QoS expected from those multimedia applications. In order to match applications requirements and the constraints of the mobile radio channel, in the last few years researches have proposed a new paradigm for the layered architecture for communications: the cross-layer design framework. In a general way, the cross-layer design paradigm refers to a protocol design in which the dependence between protocol layers is actively exploited, by breaking out the stringent rules which restrict the communication only between adjacent layers in the original reference model, and allowing direct interaction among different layers of the stack. An efficient management of the set of available radio resources demand for the implementation of efficient and low complexity packet schedulers which prioritize user’s transmissions according to inputs provided from lower as well as upper layers in the protocol stack, fully compliant with the cross-layer design paradigm. Specifically, efficiently designed packet schedulers for 4G networks should result in the maximization of the capacity available, through the consideration of the limitations imposed by the mobile radio channel and comply with the set of QoS requirements from the application layer. IEEE 802.16e standard, also named as Mobile WiMAX, seems to comply with the specifications of 4G mobile networks. The scalable architecture, low cost implementation and high data throughput, enable efficient data multiplexing and low data latency, which are attributes essential to enable broadband data services. Also, the connection oriented approach of Its medium access layer is fully compliant with the quality of service demands from such applications. Therefore, Mobile WiMAX seems to be a promising 4G mobile wireless networks candidate. In this thesis it is proposed the investigation, design and implementation of packet scheduling algorithms for the efficient management of the set of available radio resources, in time, frequency and spatial domains of the Mobile WiMAX networks. The proposed algorithms combine input metrics from physical layer and QoS requirements from upper layers, according to the crosslayer design paradigm. Proposed schedulers are evaluated by means of system level simulations, conducted in a system level simulation platform implementing the physical and medium access control layers of the IEEE802.16e standard.

The nest architecture of the ant, Pheidole oxyops Forel, 1908 (Hymenoptera : Formicidae)

Pheidole oxyops builds subterranean nests, with an external architecture that is distinctive and easily recognizable by its wide and specific entrance hole, measuring up to 12.2 cm in diameter, denoting a pitfall-trap. In order to study the nests'internal architecture, seven nests were excavated; four were identified with neutral talc, while the others were cast in cement and then excavated. Measurements were made in order to gain a better understanding of their structures, and a photographic documentation was obtained as well. The excavations revealed that the nests are perpendicular relative to the ground, beginning with a cylindrical channel with a mean length of 13.5 cm, containing irregular formations, and whose diameter becomes progressively narrower until the first chamber is formed. As the channel continues, dish-like chambers appear, interconnected by channels that become progressively narrower and longer, while the chambers are arranged at greater distances from each other as nest depth increases. Both channels and chambers are located on the vertical projection of the entrance hole. Nests may reach a depth of up to 5.09 m, with a number of chambers ranging between 4 and 14.

Iron phthalocyanine in non-aqueous medium forming layer-by-layer films: growth mechanism, molecular architecture and applications

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

On developing efficient applications using conservative distributed simulation paradigm

This paper aims to present, using a set of guidelines, how to apply the conservative distributed simulation paradigm (CMB protocol) to develop efficient applications. Using these guidelines, even a user with little experience on distributed simulation and computer architecture can have good performance on distributed simulations using conservative synchronization protocols for parallel processes.The set of guidelines is focus on a specific application domain, the performance evaluation of computer systems, considering models with coarse granularity and few logical processes and running over two platforms: parallel (high performance communication environment) and distributed (low performance communication environment).

A multisampling time-domain CMOS imager with synchronous readout circuit

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Abordagem dirigida a modelos para redes de sensores sem fio

Research on Wireless Sensor Networks (WSN) has evolved, with potential applications in several domains. However, the building of WSN applications is hampered by the need of programming in low-level abstractions provided by sensor OS and of specific knowledge about each application domain and each sensor platform. We propose a MDA approach do develop WSN applications. This approach allows domain experts to directly contribute in the developing of applications without needing low level knowledge on WSN platforms and, at the same time, it allows network experts to program WSN nodes to met application requirements without specific knowledge on the application domain. Our approach also promotes the reuse of the developed software artifacts, allowing an application model to be reused across different sensor platforms and a platform model to be reused for different applications

Abordagem de construção de arquitetura homogênea para comitês via meta-aprendizagem

In the world we are constantly performing everyday actions. Two of these actions are frequent and of great importance: classify (sort by classes) and take decision. When we encounter problems with a relatively high degree of complexity, we tend to seek other opinions, usually from people who have some knowledge or even to the extent possible, are experts in the problem domain in question in order to help us in the decision-making process. Both the classification process as the process of decision making, we are guided by consideration of the characteristics involved in the specific problem. The characterization of a set of objects is part of the decision making process in general. In Machine Learning this classification happens through a learning algorithm and the characterization is applied to databases. The classification algorithms can be employed individually or by machine committees. The choice of the best methods to be used in the construction of a committee is a very arduous task. In this work, it will be investigated meta-learning techniques in selecting the best configuration parameters of homogeneous committees for applications in various classification problems. These parameters are: the base classifier, the architecture and the size of this architecture. We investigated nine types of inductors candidates for based classifier, two methods of generation of architecture and nine medium-sized groups for architecture. Dimensionality reduction techniques have been applied to metabases looking for improvement. Five classifiers methods are investigated as meta-learners in the process of choosing the best parameters of a homogeneous committee.

Nest architecture of Pachycondyla striata Fr. Smith, 1858 (Formicidae, Ponerinae)

Nine nests of Pachycondyla striata Fr. Smith, 1858 were excavated between 2006 and 2007 at the UNESP university campus in Rio Claro, SP, southeastern Brazil. The P. striata population was larger in the two nests excavated in the months of August and November, 2006. The nests of this species are simple and poorly elaborated, with chambers and tunnels close to the ground surface. P. striata places the pupae in chambers isolated from the other individuals. The lack of chambers with the specific purpose of conditioning food and garbage underscores the simplicity of these nests.

Common architecture for discrete wavelet transform analysis and synthesis with sequential and constant processing elements

This paper adresses the problem on processing biological data such as cardiac beats, audio and ultrasonic range, calculating wavelet coefficients in real time, with processor clock running at frequency of present ASIC's and FPGA. The Paralell Filter Architecture for DWT has been improved, calculating wavelet coefficients in real time with hardware reduced to 60%. The new architecture, which also processes IDWT, is implemented with the Radix-2 or the Booth-Wallace Constant multipliers. Including series memory register banks, one integrated circuit Signal Analyzer, ultrasonic range, is presented.

Kaposi's sarcoma-associated herpesvirus latency-associated nuclear antigen 1 mimics Epstein-Barr virus EBNA1 immune evasion through central repeat domain effects on protein processing

Kaposi's sarcoma-associated herpesvirus (KSHV/human herpesvirus 8 [HHV8]) and Epstein-Barr virus (EBV/HHV4) are distantly related gammaherpesviruses causing tumors in humans. KSHV latency-associated nuclear antigen 1 (LANA1) is functionally similar to the EBV nuclear antigen-1 (EBNA1) protein expressed during viral latency, although they have no amino acid similarities. EBNA1 escapes cytotoxic lymphocyte (CTL) antigen processing by inhibiting its own proteosomal degradation and retarding its own synthesis to reduce defective ribosomal product processing. We show here that the LANA1 QED-rich central repeat (CR) region, particularly the CR2CR3 subdomain, also retards LANA1 synthesis and markedly enhances LANA1 stability in vitro and in vivo. LANA1 isoforms have half-lives greater than 24 h, and fusion of the LANA1 CR2CR3 domain to a destabilized heterologous protein markedly decreases protein turnover. Unlike EBNA1, the LANA1 CR2CR3 subdomain retards translation regardless of whether it is fused to the 5′ or 3′ end of a heterologous gene construct. Manipulation of sequence order, orientation, and composition of the CR2 and CR3 subdomains suggests that specific peptide sequences rather than RNA structures are responsible for synthesis retardation. Although mechanistic differences exist between LANA1 and EBNA1, the primary structures of both proteins have evolved to minimize provoking CTL immune responses. Simple strategies to eliminate these viral inhibitory regions may markedly improve vaccine effectiveness by maximizing CTL responses. Copyright © 2007, American Society for Microbiology. All Rights Reserved.

A multisampling time-domain CMOS imager with synchronous readout circuit

A novel multisampling time-domain architecture for CMOS imagers with synchronous readout and wide dynamic range is proposed. The architecture was implemented in a prototype of imager with 32x32 pixel array fabricated in AMS CMOS 0.35νm and was characterized for sensitivity and color response. The pixel is composed of an n+/psub photodiode, a comparator and a D flip-flop having 16% fill-factor and 30νmx26νm dimensions. The multisampling architecture requires only a 1 bit per pixel memory instead of 8 bits which is typical for time-domain active pixel architectures. The advantage is that the number of transistors in the pixel is low, saving area and providing higher fill-factor. The maximum frame rate is analyzed as a function of number of bits and array size. The analysis shows that it is possible to achieve high frame rates and operation in video mode with 10 bits. Also, we present analysis for the impact of comparator offset voltage in the fixed pattern noise. Copyright 2007 ACM.

Studies of Author Cocitation Analysis: A Bibliometric Approach for Domain Analysis

Author Cocitation Analysis (ACA) can be defined as the analysis of a group of actors, writers or researchers structurally organized in a (social and cognitive) network of a particular scientific community. The greater the number of researchers selected, the greater the amplitude and the domain boundary under consideration; the more restricted the number of researchers chosen as representative and appropriate, the less extensive the domain. From the perspective of the first axis of Tennis (2003), the selection of authors involves setting parameters on the extent of the domain, i.e., its total scope and amplitude. Thus, from the point of view of Tennis’s (2003) approach to Domain Analysis, the selection of authors for Author Cocitation Analysis is associated with the designations and boundaries of the domain, as well as to their goals (Tennis, 2003). Still, the selection of authors through the most cited authors in the literature, reflects the core elements of a domain and constitute the most specific foundation of a domain, aligning to the Degrees of Specialization characterized by Tennis (2003). It is concluded that the Author Cocitation Analysis (ACA) is a relevant procedure to the analysis of the underlying structure of a scientific knowledge domain, which meets the theories and concepts of Domain Analysis researchers, in that it allows characterizing the science, identifying, analyzing and assessing the conditions under which scientific knowledge is constructed and socialized.