GRASSIUS: A Platform for Comparative Regulatory Genomics across the Grasses

Transcription factors (TFs) are major players in gene regulatory networks and interactions between TFs and their target genes furnish spatiotemporal patterns of gene expression. Establishing the architecture of regulatory networks requires gathering information on TFs, their targets in the genome, and the corresponding binding sites. We have developed GRASSIUS (Grass Regulatory Information Services) as a knowledge-based Web resource that integrates information on TFs and gene promoters across the grasses. In its initial implementation, GRASSIUS consists of two separate, yet linked, databases. GrassTFDB holds information on TFs from maize (Zea mays), sorghum (Sorghum bicolor), sugarcane (Saccharum spp.), and rice (Oryza sativa). TFs are classified into families and phylogenetic relationships begin to uncover orthologous relationships among the participating species. This database also provides a centralized clearinghouse for TF synonyms in the grasses. GrassTFDB is linked to the grass TFome collection, which provides clones in recombination-based vectors corresponding to full-length open reading frames for a growing number of grass TFs. GrassPROMDB contains promoter and cis-regulatory element information for those grass species and genes for which enough data are available. The integration of GrassTFDB and GrassPROMDB will be accomplished through GrassRegNet as a first step in representing the architecture of grass regulatory networks. GRASSIUS can be accessed from www.grassius.org.

Nanoparticle Platform to Modulate Reaction Mechanism of Phenothiazine Photosensitizers

Herein, we report on the synthesis of photosensitizing nanoparticles in which the generation of different oxidizing species, i.e., singlet oxygen ((1)O(2)) or radicals, was modulated. Sol gel and surface chemistry were used to obtain nanoparticles with specific ratios of dimer to monomer species of phenothiazine photosensitizers (PSs). Due to competition between the reactions involving electron transfer within dimer species and energy transfer from monomer triplets to oxygen, the efficiency of (1)O(2) generation could be controlled. Nanoparticles with an excess of dimer have an (1)O(2) generation efficiency (S(Delta)) of 0.01 while those without dimer have a S, value of 0.4. Furthermore, we demonstrate that the PS properties of the nanoparticles are not subjected to interference from the external medium as is commonly the case for free PSs, i.e., PS ground and triplet states are not reduced by NADH and ascorbate, respectively, and singlet excited states are less suppressed by bromide. The modulated (1)O(2) generation and the PS protection from external interferences make this nanoparticle platform a promising tool to aid in performing mechanistic studies in biological systems. Also, it offers potential application in technological areas in which photo-induced processes take place.

Developing a Communication link between Agents and cross Platform IDE

The main objective of this thesis work is to develop communication link between Runrev Revolution (IDE) and JADE (Multi-Agent System) through Socket programming using TCP/IP layer. These two independent platforms are connected using socket programming technique. Socket programming is considered to be newly emerging technology among these two platforms, the work done in this thesis work is considered to be a prototype.A Graphical simulation model is developed by salixphere (Company in Hedemora) to simulate logistic problems using Runrev Revolution (IDE). The simulation software/program is called “BIOSIM”. The logistic problems are complex, and conventional optimization techniques are unlikely very successful. “BIOSIM” can demonstrate the graphical representation of logistic problems depending upon the problem domains. As this simulation model is developed in revolution programming language (Transcript) which is dynamically typed and English-like language, it is quite slow compared to other high level programming languages. The object of this thesis work is to add intelligent behaviour in graphical objects and develop communication link between Runrev revolution (IDE) and JADE (Multi-Agent System) using TCP/IP layers.The test shows the intelligent behaviour in the graphical objects and successful communication between Runrev Revolution (IDE) and JADE (Multi-Agent System).

Separation and Execution of graphical engine on a cross platform IDE to enhance performance

“Biosim” is a simulation software which works to simulate the harvesting system.This system is able to design a model for any logistic problem with the combination of several objects so that the artificial system can show the performance of an individual model. The system will also describe the efficiency, possibility to be chosen for real life application of that particular model. So, when any one wish to setup a logistic model like- harvesting system, in real life he/she may be noticed about the suitable prostitution for his plants and factories as well as he/she may get information about the least number of objects, total time to complete the task, total investment required for his model, total amount of noise produced for his establishment in advance. It will produce an advance over view for his model. But “Biosim” is quite slow .As it is an object based system, it takes long time to make its decision. Here the main task is to modify the system so that it can work faster than the previous. So, the main objective of this thesis is to reduce the load of “Biosim” by making some modification of the original system as well as to increase its efficiency. So that the whole system will be faster than the previous one and performs more efficiently when it will be applied in real life. Theconcept is to separate the execution part of ”Biosim” form its graphical engine and run this separated portion in a third generation language platform. C++ is chosenhere as this external platform. After completing the proposed system, results with different models have been observed. The results show that, for any type of plants of fields, for any number of trucks, the proposed system is faster than the original system. The proposed system takes at least 15% less time “Biosim”. The efficiency increase with the complexity of than the original the model. More complex the model, more efficient the proposed system is than original “Biosim”.Depending on the complexity of a model, the proposed system can be 56.53 % faster than the original “Biosim”.

GULF OF MEXICO'S OFFSHORE OIL PLATFORM WIND POTENTIAL

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Gulf of Mexico's Offshore Oil Platform Wind Potential

There are over 6000 natural resource drilling platforms in the Gulf of Mexico, all of which will become obsolete once their deposits are extracted. This study examined one of the possible alternate uses for these platforms, wind power potential. Using ArcGIS the number of platforms was reduced by weighting their distance from National Data Buoy Center wind speed collection points and water depth. Calculations were done to assess the optimal sites remaining, as well as provide an estimate of the energy potential for each site. Data for this project was obtained from the Minerals Management Service (MMS), United States Geological Service (USGS), and National Data Buoy Center (NDBC). A major limitation of this project was a lack of NDBC wind speed buoys, creating large data gaps and excluding many oil rigs that have otherwise high energy potential.

Why join a carbon club?: a study of the banks participating in the Brazilian “Business for Climate Platform”

Why do firms that present low levels of (direct) carbon emissions participate in “carbon clubs”, which have the goal of managing and reducing greenhouse gas (GHG) emissions? In order to answer this question, we collected data from both primary and secondary sources from firms operating in the Brazilian banking sector, which are members of the Businesses for Climate Platform (Plataforma Empresas pelo Clima e EPC). We first looked for answers in the institutional theory and resource based view of the firm (RBV). By confronting the arguments presented by these streams of scientific enquiry with empirical data, we worked on theory testing. In particular, we analyzed the institutional pressures and resources and capabilities of the focus companies, in order to understand the rationales for proactive sustainability management. We found evidences of the arguments presented by both the institutional theory and the RBV. By studying an industry that is not a frequent subject to research on socio-environmental issues e for not being considered of high impact e in an emerging market economy, the research contributes to both the further development of the institutional theory and the advancement of sustainability management in corporations.

An online platform for real-time sensor data collection, visualization, and sharing

Sharing sensor data between multiple devices and users can be^challenging for naive users, and requires knowledge of programming and use of different communication channels and/or development tools, leading to non uniform solutions. This thesis proposes a system that allows users to access sensors, share sensor data and manage sensors. With this system we intent to manage devices, share sensor data, compare sensor data, and set policies to act based on rules. This thesis presents the design and implementation of the system, as well as three case studies of its use.

Hudumia: a platform to support spontaneous volunteers' situational awareness, coordination and safety underemergency scenarios

Spontaneous volunteers always emerge under emergency scenarios and are vital to a successful community response, yet some uncertainty subsists around their role and its inherent acceptance by official entities under emergency scenarios. In our research we have identified that most of the spontaneous volunteers do have none or little support from official entities, hence they end up facing critical problems as situational awareness, safety instructions and guidance, motivation and group organization. We argue that official entities still play a crucial role and should change some of their behaviors regarding spontaneous volunteerism. We aim with this thesis to design a software architecture and a framework in order to implement a solution to support spontaneous volunteerism under emergency scenarios along with a set of guidelines for the design of open information management systems. Together with the collaboration from both citizens and emergency professionals we have been able to attain several important contributions, as the clear identification of the roles taken by both spontaneous volunteers and professionals, the importance of volunteerism in overall community response and the role which open collaborative information management systems have in the community volunteering efforts. These conclusions have directly supported the design guidelines of our software solution proposal. In what concerns to methodology, we first review literature on technologies support to emergencies and how spontaneous volunteers actually challenge these systems. Following, we have performed a field research where we have observed that the emerging of spontaneous volunteer’s efforts imposes new requirements for the design of such systems, which leaded to the creation of a cluster of design guidelines that supported our software solution proposal to address the volunteers’ requirements. Finally we have architected and developed an online open information management tool which has been evaluated via usability engineering methods, usability user tests and heuristic evaluations.

Inspeção e monitorização de estruturas em engenharia civil: utilização de UAV na inspeção e monitorização

Nesta tese são abordadas as tipologias e metodologias de monitorização e observação de infraestruturas em engenharia civil, nomeadamente através de aplicação de vários métodos de medição, de ensaios e também com implementação de sensores. Esta tese pretende abordar de uma forma mais concreta a utilização de plataformas UAV (Unmanned Aerial Vehicle) que apresentam vantagens consideráveis para ser utilizado na monitorização de infraestruturas devido à rapidez de aquisição de dados, mobilidade, segurança e ao baixo custo de aquisição e exploração. A monitorização com UAV consiste no aproveitamento de uma plataforma que pode transportar variadíssimos equipamentos para registo de dados, como câmaras e sensores de várias ordens, de uma forma rápida, económica e segura. Os UAV’s possibilitam o tratamento rápido da informação por eles recolhida, em tempo real ou em pós-processamento. Os dados recolhidos, dependendo do tipo de infraestruturas e objetivos, podem ser analisados com diversas aplicações que tratam os dados de acordo com as necessidades, tais como, modelação em 3D, modelos de elevação, cálculo de áreas, termografia, fotogrametria, etc. Nesta tese são apresentados alguns casos práticos onde se evidencia a vantagem da utilização do UAV na monitorização de infraestruturas, onde se verifica a rapidez, eficiência e qualidade na recolha de informação com o reduzido custo de exploração.

Breadcrumbs: location and context aware mobile platform for story sharing

With the current proliferation of sensor equipped mobile devices such as smartphones and tablets, location aware services are expanding beyond the mere efficiency and work related needs of users, evolving in order to incorporate fun, culture and the social life of users. Today people on the move have more and more connectivity and are expected to be able to communicate with their usual and familiar social networks. That means communications not only with their peers and colleagues, friends and family but also with unknown people that might share their interests, curiosities or happen to use the same social network. Through social networks, location aware blogging, cultural mobile applications relevant information is now available at specific geographical locations and open to feedback and conversations among friends as well as strangers. In fact, nowadays smartphone technologies aloud users to post and retrieve content while on the move, often relating to specific physical landmarks or locations, engaging and being engaged in conversations with strangers as much as their own social network. The use of such technologies and applications while on the move can often lead people to serendipitous discoveries and interactions. Throughout our thesis we are engaging on a two folded investigation: how can we foster and support serendipitous discoveries and what are the best interfaces for it? In fact, to read and write content while on the move is a cognitively intensive task. While the map serves the function of orienting the user, it also absorbs most of the user’s concentration. In order to address this kind of cognitive overload issue with Breadcrumbs we propose a 360 degrees interface that enables the user to find content around them by means of scanning the surrounding space with the mobile device. By using a loose metaphor of a periscope, harnessing the power of the smartphone sensors we designed an interactive interface capable of detecting content around the users and display it in the form of 2 dimensional bubbles which diameter depends on their distance from the users. Users will navigate the space in relation to the content that they are curious about, rather than in relation to the traditional geographical map. Through this model we envisage alleviating a certain cognitive overload generated by having to continuously confront a two dimensional map with the real three dimensional space surrounding the user, but also use the content as a navigational filter. Furthermore this alternative mean of navigating space might bring serendipitous discovery about places that user where not aware of or intending to reach. We hence conclude our thesis with the evaluation of the Breadcrumbs application and the comparison of the 360 degrees interface with a traditional 2 dimensional map displayed on the devise screen. Results from the evaluation are compiled in findings and insights for future use in designing and developing context aware mobile applications.

Thermochronology of the South American platform in the state of São Paulo, Brazil, through apatite fission tracks

The fission-track method (FTM) in apatite was applied to 45 samples collected in the Serra da Mantiqueira (Mantiqueira mountain range), the Serra do Mar (Mar mountain range), regions next to these mountain ranges and the coastal region between Ubatuba and Santos in the State of São Paulo, Brazil, to study the thermochronology of the South American Platform in southeast Brazil and its influence on Santos and Campos basins. The data presented in this work complement the previously presented data on the same region (Tello Saenz et al., 2003. J. S. Am. Earth Sci. 15, 765-774) with 31 new samples analyzed. The weighted mean of the corrected ages from high Mantiqueira (around 1000 m), (121 +/- 6) Ma, coincides with the South Atlantic opening. The fact that its thermal history starts at a relatively low temperature (similar to 80 degrees C) suggests that the age of similar to 120 Ma would be the formation age of Serra da Mantiqueira due to a rapid pulse, in which tracks had no time to be retained at the closure temperature, that is similar to 120 degrees C. The Serra do Mar presents a more complicated thermal history, with several reactivations indicated by the changes in the slope of its cooling curve. The thermal histories obtained in the regions next to these mountain ranges are compatible with the results mentioned above. The Santos Basin has unconformities that agree with changes in the slope thermal histories of the studied region. (c) 2005 Elsevier Ltd. All rights reserved.