Streamlining code smells: Using collective intelligence and visualization

Context. Code smells are seen as major source of technical debt and, as such, should be detected and removed. Code smells have long been catalogued with corresponding mitigating solutions called refactoring operations. However, while the latter are supported in current IDEs (e.g., Eclipse), code smells detection scaffolding has still many limitations. Researchers argue that the subjectiveness of the code smells detection process is a major hindrance to mitigate the problem of smells-infected code. Objective. This thesis presents a new approach to code smells detection that we have called CrowdSmelling and the results of a validation experiment for this approach. The latter is based on supervised machine learning techniques, where the wisdom of the crowd (of software developers) is used to collectively calibrate code smells detection algorithms, thereby lessening the subjectivity issue. Method. In the context of three consecutive years of a Software Engineering course, a total “crowd” of around a hundred teams, with an average of three members each, classified the presence of 3 code smells (Long Method, God Class, and Feature Envy) in Java source code. These classifications were the basis of the oracles used for training six machine learning algorithms. Over one hundred models were generated and evaluated to determine which machine learning algorithms had the best performance in detecting each of the aforementioned code smells. Results. Good performances were obtained for God Class detection (ROC=0.896 for Naive Bayes) and Long Method detection (ROC=0.870 for AdaBoostM1), but much lower for Feature Envy (ROC=0.570 for Random Forrest). Conclusions. Obtained results suggest that Crowdsmelling is a feasible approach for the detection of code smells, but further validation experiments are required to cover more code smells and to increase external validityContexto. Os cheiros de código são a principal causa de dívida técnica (technical debt), como tal, devem ser detectados e removidos. Os cheiros de código já foram há muito tempo catalogados juntamente com as correspondentes soluções mitigadoras chamadas operações de refabricação (refactoring). No entanto, embora estas últimas sejam suportadas nas IDEs actuais (por exemplo, Eclipse), a deteção de cheiros de código têm ainda muitas limitações. Os investigadores argumentam que a subjectividade do processo de deteção de cheiros de código é um dos principais obstáculo à mitigação do problema da qualidade do código. Objectivo. Esta tese apresenta uma nova abordagem à detecção de cheiros de código, a que chamámos CrowdSmelling, e os resultados de uma experiência de validação para esta abordagem. A nossa abordagem de CrowdSmelling baseia-se em técnicas de aprendizagem automática supervisionada, onde a sabedoria da multidão (dos programadores de software) é utilizada para calibrar colectivamente algoritmos de detecção de cheiros de código, diminuindo assim a questão da subjectividade. Método. Em três anos consecutivos, no âmbito da Unidade Curricular de Engenharia de Software, uma "multidão", num total de cerca de uma centena de equipas, com uma média de três membros cada, classificou a presença de 3 cheiros de código (Long Method, God Class, and Feature Envy) em código fonte Java. Estas classificações foram a base dos oráculos utilizados para o treino de seis algoritmos de aprendizagem automática. Mais de cem modelos foram gerados e avaliados para determinar quais os algoritmos de aprendizagem de máquinas com melhor desempenho na detecção de cada um dos cheiros de código acima mencionados. Resultados. Foram obtidos bons desempenhos na detecção do God Class (ROC=0,896 para Naive Bayes) e na detecção do Long Method (ROC=0,870 para AdaBoostM1), mas muito mais baixos para Feature Envy (ROC=0,570 para Random Forrest). Conclusões. Os resultados obtidos sugerem que o Crowdsmelling é uma abordagem viável para a detecção de cheiros de código, mas são necessárias mais experiências de validação para cobrir mais cheiros de código e para aumentar a validade externa

NPK RESIDUAL EFFECTS IN THE PSAMENTIC HAPLUSDALF WITH UNIRRIGATED FORAGE SORGHUM (Sorghum bicolor (L.) Moench) IN ROTATION WITH POTATO (Solanum tuberosum L.)

The objectives of this research were to know the residual effects of the macronutrients N P K, applied in the non-irrigated Psamentic Haplusdalf, initially cropped with potato (Solanum tuberosum L.) and later with forage sorghum (Sorghum bicolor (L.) Moench, evaluating dry matter accumulation, plant height, leaf area index, leaf area ratio and the water use efficiency. The trials with sorghum were conducted in 1998 and 2000. It was used a randomized block design with 33 factorial arrangement of the W group of confounding and two replications. The fertilizers were applied from 1995 to 1997, excepting phosphorus, which was applied only in 1995. In 1998 the residual effect of nitrogen over 100kg ha-1 reduced dry matter production and the one for phosphorus increased. However, for the variable water use efficiency, the nitrogen was less efficient than phosphorus. Considering the potassium factor, the only significant response was found for the variable leaf area ratio. In the year 2000, only the nitrogen reduced significantly the variable leaf area ratio. Based on these findings, it is clear that the residual effects of the fertilizers should be considered in future crops, since it means, evidently, economy to farmers

Práticas artísticas no ensino básico e secundário

O terceiro número da Revista Matéria-Prima afirma-se como mais uma plataforma de disseminação e de registo na área da educação e ensino artísticos. Ao propor-se o desafio da Matéria-Prima está a lançar-se um repto de intervenção e partilha a três tipos de intervenientes na educação pela arte: — Os professores, profissionais experimentados; — Os que se iniciam na profissão, através da frequência de mestrados e estágios formativos; — Os investigadores e professores universitários desta área. Esta chamada coloca em cima da mesa a partilha das experiências didácticas em sala de aula, a pesquisa sobre práticas profissionais. Experiências, algumas bem-sucedidas, outras menos, porventura, todas com um mérito substancial, que é a vontade de estabelecer comunidade entre os interessados pela educação artística. Este conjunto de textos poderá ajudar a cartografar práticas que se observam bastante distintas, entre as realidades dos países representados, Portugal, Espanha, Brasil, Argentina. Observa-se também que a prática dos educadores está longe de ser homogénea. É surpreendente determinar as diferenças entre contextos e regiões. Se umas são mais metódicas, e por isso consistentes, outras abrem-se à descoberta. Em todas um ponto de encontro: a revista Matéria-Prima, que assim assume cada vez mais o seu nome como um desígnio de intervenção.info:eu-repo/semantics/publishedVersio

Pervasive gaps in Amazonian ecological research

Biodiversity loss is one of the main challenges of our time,1,2 and attempts to address it require a clear un derstanding of how ecological communities respond to environmental change across time and space.3,4 While the increasing availability of global databases on ecological communities has advanced our knowledge of biodiversity sensitivity to environmental changes,5–7 vast areas of the tropics remain understudied.8–11 In the American tropics, Amazonia stands out as the world’s most diverse rainforest and the primary source of Neotropical biodiversity,12 but it remains among the least known forests in America and is often underrepre sented in biodiversity databases.13–15 To worsen this situation, human-induced modifications16,17 may elim inate pieces of the Amazon’s biodiversity puzzle before we can use them to understand how ecological com munities are responding. To increase generalization and applicability of biodiversity knowledge,18,19 it is thus crucial to reduce biases in ecological research, particularly in regions projected to face the most pronounced environmental changes. We integrate ecological community metadata of 7,694 sampling sites for multiple or ganism groups in a machine learning model framework to map the research probability across the Brazilian Amazonia, while identifying the region’s vulnerability to environmental change. 15%–18% of the most ne glected areas in ecological research are expected to experience severe climate or land use changes by 2050. This means that unless we take immediate action, we will not be able to establish their current status, much less monitor how it is changing and what is being lostinfo:eu-repo/semantics/publishedVersio

ATLANTIC EPIPHYTES: a data set of vascular and non-vascular epiphyte plants and lichens from the Atlantic Forest

Epiphytes are hyper-diverse and one of the frequently undervalued life forms in plant surveys and biodiversity inventories. Epiphytes of the Atlantic Forest, one of the most endangered ecosystems in the world, have high endemism and radiated recently in the Pliocene. We aimed to (1) compile an extensive Atlantic Forest data set on vascular, non-vascular plants (including hemiepiphytes), and lichen epiphyte species occurrence and abundance; (2) describe the epiphyte distribution in the Atlantic Forest, in order to indicate future sampling efforts. Our work presents the first epiphyte data set with information on abundance and occurrence of epiphyte phorophyte species. All data compiled here come from three main sources provided by the authors: published sources (comprising peer-reviewed articles, books, and theses), unpublished data, and herbarium data. We compiled a data set composed of 2,095 species, from 89,270 holo/hemiepiphyte records, in the Atlantic Forest of Brazil, Argentina, Paraguay, and Uruguay, recorded from 1824 to early 2018. Most of the records were from qualitative data (occurrence only, 88%), well distributed throughout the Atlantic Forest. For quantitative records, the most common sampling method was individual trees (71%), followed by plot sampling (19%), and transect sampling (10%). Angiosperms (81%) were the most frequently registered group, and Bromeliaceae and Orchidaceae were the families with the greatest number of records (27,272 and 21,945, respectively). Ferns and Lycophytes presented fewer records than Angiosperms, and Polypodiaceae were the most recorded family, and more concentrated in the Southern and Southeastern regions. Data on non-vascular plants and lichens were scarce, with a few disjunct records concentrated in the Northeastern region of the Atlantic Forest. For all non-vascular plant records, Lejeuneaceae, a family of liverworts, was the most recorded family. We hope that our effort to organize scattered epiphyte data help advance the knowledge of epiphyte ecology, as well as our understanding of macroecological and biogeographical patterns in the Atlantic Forest. No copyright restrictions are associated with the data set. Please cite this Ecology Data Paper if the data are used in publication and teaching events. © 2019 The Authors. Ecology © 2019 The Ecological Society of Americ

Pervasive gaps in Amazonian ecological research

Biodiversity loss is one of the main challenges of our time,1,2 and attempts to address it require a clear understanding of how ecological communities respond to environmental change across time and space.3,4 While the increasing availability of global databases on ecological communities has advanced our knowledge of biodiversity sensitivity to environmental changes,5,6,7 vast areas of the tropics remain understudied.8,9,10,11 In the American tropics, Amazonia stands out as the world's most diverse rainforest and the primary source of Neotropical biodiversity,12 but it remains among the least known forests in America and is often underrepresented in biodiversity databases.13,14,15 To worsen this situation, human-induced modifications16,17 may eliminate pieces of the Amazon's biodiversity puzzle before we can use them to understand how ecological communities are responding. To increase generalization and applicability of biodiversity knowledge,18,19 it is thus crucial to reduce biases in ecological research, particularly in regions projected to face the most pronounced environmental changes. We integrate ecological community metadata of 7,694 sampling sites for multiple organism groups in a machine learning model framework to map the research probability across the Brazilian Amazonia, while identifying the region's vulnerability to environmental change. 15%–18% of the most neglected areas in ecological research are expected to experience severe climate or land use changes by 2050. This means that unless we take immediate action, we will not be able to establish their current status, much less monitor how it is changing and what is being lost

Efeito da glicose na histomorfologia do peritônio durante a diálise peritoneal

The peritoneum alterations in patients submitted to peritoneal dialysis for long periods begin with the mesothelium modifications and latter involves alterations of the submesothelium, fibrosis and vascular system. These alterations could be explained by the high concentration of glucose in the dialysis solution, and by other things. Therefore, the aim of this study was to study the histomorfological alterations of the peritoneal membrane in rats submitted to peritoneal dialysis, with the glucose solution at the local temperature. 20 Wistar rats were used, divided into two groups: control group (CG) with eight animals that didn’t receive intraperitoneal injection and the concentrated solution group (CSG) with 12 animals that received 10ml of the dialysis fluid with 4.25% of glucose once a day for 30 days. The visceral peritoneum of the spleen and the parietal peritoneum of the abdominal wall in the animals of CSG presented epithelial alterations with cubic transformation of the mesothelium cells and the thickness of the submesothelium layer, respectively. The dialysis solution of glucose at 4.25% in local temperature, done once a day, during 30 days, altered the histomorfology of the peritoneum.As alterações peritoneais em pacientes submetidos a diálise peritoneal por longos períodos começam com as modificações mesoteliais e mais tarde envolvem alterações submesoteliais, fibrose e vasculopatias. Essas alterações podem ser decorrentes entre outras coisas da alta concentração de glicose da solução de diálise. Desta forma, o objetivo desse trabalho foi estudar as alterações histomorfológicas na membrana peritoneal de ratos submetidos a diálise peritoneal, com solução de glicose a temperatura ambiente. Foram utilizados 20 ratos Wistar divididos em dois grupos: grupo controle (GC) com oito animais que não receberam nenhuma injeção intraperitoneal e grupo solução concentrada (GSC) com 12 animais que receberam 10 ml de fluido de diálise com 4,25% de glicose uma vez por dia durante 30 dias. O peritônio visceral do baço e o peritônio parietal da parede abdominal nos animais do GSC apresentaram respectivamente alterações epiteliais com transformação cúbica das células mesoteliais e espessamento na camada submesotelial. A solução de diálise com 4,25% de glicose em temperatura ambiente realizada uma vez por dia durante 30 dias alterou a histomorfologia do peritônio

Prognostic Factors and Markers in Non-Small Cell Lung Cancer: Recent Progress and Future Challenges

Lung cancer is a highly aggressive neoplasm and, despite the development of recent therapies, tumor progression and recurrence following the initial response remains unsolved. Several questions remain unanswered about non-small cell lung cancer (NSCLC): (1) Which patients will actually benefit from therapy? (2) What are the predictive factors of response to MAbs and TKIs? (3) What are the best combination strategies with conventional treatments or new antineoplastic drugs? To answer these questions, an integrative literature review was carried out, searching articles in PUBMED, NCBI-PMC, Google Academic, and others. Here, we will examine the molecular genetics of lung cancer, emphasizing NSCLC, and delineate the primary categories of inhibitors based on their molecular targets, alongside the main treatment alternatives depending on the type of acquired resistance. We highlighted new therapies based on epigenetic information and a single-cell approach as a potential source of new biomarkers. The current and future of NSCLC management hinges upon genotyping correct prognostic markers, as well as on the evolution of precision medicine, which guarantees a tailored drug combination with precise targeting