Variation Factors in the Design and Analysis of Replicated Controlled Experiments - Three (Dis)similar Studies on Inspections versus Unit Testing

Background. In formal experiments on software engineering, the number of factors that may impact an outcome is very high. Some factors are controlled and change by design, while others are are either unforeseen or due to chance. Aims. This paper aims to explore how context factors change in a series of for- mal experiments and to identify implications for experimentation and replication practices to enable learning from experimentation. Method. We analyze three experiments on code inspections and structural unit testing. The first two experiments use the same experimental design and instrumentation (replication), while the third, conducted by different researchers, replaces the programs and adapts defect detection methods accordingly (reproduction). Experimental procedures and location also differ between the experiments. Results. Contrary to expectations, there are significant differences between the original experiment and the replication, as well as compared to the reproduction. Some of the differences are due to factors other than the ones designed to vary between experiments, indicating the sensitivity to context factors in software engineering experimentation. Conclusions. In aggregate, the analysis indicates that reducing the complexity of software engineering experiments should be considered by researchers who want to obtain reliable and repeatable empirical measures

The Taf14 YEATS domain is a reader of histone crotonylation

The discovery of new histone modifications is unfolding at startling rates, however, the identification of effectors capable of interpreting these modifications has lagged behind. Here we report the YEATS domain as an effective reader of histone lysine crotonylation – an epigenetic signature associated with active transcription. We show that the Taf14 YEATS domain engages crotonyllysine via a unique π-π-π-stacking mechanism and that other YEATS domains have crotonyllysine binding activity

Associations of common breast cancer susceptibility alleles with risk of breast cancer subtypes in BRCA1 and BRCA2 mutation carriers

Introduction: More than 70 common alleles are known to be involved in breast cancer (BC) susceptibility, and several exhibit significant heterogeneity in their associations with different BC subtypes. Although there are differences in the association patterns between BRCA1 and BRCA2 mutation carriers and the general population for several loci, no study has comprehensively evaluated the associations of all known BC susceptibility alleles with risk of BC subtypes in BRCA1 and BRCA2 carriers. Methods: We used data from 15,252 BRCA1 and 8,211 BRCA2 carriers to analyze the associations between approximately 200,000 genetic variants on the iCOGS array and risk of BC subtypes defined by estrogen receptor (ER), progesterone receptor (PR), human epidermal growth factor receptor 2 (HER2) and triple-negative- (TN) status; morphologic subtypes; histological grade; and nodal involvement. Results: The estimated BC hazard ratios (HRs) for the 74 known BC alleles in BRCA1 carriers exhibited moderate correlations with the corresponding odds ratios from the general population. However, their associations with ER-positive BC in BRCA1 carriers were more consistent with the ER-positive as

Associations of common breast cancer susceptibility alleles with risk of breast cancer subtypes in BRCA1 and BRCA2 mutation carriers

Abstract Introduction More than 70 common alleles are known to be involved in breast cancer (BC) susceptibility, and several exhibit significant heterogeneity in their associations with different BC subtypes. Although there are differences in the association patterns between BRCA1 and BRCA2 mutation carriers and the general population for several loci, no study has comprehensively evaluated the associations of all known BC susceptibility alleles with risk of BC subtypes in BRCA1 and BRCA2 carriers. Methods We used data from 15,252 BRCA1 and 8,211 BRCA2 carriers to analyze the associations between approximately 200,000 genetic variants on the iCOGS array and risk of BC subtypes defined by estrogen receptor (ER), progesterone receptor (PR), human epidermal growth factor receptor 2 (HER2) and triple-negative- (TN) status; morphologic subtypes; histological grade; and nodal involvement. Results The estimated BC hazard ratios (HRs) for the 74 known BC alleles in BRCA1 carriers exhibited moderate correlations with the corresponding odds ratios from the general population. However, their associations with ER-positive BC in BRCA1 carriers were more consistent with the ER-positive associations in the general population (intraclass correlation (ICC) = 0.61, 95% confidence interval (CI): 0.45 to 0.74), and the same was true when considering ER-negative associations in both groups (ICC = 0.59, 95% CI: 0.42 to 0.72). Similarly, there was strong correlation between the ER-positive associations for BRCA1 and BRCA2 carriers (ICC = 0.67, 95% CI: 0.52 to 0.78), whereas ER-positive associations in any one of the groups were generally inconsistent with ER-negative associations in any of the others. After stratifying by ER status in mutation carriers, additional significant associations were observed. Several previously unreported variants exhibited associations at P <10−6 in the analyses by PR status, HER2 status, TN phenotype, morphologic subtypes, histological grade and nodal involvement. Conclusions Differences in associations of common BC susceptibility alleles between BRCA1 and BRCA2 carriers and the general population are explained to a large extent by differences in the prevalence of ER-positive and ER-negative tumors. Estimates of the risks associated with these variants based on population-based studies are likely to be applicable to mutation carriers after taking ER status into account, which has implications for risk prediction

A Rule-Based Software Testing Method for VHDL Models

The verification of behavioral models is an important step before transferring a hardware design to the layout. A popular approach is to use a variety of code coverage measures to evaluate how much of the design has been simulated. Common coverage measures include branch coverage and bit toggle coverage. This paper presents a test pattern generation approach based on controlflow and dataflow analysis. Heuristic rules use the results of the static analysis to generate new patterns. We applied this technique to a sizable VHDL design and compared resulting coverage to other methods. The results showed that this new method achieved higher branch coverage. 1

Requirements Prioritization

This chapter provides an overview of techniques for prioritization of requirements for software products. Prioritization is a crucial step towards making good decisions regarding product planning for single and multiple releases. Various aspects of functionality are considered, such as importance, risk, cost, etc. Prioritization decisions are made by stakeholders, including users, managers, developers, or their representatives. Methods are given how to combine individual prioritizations based on overall objectives and constraints. A range of different techniques and aspects are applied to an example to illustrate their use. Finally, limitations and shortcomings of current methods are pointed out, and open research questions in the area of requirements prioritization are discussed

Requirements Prioritization

This chapter provides an overview of techniques for prioritization of requirements for software products. Prioritization is a crucial step towards making good decisions regarding product planning for single and multiple releases. Various aspects of functionality are considered, such as importance, risk, cost, etc. Prioritization decisions are made by stakeholders, including users, managers, developers, or their representatives. Methods are given how to combine individual prioritizations based on overall objectives and constraints. A range of different techniques and aspects are applied to an example to illustrate their use. Finally, limitations and shortcomings of current methods are pointed out, and open research questions in the area of requirements prioritization are discussed

Active World Model for Testing Autonomous Systems Using CEFSM

Abstract-This paper describes a model-based test generation approach for testing autonomous systems interacting with their environment (i.e., world). Unlike other approaches that assume a static world with attributes and values, we present and test a dynamic world. We use Communicating Extended Finite State Machine (CEFSM) to illustrate an active world model that describes behaviors of environmental factors (i.e., actors). Abstract World Behavioral Test Cases (AWBTCs) are then generated by covering the active world model using graph coverage criteria. We also generate test-data by input-space partitioning to transform the generated AWBTCs into executable test cases. We apply the World Model-based Test Generation (WMBTG) technique to a case study from the Human-Robot Interaction domain (HRI) specifically a tour-guide robot. Reachability of the active world model and efficiency of coverage criteria are also discussed

Requirements Trade-offs During UML Design

Designs almost always require trade-offs between competing design choices to meet pervasive system dependability requirements (e.g., security, performance and fault tolerance system goals). In some cases, dependability requirements are realized by functionality that cross-cuts designs. Aspect-Oriented Modeling (AOM) methods allow developers to localize such cross-cutting functionality in design modeling views called aspects. Aspects can be composed with other design views to obtain an integrated view of a design. This paper presents a technique that extends such methods to cover dependability requirements that are not directly realized by functional structures in a design. Performance goals provide examples of such requirements. We also present a trade-off mechanism to rank feasible solutions with respect to requirements priorities between different dependability requirements. The paper applies this technique to an example that has performance, fault-tolerance, and security requirements