Ground truth deficiencies in software engineering:when codifying the past can be counterproductive

Abstract Many software engineering tools build and evaluate their models based on historical data to support development and process decisions. These models help us answer numerous interesting questions, but have their own caveats. In a real-life setting, the objective function of human decision-makers for a given task might be influenced by a whole host of factors that stem from their cognitive biases, subverting the ideal objective function required for an optimally functioning system. Relying on this data as ground truth may give rise to systems that end up automating software engineering decisions by mimicking past sub-optimal behaviour. We illustrate this phenomenon and suggest mitigation strategies to raise awareness

Technical debt diffuseness in the Apache ecosystem:a differentiated replication

Abstract Technical debt management is a critical activity that is gaining the attention of both practitioners and researchers. Several tools providing automatic support for technical debt management have been introduced over the last years. SonarQube is one of the most widely applied tools to automatically measure technical debt in software systems. SonarQube has been adopted to quantify the diffuseness of technical debt in projects of the Apache Software Foundation ecosystem. Lenarduzzi et al. [1] found that the vast majority of technical debt issues in the code are code smells and that, surprisingly, developers tend to take more time to remove severe issues than the less-severe ones. While this study provides very interesting insights both for researchers and practitioners interested in technical debt management, we identified some major limitations that could have led to results that do not perfectly reflect reality. This study aims to address such limitations by presenting a differentiated replication study. Our findings have pointed out significant differences with the reference work. The results show that technical debt issues appear much more rarely than what the reference work reported. In this study, we implemented a new methodology to calculate the diffuseness of SonarQube issues at project and commit level, based on the reconstruction of the SonarQube quality profile in order to understand how the quality profile has evolved and to compare the number of active rules per category and severity level with the respective number of issues found. The results show that over 50% of rules active in the quality profile, are Code Smell rules and that over 90% of the issues belong to Code Smell category. Furthermore, analyzing the life span of the issues, we found that developers take into account the level of severity of the issues only for the Bug category, thus fixing the issues starting from the most severe, which is not the case for the other categories

On researcher bias in Software Engineering experiments

Abstract Researcher bias occurs when researchers influence the results of an empirical study based on their expectations, either consciously or unconsciously. Researcher bias might be due to the use of Questionable Research Practices (QRPs). In research fields like medicine, blinding techniques have been applied to counteract researcher bias. In this paper, we present two studies to increase our body of knowledge on researcher bias in Software Engineering (SE) experiments, including: (i) QRPs potentially leading to researcher bias; (ii) causes behind researcher bias; and (iii) possible actions to counteract researcher bias with a focus on, but not limited to, blinding techniques. The former is an interview study, intended as an exploratory study, with nine experts of the empirical SE community. The latter is a quantitative survey with 51 respondents, who were experts of the above-mentioned community. The findings from the exploratory study represented the starting point to design the survey. In particular, we defined the questionnaire of this survey to support the findings from the exploratory study. From the interview study, it emerged that some QRPs (e.g., post-hoc outlier criteria) are acceptable in certain cases. Also, it appears that researcher bias is perceived in SE and, to counteract researcher bias, a number of solutions have been highlighted. For example, duplicating the data analysis in SE experiments or fostering open data policies in SE conferences/journals. The findings from the interview study are mostly confirmed by those from the survey, and allowed us to delineate recommendations to counteract researcher bias in SE experiments. Some recommendations are intended for SE researchers, while others are purposeful for the boards of SE research venues

Studying test-driven development and its retainment over a six-month time span

Abstract In this paper, we investigate the effect of TDD, as compared to a non-TDD approach, as well as its retainment (or retention) over a time span of (about) six months. To pursue these objectives, we conducted a (quantitative) longitudinal cohort study with 30 novice developers (i.e., third-year undergraduate students in Computer Science). We observed that TDD affects neither the external quality of software products nor developers’ productivity. However, we observed that the participants applying TDD produced significantly more tests, with a higher fault-detection capability, than those using a non-TDD approach. As for the retainment of TDD, we found that TDD is retained by novice developers for at least six months

Resolving security issues via quality-oriented refactoring:a user study

Abstract Software quality is crucial in software development: if not addressed in early phases of the software development life cycle, it may even lead to technical bankruptcy, i.e., a situation in which modifications cost more than redeveloping the application from scratch. In addition, code security must also be addressed to reduce software vulnerabilities and to comply with legal requirements. In this work, we aim to investigate the relationship between refactoring code quality and software security, with the purpose of understanding whether and to what extent improving software quality could have a positive impact on software security as well. Specifically, we investigate to what extent rule violations of a software quality tool such as SonarQube overlap with rule violations of a software vulnerability tool like Fortify Static Code Analyzer. We first compared the rules encoded in the quality models of both tools, to discover possible overlapping cases. Later, we compared the issues raised by both tools on a set of open source Java projects; we also investigated the cases in which a quality refactoring process impacts over software security (thus removing one or more vulnerabilities). We furthermore validated our results statistically. Our results show that resolving software quality issues might also resolve security issues but only in part: many security issues still persist in the source code; also, some quality aspects are more likely to be improved in respect to others. In addition, this empirical study uncovers rule co-occurrences between the two tools. This study confirms the need for using a security-oriented static analysis tool to enforce software security instead of relying only on a quality-oriented one. Results have highlighted important insights for practitioners

The Influence of Age and Sex on Genetic Associations with Adult Body Size and Shape: A Large-Scale Genome-Wide Interaction Study.

Genome-wide association studies (GWAS) have identified more than 100 genetic variants contributing to BMI, a measure of body size, or waist-to-hip ratio (adjusted for BMI, WHRadjBMI), a measure of body shape. Body size and shape change as people grow older and these changes differ substantially between men and women. To systematically screen for age- and/or sex-specific effects of genetic variants on BMI and WHRadjBMI, we performed meta-analyses of 114 studies (up to 320,485 individuals of European descent) with genome-wide chip and/or Metabochip data by the Genetic Investigation of Anthropometric Traits (GIANT) Consortium. Each study tested the association of up to ~2.8M SNPs with BMI and WHRadjBMI in four strata (men ≤50y, men >50y, women ≤50y, women >50y) and summary statistics were combined in stratum-specific meta-analyses. We then screened for variants that showed age-specific effects (G x AGE), sex-specific effects (G x SEX) or age-specific effects that differed between men and women (G x AGE x SEX). For BMI, we identified 15 loci (11 previously established for main effects, four novel) that showed significant (FDR<5%) age-specific effects, of which 11 had larger effects in younger (<50y) than in older adults (≥50y). No sex-dependent effects were identified for BMI. For WHRadjBMI, we identified 44 loci (27 previously established for main effects, 17 novel) with sex-specific effects, of which 28 showed larger effects in women than in men, five showed larger effects in men than in women, and 11 showed opposite effects between sexes. No age-dependent effects were identified for WHRadjBMI. This is the first genome-wide interaction meta-analysis to report convincing evidence of age-dependent genetic effects on BMI. In addition, we confirm the sex-specificity of genetic effects on WHRadjBMI. These results may provide further insights into the biology that underlies weight change with age or the sexually dimorphism of body shape

Appropriateness of antiplatelet therapy for primary and secondary cardio- and cerebrovascular prevention in acutely hospitalized older people

Aims: Antiplatelet therapy is recommended for the secondary prevention of cardio- and cerebrovascular disease, but for primary prevention it is advised only in patients at very high risk. With this background, this study aims to assess the appropriateness of antiplatelet therapy in acutely hospitalized older people according to their risk profile. Methods: Data were obtained from the REPOSI register held in Italian and Spanish internal medicine and geriatric wards in 2012 and 2014. Hospitalized patients aged 6565 assessable at discharge were selected. Appropriateness of the antiplatelet therapy was evaluated according to their primary or secondary cardiovascular prevention profiles. Results: Of 2535 enrolled patients, 2199 were assessable at discharge. Overall 959 (43.6%, 95% CI 41.5\u201345.7) were prescribed an antiplatelet drug, aspirin being the most frequently chosen. Among patients prescribed for primary prevention, just over half were inappropriately prescribed (52.1%), being mainly overprescribed (155/209 patients, 74.2%). On the other hand, there was also a high rate of inappropriate underprescription in the context of secondary prevention (222/726 patients, 30.6%, 95% CI 27.3\u201334.0%). Conclusions: This study carried out in acutely hospitalized older people shows a high degree of inappropriate prescription among patients prescribed with antiplatelets for primary prevention, mainly due to overprescription. Further, a large proportion of patients who had had overt cardio- or cerebrovascular disease were underprescribed, in spite of the established benefits of antiplatelet drugs in the context of secondary prevention

Correction: The Influence of Age and Sex on Genetic Associations with Adult Body Size and Shape: A Large-Scale Genome-Wide Interaction Study

[This corrects the article DOI: 10.1371/journal.pgen.1005378.].status: publishe

Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility

To access publisher's full text version of this article click on the hyperlink at the bottom of the pageTo further understanding of the genetic basis of type 2 diabetes (T2D) susceptibility, we aggregated published meta-analyses of genome-wide association studies (GWAS), including 26,488 cases and 83,964 controls of European, east Asian, south Asian and Mexican and Mexican American ancestry. We observed a significant excess in the directional consistency of T2D risk alleles across ancestry groups, even at SNPs demonstrating only weak evidence of association. By following up the strongest signals of association from the trans-ethnic meta-analysis in an additional 21,491 cases and 55,647 controls of European ancestry, we identified seven new T2D susceptibility loci. Furthermore, we observed considerable improvements in the fine-mapping resolution of common variant association signals at several T2D susceptibility loci. These observations highlight the benefits of trans-ethnic GWAS for the discovery and characterization of complex trait loci and emphasize an exciting opportunity to extend insight into the genetic architecture and pathogenesis of human diseases across populations of diverse ancestry.Canadian Institutes of Health Research Medical Research Council UK G0601261 Mexico Convocatoria SSA/IMMS/ISSSTE-CONACYT 2012-2 clave 150352 IMSS R-2011-785-018 CONACYT Salud-2007-C01-71068 US National Institutes of Health DK062370 HG000376 DK085584 DK085545 DK073541 DK085501 Wellcome Trust WT098017 WT090532 WT090367 WT098381 WT081682 WT085475info:eu-repo/grantAgreement/EC/FP7/20141