Chromatographic alignment of LC-MS and LC-MS/MS datasets by genetic algorithm feature extraction

Liquid chromatography-mass spectrometry (LC-MS) datasets can be compared or combined following chromatographic alignment. Here we describe a simple solution to the specific problem of aligning one LC-MS dataset and one LC-MS/MS dataset, acquired on separate instruments from an enzymatic digest of a protein mixture, using feature extraction and a genetic algorithm. First, the LC-MS dataset is searched within a few ppm of the calculated theoretical masses of peptides confidently identified by LC-MS/MS. A piecewise linear function is then fitted to these matched peptides using a genetic algorithm with a fitness function that is insensitive to incorrect matches but sufficiently flexible to adapt to the discrete shifts common when comparing LC datasets. We demonstrate the utility of this method by aligning ion trap LC-MS/MS data with accurate LC-MS data from an FTICR mass spectrometer and show how hybrid datasets can improve peptide and protein identification by combining the speed of the ion trap with the mass accuracy of the FTICR, similar to using a hybrid ion trap-FTICR instrument. We also show that the high resolving power of FTICR can improve precision and linear dynamic range in quantitative proteomics. The alignment software, msalign, is freely available as open source.

Solving complex optimal control problems at no cost with PSOPT

This paper introduces PSOPT, an open source optimal control solver written in C++. PSOPT uses pseudospectral and local discretizations, sparse nonlinear programming, automatic differentiation, and it incorporates automatic scaling and mesh refinement facilities. The software is able to solve complex optimal control problems including multiple phases, delayed differential equations, nonlinear path constraints, interior point constraints, integral constraints, and free initial and/or final times. The software does not require any non-free platform to run, not even the operating system, as it is able to run under Linux. Additionally, the software generates plots as well as LATEX code so that its results can easily be included in publications. An illustrative example is provided.

Capturing and sharing our collective expertise on climate data: the CHARMe project

For users of climate services, the ability to quickly determine the datasets that best fit one's needs would be invaluable. The volume, variety and complexity of climate data makes this judgment difficult. The ambition of CHARMe ("Characterization of metadata to enable high-quality climate services") is to give a wider interdisciplinary community access to a range of supporting information, such as journal articles, technical reports or feedback on previous applications of the data. The capture and discovery of this "commentary" information, often created by data users rather than data providers, and currently not linked to the data themselves, has not been significantly addressed previously. CHARMe applies the principles of Linked Data and open web standards to associate, record, search and publish user-derived annotations in a way that can be read both by users and automated systems. Tools have been developed within the CHARMe project that enable annotation capability for data delivery systems already in wide use for discovering climate data. In addition, the project has developed advanced tools for exploring data and commentary in innovative ways, including an interactive data explorer and comparator ("CHARMe Maps") and a tool for correlating climate time series with external "significant events" (e.g. instrument failures or large volcanic eruptions) that affect the data quality. Although the project focuses on climate science, the concepts are general and could be applied to other fields. All CHARMe system software is open-source, released under a liberal licence, permitting future projects to re-use the source code as they wish.

Using social software to support the teaching of IT professional practice

Social software has been used to support problem-based learning activities in a wholly online information technology (IT) professional practice course at Deakin University since 2006. When the course was first delivered, the authentic learning environment was a website, with an intranet and team forums created in Drupal, the open source content management system (CMS). Although this environment was suitable, feedback from students and teaching staff highlighted areas where improvements could be made. In the second year of the course, Joomla!, the open source CMS, in combination with Simple Machines Forum (SMF), the open source online discussion community software, was used to provide the website, as well as the intranet and team forums respectively. Feedback in 2007 was more positive, suggesting that the Joomla!-SMF social software combination and the features implemented, improved the learning and teaching experience in comparison to the 2006 version of the course.

Numerical Simulation Of Sediment Transport And Bedmorphology Around A Hydraulic Structure On A River

Scour around hydraulic structures is a critical problem in hydraulic engineering. Under prediction of scour depth may lead to costly failures of the structure, while over prediction might result in unnecessary costs. Unfortunately, up-to-date empirical scour prediction formulas are based on laboratory experiments that are not always able to reproduce field conditions due to complicated geometry of rivers and temporal and spatial scales of a physical model. However, computational fluid dynamics (CFD) tools can perform using real field dimensions and operating conditions to predict sediment scour around hydraulic structures. In Korea, after completing the Four Major Rivers Restoration Project, several new weirs have been built across Han, Nakdong, Geum and Yeongsan Rivers. Consequently, sediment deposition and bed erosion around such structures have became a major issue in these four rivers. In this study, an application of an open source CFD software package, the TELEMAC-MASCARET, to simulate sediment transport and bed morphology around Gangjeong weir, which is the largest multipurpose weir built on Nakdong River. A real bathymetry of the river and a geometry of the weir have been implemented into the numerical model. The numerical simulation is carried out with a real hydrograph at the upstream boundary. The bedmorphology obtained from the numerical results has been validated against field observation data, and a maximum of simulated scour depth is compared with the results obtained by empirical formulas of Hoffmans. Agreement between numerical computations, observed data and empirical formulas is judged to be satisfactory on all major comparisons. The outcome of this study does not only point out the locations where deposition and erosion might take place depending on the weir gate operation, but also analyzes the mechanism of formation and evolution of scour holes after the weir gates.

Temperature Dynamics Investigation At Small And Shallow Lakes Using Hydrodynamic Model

A three-dimensional time-dependent hydrodynamic and heat transport model of Lake Binaba, a shallow and small dam reservoir in Ghana, emphasizing the simulation of dynamics and thermal structure has been developed. Most numerical studies of temperature dynamics in reservoirs are based on one- or two-dimensional models. These models are not applicable for reservoirs characterized with complex flow pattern and unsteady heat exchange between the atmosphere and water surface. Continuity, momentum and temperature transport equations have been solved. Proper assignment of boundary conditions, especially surface heat fluxes, has been found crucial in simulating the lake’s hydrothermal dynamics. This model is based on the Reynolds Average Navier-Stokes equations, using a Boussinesq approach, with a standard k − ε turbulence closure to solve the flow field. The thermal model includes a heat source term, which takes into account the short wave radiation and also heat convection at the free surface, which is function of air temperatures, wind velocity and stability conditions of atmospheric boundary layer over the water surface. The governing equations of the model have been solved by OpenFOAM; an open source, freely available CFD toolbox. As its core, OpenFOAM has a set of efficient C++ modules that are used to build solvers. It uses collocated, polyhedral numerics that can be applied on unstructured meshes and can be easily extended to run in parallel. A new solver has been developed to solve the hydrothermal model of lake. The simulated temperature was compared against a 15 days field data set. Simulated and measured temperature profiles in the probe locations show reasonable agreement. The model might be able to compute total heat storage of water bodies to estimate evaporation from water surface.

Entry mode choice and market selection of born globals in developing countries: a multiple-case study of the ecuadorian software sector

O fenômeno "Born global" refere-se a empresas que consideram o mercado global como seu contexto natural e que iniciam seu processo de internacionalização muito cedo após sua criação. As teorias tradicionais como o modelo de Uppsala não conseguem explicar este processo. Portanto, outras teorias têm surgido, como a perspectiva de redes. Existem alguns estudos relacionados a esta área, principalmente realizados em países desenvolvidos com pequenos mercados e economias abertas. No entanto, poucos estudos têm sido feitos em economias em desenvolvimento. Além disso, o número de pesquisas quanto à escolha do modo de entrada e seleção de mercados das empresas “born global” é bastante limitado. Consequentemente, este estudo pretende descrever os principais fatores que influenciam a escolha do modo de entrada e seleção de mercados das empresas, de economias em desenvolvimento, nascidas globais. O foco da pesquisa é a indústria de software e um estudo de casos múltiplo foi realizado com três empresas no Equador. A metodologia incluiu entrevistas com fundadores, bem como a coleta de dados secundários. Com base na evidência empírica, verificou-se que os principais fatores que influenciam a escolha do modo de entrada são as restrições financeiras, as receitas esperadas, a velocidade de internacionalização, mercados nicho e a experiência empresarial anterior dos fundadores. Por outro lado, a seleção de mercado é influenciada por semelhanças de língua e cultura, mercados nicho e relações em rede.

Avaliação da contribuição de desenvolvedores para projetos de software usando mineração de repositórios de software e mineração de processos

Software Repository Mining (MSR) is a research area that analyses software repositories in order to derive relevant information for the research and practice of software engineering. The main goal of repository mining is to extract static information from repositories (e.g. code repository or change requisition system) into valuable information providing a way to support the decision making of software projects. On the other hand, another research area called Process Mining (PM) aims to find the characteristics of the underlying process of business organizations, supporting the process improvement and documentation. Recent works have been doing several analyses through MSR and PM techniques: (i) to investigate the evolution of software projects; (ii) to understand the real underlying process of a project; and (iii) create defect prediction models. However, few research works have been focusing on analyzing the contributions of software developers by means of MSR and PM techniques. In this context, this dissertation proposes the development of two empirical studies of assessment of the contribution of software developers to an open-source and a commercial project using those techniques. The contributions of developers are assessed through three different perspectives: (i) buggy commits; (ii) the size of commits; and (iii) the most important bugs. For the opensource project 12.827 commits and 8.410 bugs have been analyzed while 4.663 commits and 1.898 bugs have been analyzed for the commercial project. Our results indicate that, for the open source project, the developers classified as core developers have contributed with more buggy commits (although they have contributed with the majority of commits), more code to the project (commit size) and more important bugs solved while the results could not indicate differences with statistical significance between developer groups for the commercial project

Dihydrolipoyl dehydrogenase as a source of reactive oxygen species inhibited by caloric restriction and involved in Saccharomyces cerevisiae aging

Replicative life span in Saccharomyces cerevisiae is increased by glucose (G1c) limitation [ calorie restriction (CR)] and by augmented NAD(+). Increased survival promoted by CR was attributed previously to the NAD(+)-dependent histone deacetylase activity of sirtuin family protein Sir2p but not to changes in redox state. Here we show that strains defective in NAD(+) synthesis and salvage pathways (pnc1 Delta, npt1 Delta, and bna6 Delta) exhibit decreased oxygen consumption and increased mitochondrial H2O2 release, reversed over time by CR. These null mutant strains also present decreased chronological longevity in a manner rescued by CR. Furthermore, we observed that changes in mitochondrial H2O2 release alter cellular redox state, as attested by measurements of total, oxidized, and reduced glutathione. Surprisingly, our results indicate that matrix-soluble dihydrolipoyl-dehydrogenases are an important source of CR-preventable mitochondrial reactive oxygen species (ROS). Indeed, deletion of the LPD1 gene prevented oxidative stress in npt1 Delta and bna6 Delta mutants. Furthermore, pyruvate and alpha-ketoglutarate, substrates for dihydrolipoyl dehydrogenase-containing enzymes, promoted pronounced reactive oxygen release in permeabilized wild-type mitochondria. Altogether, these results substantiate the concept that mitochondrial ROS can be limited by caloric restriction and play an important role in S. cerevisiae senescence. Furthermore, these findings uncover dihydrolipoyl dehydrogenase as an important and novel source of ROS leading to life span limitation.

Structural complexity of the nitrogen source and influence on yeast growth and fermentation

The structural complexity of the nitrogen source strongly affects both biomass and ethanol production by industrial strains of Saccharomyces cerevisiae, during fermentation in media containing glucose or maltose, and supplemented with a nitrogen source varying from a single ammonium salt (ammonium sulfate) to free amino acids (casamino acids) and peptides (peptone). Diauxie was observed at low glucose and maltose concentrations independent of nitrogen supplementation. At high sugar concentrations diauxie was not easily observed. and growth and ethanol production depended on the nature of the nitrogen source. This was different for baking and brewing ale and lager yeast strains. Sugar concentration had a strong effect on the shift from oxido-fermentative to oxidative metabolism. At low sugar concentrations, biomass production was similar under both peptone and casamino acid supplementation. Under casamino acid supplementation, the time for metabolic shift increased with the glucose concentration, together with a decrease in the biomass production. This drastic effect on glucose fermentation resulted in the extinction of the second growth phase, probably due to the loss of cell viability. Ammonium salts always induced poor yeast performance. In general, supplementation with a nitrogen source in the peptide form (peptone) was more positive for yeast metabolism, inducing higher biomass and ethanol production, and preserving yeast viability, in both glucose and maltose media, for baking and brewing ale and lager yeast strains. Determination of amino acid utilization showed that most free and peptide amino acids present, in peptone and casamino acids, were utilized by the yeast, suggesting that the results described in this work were not due to a nutritional status induced by nitrogen limitation.

A development process proposal for the ERP5 system

Modeling ERP software means capturing the information necessary for supporting enterprise management. This modeling process goes down through different abstraction layers, from enterprise modeling to code generation. Thus ERP is the kind of system where enterprise engineering undoubtedly has, or should have, a strong influence. For the case of Free/Open Source ERP, the lack of proper modeling methods and tools can jeopardize the advantage brought by source code availability. Therefore, the aim of this paper is to present a development process proposal for the Open Source ERP5 system. The proposed development process aims to cover different abstraction levels, taking into account well established standards and common practices, as well as platform issues. Its main goal is to provide an adaptable meta-process to ERP5 adopters. © 2006 IEEE.

Mobile application as a tool for urban traffic data collection and generation to advanced traveler information systems using Wi-Fi networks available in urban centers

This paper presents an Advanced Traveler Information System (ATIS) developed on Android platform, which is open source and free. The developed application has as its main objective the free use of a Vehicle-to- Infrastructure (V2I) communication through the wireless network access points available in urban centers. In addition to providing the necessary information for an Intelligent Transportation System (ITS) to a central server, the application also receives the traffic data close to the vehicle. Once obtained this traffic information, the application displays them to the driver in a clear and efficient way, allowing the user to make decisions about his route in real time. The application was tested in a real environment and the results are presented in the article. In conclusion we present the benefits of this application. © 2012 IEEE.

Free Amino Acids in Pacu, Piaractus mesopotamicus, Eggs and Larvae

Free amino acids (FAA) are used principally as substrate in protein synthesis and the source of energy in aerobic catabolism. In marine fish, embryo and larvae FAA are used to maintain body fluid osmolality during fish early development. However, there is essentially no information about FAA concentrations in early ontogeny of freshwater neotropical species in comparison to marine fishes. Therefore, the aim of this study was to evaluate the FAA concentrations in pacu, Piaractus mesopotamicus, eggs and larvae. Broodstock fish were induced to spawn and ovulated females were stripped of their eggs and immediately sampled for analysis. Larvae were sampled right after hatching (HL) and after the completion of the yolk-sac absorption (YSA). The wet weight of the HL and YSA larvae amounted to 0.5±0.1mg and 1.1±0.3mg, respectively. HL larvae showed higher levels of most of the indispensable amino acids (IAA) in comparison to eggs and YSA larvae. Exceptions were observed with His and Trp that showed higher or similar levels, respectively, in YSA larvae. The FAA Orn, Tau, Glu, Gln, Gly, and Tyr increased concentrations in both larval stages while that of Tau was found in higher concentration in all analyzed stages. Also, the concentrations of Asn, Ala, Pro, Ser, and Asp were higher in HL larvae. Both larval stages displayed a rise in total free IAA/total free DAA (dispensable amino acids) ratio. The authors conclude that the highest level of FAA in HL pacu larvae is indicative of active proteolysis of yolk reserves and a probable catabolism regulation of some FAA through spare-effect. In addition, Tau is one of the major FAA occurring during pacu ontogeny and may be performing regulation on body fluid osmolality regulation. © Copyright by the World Aquaculture Society 2013.

Sistema WEB para gerenciamento de informações agrícolas

Pós-graduação em Agronomia (Energia na Agricultura) - FCA

Um software de reconhecimento de voz para português brasileiro

Descreve a implementação de um software de reconhecimento de voz para o Português Brasileiro. Dentre os objetivos do trabalho tem-se a construção de um sistema de voz contínua para grandes vocabulários, apto a ser usado em aplicações em tempo-real. São apresentados os principais conceitos e características de tais sistemas, além de todos os passos necessários para construção. Como parte desse trabalho foram produzidos e disponibilizados vários recursos: modelos acústicos e de linguagem, novos corpora de voz e texto. O corpus de texto vem sendo construído através da extração e formatação automática de textos de jornais na Internet. Além disso, foram produzidos dois corpora de voz, um baseado em audiobooks e outro produzido especificamente para simular testes em tempo-real. O trabalho também propõe a utilização de técnicas de adaptação de locutor para resolução de problemas de descasamento acústico entre corpora de voz. Por último, é apresentada uma interface de programação de aplicativos que busca facilitar a utilização do decodificador Julius. Testes de desempenho são apresentados, comparando os sistemas desenvolvidos e um software comercial.