Software systems are designed according to guidelines and constraints defined by business rules. Some of these constraints define the allowable or required values for data handled by the systems. These data constraints usually originate from the problem domain (e.g., regulations), and developers must write code that enforces them. Understanding how data constraints are implemented is essential for testing, debugging, and software change. Unfortunately, there are no widely-accepted guidelines or best practices on how to implement data constraints. This paper presents an empirical study that investigates how data constraints are implemented in Java. We study the implementation of 187 data constraints extracted from the documentation of eight real-world Java software systems. First, we perform a qualitative analysis of the textual description of data constraints and identify four data constraint types. Second, we manually identify the implementations of these data constraints and reveal that they can be grouped into 31 implementation patterns. The analysis of these implementation patterns indicates that developers prefer a handful of patterns when implementing data constraints. We also found evidence suggesting that deviations from these patterns are associated with unusual implementation decisions or code smells. Third, we develop a tool-assisted protocol that allows us to identify 256 additional trace links for the data constraints implemented using the 13 most common patterns. We find that almost half of these data constraints have multiple enforcing statements, which are code clones of different types. Finally, a study with 16 professional developers indicates that the patterns we describe can be easily and accurately recognized in Java code.

This research attempted to determine the efficacy of the tetrazolium test in the evaluation of the seed viability of two varieties of Coffea arabica L. (‘Castillo’ and ‘Cenicafé’). The fruits were obtained from crops located in the municipalities of Salazar de las Palmas and Arboledas (Norte de Santander - Colombia). The test was carried out with embryos manually extracted from the seeds using tweezers. Three pretreatments were established: distilled water, sodium hypochlorite (2.5 %), sucrose (10 %), and a control (no pretreatment). Embryos were placed in a cysteine solution (0.5 %) to prevent oxidation, then immersed in tetrazolium solutions with concentrations of 0.035 %, 0.075 %, and 0.1 % for a period of 6, 9, and 12 hours in darkness. The results of the viability test were validated with seed germination, using the wet paper towel method in darkness. The best viability percentages were found with the application of sodium hypochlorite (NaClO 2.5 %), with a high correlation with the germination percentage. The use of pretreatments improved the efficiency of the viability test and allowed the use of low concentrations of the reagent (0.035 %), giving the farmer a quick and less expensive alternative to determine germination capacity.

In theory, (good) documentation is an invaluable asset to any software project, as it helps stakeholders to use, understand, maintain, and evolve a system. In practice, however, documentation is generally affected by numerous shortcomings and issues, such as insufficient and inadequate content and obsolete, ambiguous information. To counter this, researchers are investigating the development of advanced recommender systems that automatically suggest high-quality documentation, useful for a given task. A crucial first step is to understand what quality means for practitioners and what information is actually needed for specific tasks. We present two surveys performed with 146 practitioners to investigate (i) the documentation issues they perceive as more relevant together with solutions they apply when these issues arise; and (ii) the types of documentation considered as important in different tasks. Our findings can help researchers in designing the next generation of documentation recommender systems.

Diazotrophic bacteria can stimulate the growth of the tomato (Lycopersicon esculentum Mill.) crop by hormone synthesis, with N fixation and the production of siderophores, or other processes. The predominant diazotrophic bacteria in agroecosystems may be potential biofertilizers. The aim of this study was to quantify and characterize the population of rhizospheric diatrophic bacteria in samples of rhizospheric soil (RS) and endophytic diazotrophic bacteria in root (R) and foliar material (FM) samples, with phenotypical and molecular tests. The study was exploratory and with random sampling, with 18 RS, roots (R) and FM samples of tomato plantations in six farms. The differences in the most probable number (MPN) of diazotrophic bacteria were not significant between the FM and R sampling sites. The mean of the Mfb displayed highly significant differences in Azotobacter sp. and Azospirillum sp. between the RS, R and FM samples, with a higher and lower MPN in RS and FM. This relates with the phenotypical and biochemical characterization of RS, in which 14 isolations were identified as Azotobacter sp., and seven as Azospirillum sp. The genera Burkholderia and Gluconacetobacter showed no significant differences in the number of isolations between RS and R samples, but they did with FM, with the lower cell population. The differences between the farms were not significant in the soil parameters, related to the dissimilarity of the MPN. Molecular characterization helped identify A. chroococcum, A. nigricans, A. vinelandii, A. brasilense, B. glumae and G. azotocaptans/G. johannae in samples of RS; B. glumae, G. azotocaptans/G. johannae in samples of R and G. azotocaptans/G. johannae in FM samples.

Las bacterias diazotróficas pueden estimular el crecimiento del cultivo del tomate (Lycopersicon esculentum Mill.) mediante la síntesis de hormonas, fijación de N y producción de sideróforos, u otros procesos. Las bacterias diazotróficas predominantes en los agroecosistemas pueden ser biofertilizantes potenciales. El objetivo del estudio fue cuantificar y caracterizar la población de bacterias diazotróficas rizosféricas en muestras de suelo rizosférico (SR) y bacterias diazotróficas endófitas en muestras de raíces (R) y material foliar (MF), mediante pruebas fenotípicas y moleculares. El estudio fue exploratorio y con un muestreo aleatorio, con 18 muestras SR, raíces (R) y MF de cultivos de tomate en seis fincas. Las diferencias en el número más probable (NMP) de bacterias diazotróficas no fueron significativas entre los sitios de las muestras de MF y R. La media de NFb mostró diferencias altamente significativas en Azotobacter sp. y Azospirillum sp. entre las muestras de SR, R y MF, con un NMP mayor y menor en SR y MF. Esto se relaciona con la caracterización fenotípica y bioquímica de SR donde se identificaron 14 aislados como Azotobacter sp. y siete como Azospirillum sp. Los géneros Burkholderia y Gluconacetobacter no mostraron diferencias significativas en el número de aislados entre muestras de SR y R, pero sí respecto a MF, con la población celular menor. Las diferencias entre las fincas no fueron significativas en las variables del suelo relacionadas con la disimilitud de NMP. La caracterización molecular permitió identificar A. chroococcum, A. nigricans, A. vinelandii, A. brasilense, B. glumae y G. azotocaptans/G. johannae en muestras de SR; B. glumae, G. azotocaptans/G. johannae en muestras de R y G. azotocaptans/G. johannae en muestras de MF. Palabras claves: diazotróficas, endófitas, rizosféricas, Lycopersicon esculentum Norte de Santander.

Abstract: The aim of the present study was to determine the most suitable pretreatment to enhance the tetrazolium test in seeds of the Epidendrum genus. Initially, mature capsules were harvested at El Escorial village, in the municipality of Pamplona, Colombia. Subsequently, the seeds were subjected to five pretreatments: deionized water, 0.5% NaClO, 1.0% NaClO, 10.0% sucrose and a control group. Using the syringe method with cloth filter, the seeds were rinsed with distilled water and subjected to two concentrations of tetrazolium solution (0.25%, 1.0%) and three exposure times (6 h, 24 h and 48 h). Finally, the tetrazolium viability test results were correlated with the in vitro germination test. It was found that the use of deionized water improves the efficiency of the tetrazolium test in seeds of Epidendrum fimbriatum and E. microtum; as in seeds of E. elongatum when using 1.0% tetrazolium for 24 h. Similarly, a high correlation was found between viability and germination, using deionized water and 10.0% sucrose, with homogeneous results with each other.

(Good) Software documentation provides developers and users with a description of what a software system does, how it operates, and how it should be used. For example, technical documentation (e.g., an API reference guide) aids developers during evolution/maintenance activities, while a user manual explains how users are to interact with a system. Despite its intrinsic value, the creation and the maintenance of documentation is often neglected, negatively impacting its quality and usefulness, ultimately leading to a generally unfavorable take on documentation. Previous studies investigating documentation issues have been based on surveying developers, which naturally leads to a somewhat biased view of problems affecting documentation. We present a large scale empirical study, where we mined, analyzed, and categorized 878 documentation-related artifacts stemming from four different sources, namely mailing lists, Stack Overflow discussions, issue repositories, and pull requests. The result is a detailed taxonomy of documentation issues from which we infer a series of actionable proposals both for researchers and practitioners.

The expression of CTX-M β-lactamases belonging to groups 1 and 9 in Klebsiella pneumoniae produces high levels of resistance to ceftazidime, and they have a wide distribution worldwide.To identify and characterize the blaCTX-M-Group1 and blaCTX-M-Group9 genes in K. pneumoniae isolates resistant to ceftazidime in a hospital in San José de Cúcuta, Colombia.Primers were designed for the identification of K. pneumoniae and blaCTX-M genes by PCR. Subsequently, the genetic relationship of these isolates was analyzed by REP-PCR.A 38% of the 24 isolates identified by PCR as K. pneumoniae showed blaCTX-M-3. blaCTX-M-15 y blaCTX-M-32 genes (Group CTX-M-1) and 42% blaCTX-M14. blaCTX-M-24 y blaCTX-M-27 genes (Group CTX-M-9). The phylogenetic analysis grouped the K. pneumoniae isolates into 4 clusters, showing correlation in clusters I, II and IV, when comparing the genetic profiles with the type of sample and group of genes.We found a similar frequency of blaCTX-M-Group 1 and blaCTX-M-Group 9 genes in isolates of K. pneumoniae resistant to ceftazidime. The correlation between the REP-PCR with the CTX-M groups and the type of sample revealed the presence of three clonal patterns.

Background: The expression of CTX-M beta-lactamases belonging to groups 1 and 9 in Klebsiella pneumoniae produces high levels of resistance to ceftazidime, and they have a wide distribution worldwide. Aim: To identify and characterize the bla(CTX-M)-Group1 and bla(CTX-M)-Group9 genes in K. pneumoniae isolates resistant to ceftazidime in a hospital in San Jose de Cucuta, Colombia. Material and Methods: Primers were designed for the identification of K. pneumoniae and bla(CTX-M) genes by PCR. Subsequently, the genetic relationship of these isolates was analyzed by REP-PCR. Results: A 38% of the 24 isolates identified by PCR as K. pneumoniae showed bla(CTX-M-3). bla(CTX-M-15) y bla(CTX-M-32) genes (Group CTX-M-1) and 42% bla(CTX-M14). bla(CTX-M-24) y bla(CTX-M-27) genes (Group CTX-M-9). The phylogenetic analysis grouped the K. pneumoniae isolates into 4 clusters, showing correlation in clusters I, II and IV, when comparing the genetic profiles with the type of sample and group of genes. Discussion: We found a similar frequency of bla(CTX-M)-Group 1 and bla(CTX-M)-Group 9 genes in isolates of K. pneumoniae resistant to ceftazidime. The correlation between the REP-PCR with the CTX-M groups and the type of sample revealed the presence of three clonal patterns.

While automatic text summarization has been widely studied for more than fifty years, in software engineering, automatic summarization is an emerging area that shows great potential and poses new and exciting research challenges. This technical briefing provides an introduction to the state of the art and maps future research directions in automatic software summarization. A first version was presented at ICSE' 17 and now it is updated and enhanced, based on feedback from the audience.

Apache POI pre-processed data for the first DocGen challenge The pre-processed data for First Software Documentation Generation Challenge (DocGen), hosted at the Third International Workshop on Dynamic Software Documentation (DySDoc 3), includes the following datasets for Apache POI 3.17: Call graph between method and classes. File: call-graph-poi-3.17-all.zip CSV file with the call graph between methods and between classes. Class A calls class B if there exists a call between amethod of class A and a method of class B. The call graph was produced by the tool java-callgraph. The CSV file contains the following columns: call_type: call between (C)lasses or (M)ethods caller: the Fully Qualified Name (FQN) of the caller method_call_type: the type of method call: M for invokevirtual calls I for invokeinterface calls O for invokespecial calls S for invokestatic calls D for invokedynamic calls callee: the FQN of the callee For more details about the format and each type of method call, check the tool README. Inheritance hierarchy File: poi-3.17-inheritance.zip A CSV file with the inheritance hierarchy of POI, which was extracted using bcel 6.2 The CSV file contains the following columns: record_id: sequential number parent_class: the parent class child_class: the child class relationship_type: the type of relationship between classes, i.e., the child class 'extends' or 'implements' the parent class Issues File: bugzilla-poi-dump.zip CSV file with the list of issues of Apache POI (timestamp: Tue Feb 27, 2018, 18.41.40 UTC) The CSV file contains the following columns: record_id: sequential number issue_id: the ID that identifies the issue in the issue tracker issue_url: the URL of the issue in the issue tracker issue_title: the title of the issue xml_path: the path to the XML of the issue, which contains all the issue information provided by the issue tracker All the issues in XML format can be found in the "poi" folder in the ZIP file Commits File: poi-commits.zip A JSON file with commit information for POI 3.17 (until revision 219dff00e6, on Sept. 8, 2017). The information was extracted using the tools Historage and Kataribe. For each commit, we provide: Commit hash Parent commit hash (if exists) Commit message Commit time Committer name Method-level changes (addition/deletion/modification/renaming and method FQN). The FQN contains information about the class (CN) and method (MT) or constructor (CS) StackOverflow posts File: apache-poi-SO.zip JSON file with all 6,299 Stack Overflow threads with the apache-poi tag,

Milax gagates constituye una de las principales plagas en el cultivo de lechuga causando considerables perdidas economicas. El control con molusquicidas elimina total o parcialmente la plaga, pero genera un impacto negativo en el ambiente por su alta toxicidad. El manejo biologico tambien permite el control de la plaga, pero de manera especifica e inocua para el ambiente. Por ello, el objetivo de este trabajo fue evaluar el efecto toxico de Bacillus thuringiensis, con genes Cry1, contra M. gagates mediante la elaboracion de un bioensayo. Se tomaron 75 muestras de suelo de varios municipios de Norte de Santander, Colombia, de donde se obtuvieron 58 colonias aisladas de B. thuringiensis con caracteristicas similares. De estas colonias, cinco evidenciaron la presencia de genes Cry1, y fueron las empleadas en los bioensayos junto con el control B. thuringiensis var. Kurstaki. Los tratamientos presentaron letalidad ante M. gagates de entre 90 y 100 % a una concentracion de 500 μg∙mL-1. La CL99 calculada sugiere el uso de 820 μg∙mL-1 del biopreparado para obtener 100 % de letalidad con cualquiera de los cinco aislados estudiados

Release notes document corrections, enhancements, and, in general, changes that were implemented in a new release of a software project. They are usually created manually and may include hundreds of different items, such as descriptions of new features, bug fixes, structural changes, new or deprecated APIs, and changes to software licenses. Thus, producing them can be a time-consuming and daunting task. This paper describes ARENA (Automatic RElease Notes generAtor), an approach for the automatic generation of release notes. ARENA extracts changes from the source code, summarizes them, and integrates them with information from versioning systems and issue trackers. ARENA was designed based on the manual analysis of 990 existing release notes. In order to evaluate the quality of the release notes automatically generated by ARENA, we performed four empirical studies involving a total of 56 participants (48 professional developers and eight students). The obtained results indicate that the generated release notes are very good approximations of the ones manually produced by developers and often include important information that is missing in the manually created release notes.

Automatic text summarization has been widely studied for more than fifty years. In software engineering, automatic summarization is an emerging area that shows great potential and poses new and exciting research challenges. This technical briefing provides an introduction to the state of the art and maps future research directions in automatic software summarization.

We advocate for a paradigm shift in supporting the information needs of developers, centered around the concept of automated on-demand developer documentation. Currently, developer information needs are fulfilled by asking experts or consulting documentation. Unfortunately, traditional documentation practices are inefficient because of, among others, the manual nature of its creation and the gap between the creators and consumers. We discuss the major challenges we face in realizing such a paradigm shift, highlight existing research that can be leveraged to this end, and promote opportunities for increased convergence in research on software documentation.

Bug reports document unexpected software behaviors experienced by users. To be effective, they should allow bug triagers to easily understand and reproduce the potential reported bugs, by clearly describing the Observed Behavior (OB), the Steps to Reproduce (S2R), and the Expected Behavior (EB). Unfortunately, while considered extremely useful, reporters often miss such pieces of information in bug reports and, to date, there is no effective way to automatically check and enforce their presence. We manually analyzed nearly 3k bug reports to understand to what extent OB, EB, and S2R are reported in bug reports and what discourse patterns reporters use to describe such information. We found that (i) while most reports contain OB (i.e., 93.5%), only 35.2% and 51.4% explicitly describe EB and S2R, respectively; and (ii) reporters recurrently use 154 discourse patterns to describe such content. Based on these findings, we designed and evaluated an automated approach to detect the absence (or presence) of EB and S2R in bug descriptions. With its best setting, our approach is able to detect missing EB (S2R) with 85.9% (69.2%) average precision and 93.2% (83%) average recall. Our approach intends to improve bug descriptions quality by alerting reporters about missing EB and S2R at reporting time.

Esta investigación tuvo como objetivo cuantificar bacterias diazótrofas y comparar fisicoquímicamente suelos rizosféricos de tres cacaotales (Theobroma cacao L.) del Departamento Norte de Santander, Colombia; para lo cual se caracterizaron, diferenciándose en área cultivada, manejo agronómico y edad del cultivo. A partir de diluciones seriadas de las muestras y empleando la técnica de Número Más Probable (NMP), en medios de cultivo semiselectivos (NFb, JMV, LGI, JNFb) semisólidos, se cuantificaron las diazótrofas, evaluando como positivo la formación de una película subsuperficial en el medio contenido en viales sellados; muestras pares se enviaron al laboratorio Bioambiental (UNET) para los análisis fisicoquímicos. Como resultado, las muestras evaluadas mostraron deficiencias en el porcentaje de materia orgánica y elementos como Potasio, Fósforo y Magnesio. Se reportaron estadísticamente diferencias altamente significativas en NMP. La mayor cuantificación de diazótrofas se reportó en la finca Florilandia, que se caracterizó por tener riego por goteo. La mayor cuantificación de diazotrófas se registró en los medios NFb y JMV, demostrándose una mayor presencia de los presuntos géneros Azospirillum sp. y Burkholderia sp. los cuales son fácilmente aislados de suelos rizosféricos, a diferencia de los géneros Herbaspirillum sp. y Gluconacetobacter sp. que por su carácter endófito suelen ser menos predominantes en este tipo de muestras. Se concluye además, que las características fisicoquímicas del suelo, la humedad y las relaciones climáticas al momento de la toma de las muestras, condicionan la cantidad de exudados de las raíces y por tanto son factores que condicionaron la presencia de diazótrofas en las muestras.Palabras clave: Azospirillum, Burkholderia, cacao, rizósfera

The objective of this research was to quantify diazotrophic bacteria and compare physicochemically rhizospheric soils of three cocoa plantations (Theobroma cacao L.) in Norte de Santander Department, Colombia; for which they were characterized, differing in cultivated area, agronomic management and crop age. From serial dilutions of the samples and using the technique of Most Probable Number (MPN), In semisolid culture media (NFb, JMV, LGI, JNFb), the diazotrophs were quantified, evaluating as positive the formation of a subsurface film in the medium contained in sealed vials; equal samples were sent to the Bioambiental laboratory (UNET) for physicochemical analyzes. As a result, the evaluated samples showed deficiencies in the percentage of organic matter and elements such as Potassium, Phosphorus and Magnesium. Statistically highly significant differences in MPN were reported. The highest quantification of diazotrophs was reported in the Florilandia farm, which was characterized by drip irrigation. The highest quantification of diazotrophs was recorded in the media NFb and JMV, demonstrating a greater presence of the presumed genera Azospirillum sp. and Burkholderia sp. which are easily isolated from rhizospheric soils, unlike the genera Herbaspirillum sp. and Gluconacetobacter sp. which by their endophytic character tend to be less predominant in this type of samples. It is also concluded that the physicochemical characteristics of the soil, humidity and climatic relationships at the moment of sampling, condition the amount of root exudates and therefore are factors that conditioned the presence of diazotrophs in the samples.