Automatically fixing static analysis tools violations

Dissertação (mestrado)—Universidade de Brasília, Instituto de Ciências Exatas, Departamento de Ciência da Computação, 2019.A qualidade de software tem se tornado cada vez mais importante à medida que a so- ciedade depende mais de sistemas de software. Defeitos de software podem custar caro à organizações, especialmente quando causam falhas. Ferramentas de análise estática analisam código para encontrar desvios, ou violações, de práticas recomendadas de pro- gramação definidas como regras. Essa análise pode encontrar defeitos de software de forma antecipada, mais rápida e barata, em contraste à inspeções manuais. Para corrigir- se uma violação é necessário que o programador modifique o código problemático. Essas modificações podem ser tediosas, passíveis de erro e repetitivas. Dessa forma, a au- tomação de transformações de código é uma funcionalidade frequentemente requisitada por desenvolvedores. Esse trabalho implementa transformações automáticas para resolver violações identificadas por ferramentas de análise estática. Primeiro, nós investigamos o uso da ferramenta SonarQube, uma ferramenta amplamente utilizada, em duas grandes organizações open-source e duas instituições do Governo Federal do Brasil. Nossos re- sultados mostram que um pequeno subconjunto de regras é responsável por uma grande porção das violações resolvidas. Nós implementamos transformações automáticas para 11 regras do conjunto de regras comumente resolvidas achadas no estudo anterior. Nós submetemos 38 pull requests, incluindo 920 soluções para violações, geradas automati- camente pela nossa técnica para diversos projetos open-source na linguagem Java. Os mantenedores dos projetos aceitaram 84% das nossas transformações, sendo 95% delas sem nenhuma modificação. Esses resultados indicam que nossa abordagem é prática, e pode auxiliar desenvolvedores com resoluções automáticas, uma funcionalidade frequente- mente requisitada.Software quality is becoming more important as the reliance on software systems in- creases. Software defects may have a high cost to organizations as some can lead to software failure. Static analysis tools analyze code to find deviations, or violations, from recommended programming practices defined as rules. This analysis can find software defects earlier, faster, and cheaper than manual inspections. When fixing a violation, a programmer is required to modify the violating code. Such modifications can be tedious, error-prone, and repetitive. Unsurprisingly, automated transformations are frequently re- quested by developers. This work implements automatic transformations tailored to solve violations identified by static analysis tools. First, we investigate the use of SonarQube, a widely used Static Analysis Tool, in two large open source organizations and two Brazil- ian Government Federal Institutions. Our results show that a small subset of the rules is responsible for a large portion of the fixes. We implement automatic fixes for 11 rules from the previously found set of frequently fixed rules. We submitted 38 pull requests, including 920 fixes generated automatically by our technique for various open-source Java projects. Projects maintainers accepted 84% of our fixes (95% of them without any mod- ifications). These results indicate that our approach is feasible, and can aid developers with automatic fixes, a long requested feature

Performance of goats and sheep grazing in Brazilian semi-arid scrubland supplemented with feed-blocks

The performance of four types of animals (two ovine and two caprine) was evaluated under grazing/browsing in Brazilian Caatinga scrubland, with ad libitum feed-block supplementation. Forty noncastrated males with an initial body weight of 19.3 ± 1.9 kg were used: 20 goats (10 Savanna x local undefined breed [LUB]) and 10 Boer x LUB and 20 sheep (10 Santa-Inês x local undefined hair sheep [LUHS]) breed and 10 Dorper x LUHS. The experimental design was completely randomized blocks with four treatments and ten replications. The genotypes were compared based on growth performance and carcass characteristics. The ½ Dorper sheep had a better productive performance than the ½ Santa-Inês sheep. For goats, the ½ Boer was superior to ½ Savanna in daily gain and final body weight (P>0.05). The ½ Dorper sheep gave the best carcass characteristics of all genotypes studied. In conclusion, the Dorper (sheep) and Boer (goats) are the genotypes recommended for crossing with local animals of undefined breeds to provide animals for finishing under grazing/browsing conditions in the Caatinga ecosystem of northeast Brazil with feed-block supplementation

DELETERIOUS EFFECT OF HIGH CARNOSINE CONCENTRATIONS IN EXTENDERS DURING SPERM CRYOPRESERVATION IN DOGS / EFECTO DELETÉREO DE ALTAS CONCENTRACIONES DE CARNOSINA EN DILUYENTES DURANTE LA CRIOPRESERVACIÓN ESPERMÁTICA EN PERROS

Cryopreservation is a key process among the canine reproductive biotechnologies. However, during sperm cryopreservation an excessive reactive oxygen species (ROS) generation occurs, leading to decrease in sperm quality. Therefore, several antioxidants were tested during sperm cryopreservation to prevent such effects, however the carnosine it has not used. Carnosine is a protein present in the seminal plasma, and unlike other antioxidants has the ability to remove products of lipid peroxidation (malondialdehyde), which are as harmful as ROS. Thus, the aim of this study was to evaluate the effects of different carnosine concentrations, during sperm cryopreservation in dogs. For this purpose, six dogs in reproductive age were used, and after sperm collection the samples were cryopreserved in Control (tris-citrate egg yolk extender), Carnosine 1mM, 50mM and 100mM groups. After thawing samples were analyzed by computer-assisted analysis of sperm motility, plasma membrane (eosin/nigrosin), acrosome integrity (fast green/rose Bengal), mitochondrial activity, DNA integrity and sperm resistance to oxidative stress (by TBARS). Decrease was observed in motility sperm kinetics (total and progressive motility) and reduced lipid peroxidation products in the group treated with 50mM and 100mM. On the other hand, 1mM was similar to control group. In conclusion, higher carnosine concentration (50 and 100mM) apparently promoted impairment in energy production and consequently was harmful to sperm kinetics. Thus, future studies must be performed using different carnosine concentrations and in association with substrates for glycolysis and oxidative phosphorylation.RESUMENLa criopreservación es un proceso clave entre las biotecnologías reproductivas en caninos. Sin embargo, durante la criopreservación espermática se da una generación excesiva de especies reactivas de oxígeno (ROS), lo que lleva a una disminución en la calidad espermática. Por lo tanto, varios medios de congelación utilizando antioxidantes para evitar tales efectos han sido evaluados, aunque la carnosina todavía no se ha utilizada. La carnosina es una proteína presente en el plasma seminal que a diferencia de otros antioxidantes tiene la habilidad de remover productos de la peroxidación lipídica (malondialdehído), que son tan dañinos como los ROS. Por lo tanto, el objetivo de este estudio fue evaluar los efectos de diferentes concentraciones de carnosina durante la congelación espermática en perros. Para este propósito se utilizaron seis perros en edad reproductiva y después de la colectar los eyaculados, las muestras fueron criopreservadas en un diluyente Control (tris, citrato, yema de huevo), Carnosina 1mM, 50mM y 100 mM. Después del descongelado, las muestras fueron evaluadas mediante el análisis computerizado de la motilidad, integridad de membrana plasmática (eosina / nigrosina), integridad del acrosoma (Fast - green / rosa de Bengala), la actividad mitocondrial (3’3 Diaminobenzidina), la integridad del ADN (SCSA) y la evaluación de la resistencia al estrés oxidativo (TBARS). Se observó una disminución en la cinética de los espermatozoides (motilidad total y progresiva) y una reducción de los productos de la peroxidación lipídica en los grupos tratados con 50 mM y 100mM de carnosina. Por otro lado, el grupo con 1 mM de carnosina fue similar al control. En conclusión, una alta concentración de carnosina (50 y 100mM) parece afectar la producción de energía del espermatozoide y por lo tanto es perjudicial para la cinética del espermatozoide. Por lo tanto, futuros estudios deben realizarse utilizando diferentes concentraciones de carnosina y en asociación con sustratos para la glucólisis y la fosforilación oxidativa

A Fine-grained Data Set and Analysis of Tangling in Bug Fixing Commits

Context: Tangled commits are changes to software that address multiple concerns at once. For researchers interested in bugs, tangled commits mean that they actually study not only bugs, but also other concerns irrelevant for the study of bugs. Objective: We want to improve our understanding of the prevalence of tangling and the types of changes that are tangled within bug fixing commits. Methods: We use a crowd sourcing approach for manual labeling to validate which changes contribute to bug fixes for each line in bug fixing commits. Each line is labeled by four participants. If at least three participants agree on the same label, we have consensus. Results: We estimate that between 17% and 32% of all changes in bug fixing commits modify the source code to fix the underlying problem. However, when we only consider changes to the production code files this ratio increases to 66% to 87%. We find that about 11% of lines are hard to label leading to active disagreements between participants. Due to confirmed tangling and the uncertainty in our data, we estimate that 3% to 47% of data is noisy without manual untangling, depending on the use case. Conclusion: Tangled commits have a high prevalence in bug fixes and can lead to a large amount of noise in the data. Prior research indicates that this noise may alter results. As researchers, we should be skeptics and assume that unvalidated data is likely very noisy, until proven otherwise.Comment: Status: Accepted at Empirical Software Engineerin

TRY plant trait database – enhanced coverage and open access

Plant traits - the morphological, anatomical, physiological, biochemical and phenological characteristics of plants - determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait‐based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits - almost complete coverage for ‘plant growth form’. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait–environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives

Produção de gás de síntese a partir do etanol

34

Produção de gás de síntese a partir do etanol

34

Variabilidade espacial de atributos de solos coesos do leste maranhense

The national and international demand for maps of soil properties has increased. The aim of this study was to characterize cohesive soils and associate their variability of particle size, chemical properties, and color to different landforms in agricultural areas and native vegetation using geostatistical techniques. To set up the experiment, we selected three areas of soil consisting of an area planted to soybeans and, contiguous to it, another area with plant cover remaining from three types of cerrado (tropical savanna), designated Cerradão (A), Cerrado (B), and Campo Cerrado (C). The areas A and B are located on a concave landform, while area C is on a convex landform. Sampling grids with 121 points were established in each area, and in areas with native vegetation, transects were constructed with five points spaced at 20 m. The largest mean ranges, considering both depths evaluated, were found for area A, with 115 m for particle size, 157 m for chemical attributes, and 168 m for soil color. Area B had mean ranges of 95, 64, and 160 m for grain size, chemical attribute, and soil color, respectively. For its part, area C exhibited the mean ranges of 63, 65, and 58 m in grain size, chemical attributes, and soil color, respectively. The environment with the greatest variability (area C) is related to locations with the occurrence of Campo Cerrado vegetation and a convex landform. This same site had the lowest responsiveness to soybean crop management, shown by soil fertility indicators for this crop, especially the low values for organic matter (9.20 mg kg-1) and CEC (29.60 mmol c dm-3). Thus, it can be stated that for the geological compartment studied, the environments of high variability will always be associated with areas with lower response to soil management for soybean.A demanda nacional e internacional por mapas de atributos do solo tem aumentado. Os objetivos deste trabalho foram caracterizar e associar a variabilidade da granulometria, os atributos químicos e a cor de solos coesos a diferentes formas de paisagem, em áreas agrícolas e de vegetação nativa, por meio de técnicas geoestatísticas. Para a instalação do experimento, foram escolhidas três áreas representadas por uma área cultivada com soja e, contígua a essa, uma com cobertura vegetal remanescente de três feições de cerrado, designadas de Cerradão (A), Cerrado (B) e Campo Cerrado (C). As áreas A e B estão localizadas em pedoforma côncava e a área C, na convexa. Em cada área, foram estabelecidas malhas de amostragem com 121 pontos; nas áreas com cobertura vegetal construíram-se transeções com cinco pontos espaçados em 20 m. Os maiores alcances médios, considerando ambas as profundidades avaliadas, foram encontrados para a área A, sendo de 115 m para granulometria, 157 m para atributos químicos e 168 m para a cor do solo. A área B apresentou alcances médios de 95, 64 e 160 m para granulometria, atributos químicos e cor do solo, respectivamente. A área C, por sua vez, exibiu alcances médios de 63, 65 e 58 m para granulometria, atributos químicos e cor do solo, respectivamente. O ambiente com maior variabilidade (área C) está relacionado com locais de ocorrência de vegetação do tipo Campo Cerrado e pedoforma convexa. Esse mesmo local evidenciou a menor capacidade de resposta ao manejo da cultura de soja, evidenciado pelos índices de fertilidade do solo para essa cultura, com destaque para os baixos valores de matéria orgânica (9,20 mg kg-1) e CTC (29,60 mmol c dm-3). Assim, pode-se afirmar que para o compartimento geológico estudado, os ambientes de alta variabilidade sempre estão associados a áreas com menor resposta ao manejo do solo para a cultura da soja.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES