Architecture Information Communication in Two OSS Projects: the Why, Who, When, and What

Architecture information is vital for Open Source Software (OSS) development, and mailing list is one of the widely used channels for developers to share and communicate architecture information. This work investigates the nature of architecture information communication (i.e., why, who, when, and what) by OSS developers via developer mailing lists. We employed a multiple case study approach to extract and analyze the architecture information communication from the developer mailing lists of two OSS projects, ArgoUML and Hibernate, during their development life-cycle of over 18 years. Our main findings are: (a) architecture negotiation and interpretation are the two main reasons (i.e., why) of architecture communication; (b) the amount of architecture information communicated in developer mailing lists decreases after the first stable release (i.e., when); (c) architecture communications centered around a few core developers (i.e., who); (d) and the most frequently communicated architecture elements (i.e., what) are Architecture Rationale and Architecture Model. There are a few similarities of architecture communication between the two OSS projects. Such similarities point to how OSS developers naturally gravitate towards the four aspects of architecture communication in OSS development.Comment: Preprint accepted for publication in Journal of Systems and Software, 202

A Survey of Architecture Design Rationale

Many claims have been made about the problems caused by not documenting design rationale. The general perception is that designers and architects usually do not fully understand the critical role of systematic use and capture of design rationale. However, there is to date little empirical evidence available on what design rationale mean to practitioners, how valuable they consider them, and how they use and document design rationale during the design process. This paper reports an empirical study that surveyed practitioners to probe their perception of the value of design rationale and how they use and document background knowledge related to their design decisions. Based on eighty-one valid responses, this study has discovered that practitioners recognize the importance of documenting design rationale and frequently use them to reason about their design choices. However, they have indicated barriers to the use and documentation of design rationale. Based on the findings, we conclude that much research is needed to develop methodology and tool support for design rationale capture and usage. Furthermore, we put forward some research questions that would benefit from further investigation into design rationale in order to support practice in industry

Evidence Favoring a Positive Feedback Loop for Physiologic Auto Upregulation of hnRNP-E1 during Prolonged Folate Deficiency in Human Placental Cells

Background: Previously, we determined that heterogeneous nuclear ribonucleoprotein E1 (hnRNP-E1) functions as an intracellular physiologic sensor of folate deficiency. In this model, l-homocysteine, which accumulates intracellularly in proportion to the extent of folate deficiency, covalently binds to and thereby activates homocysteinylated hnRNP-E1 to interact with folate receptor-α mRNA; this high-affinity interaction triggers the translational upregulation of cell surface folate receptors, which enables cells to optimize folate uptake from the external milieu. However, integral to this model is the need for ongoing generation of hnRNP-E1 to replenish homocysteinylated hnRNP-E1 that is degraded.Objective: We searched for an interrelated physiologic mechanism that could also maintain the steady-state concentration of hnRNP-E1 during prolonged folate deficiency.Methods: A novel RNA-protein interaction was functionally characterized by using molecular and biochemical approaches in vitro and in vivo.Results: l-homocysteine triggered a dose-dependent high-affinity interaction between hnRNP-E1 and a 25-nucleotide cis element within the 5'-untranslated region of hnRNP-E1 mRNA; this led to a proportionate increase in these RNA-protein complexes, and translation of hnRNP-E1 both in vitro and within placental cells. Targeted perturbation of this RNA-protein interaction either by specific 25-nucleotide antisense oligonucleotides or mutation within this cis element or by small interfering RNA to hnRNP-E1 mRNA significantly reduced cellular biosynthesis of hnRNP-E1. Conversely, transfection of hnRNP-E1 mutant proteins that mimicked homocysteinylated hnRNP-E1 stimulated both cellular hnRNP-E1 and folate receptor biosynthesis. In addition, ferrous sulfate heptahydrate [iron(II)], which also binds hnRNP-E1, significantly perturbed this l-homocysteine-triggered RNA-protein interaction in a dose-dependent manner. Finally, folate deficiency induced dual upregulation of hnRNP-E1 and folate receptors in cultured human cells and tumor xenografts, and more selectively in various fetal tissues of folate-deficient dams.Conclusions: This novel positive feedback loop amplifies hnRNP-E1 during prolonged folate deficiency and thereby maximizes upregulation of folate receptors in order to restore folate homeostasis toward normalcy in placental cells. It will also functionally impact several other mRNAs of the nutrition-sensitive, folate-responsive posttranscriptional RNA operon that is orchestrated by homocysteinylated hnRNP-E1

Chapter 4 Traceability in the Co-evolution of Architectural Requirements and Design

Abstract Requirements and architectural design specifications can be conflicting and inconsistent, especially during the design period when requirements and architectural design are co-evolving. One reason is that stakeholders do not have up-to-date knowledge of each other’s work to fully understand potential conflicts and inconsistencies. Specifications are often documented in a natural language, which also makes it difficult for tracing related information automatically. In this chapter, we introduce a general-purpose ontology that we have developed to address this problem. We demonstrate an implementation of semantic wiki that supports traceability of co-evolving requirements specifications and architecture design. Let us begin by considering a typical software architecting scenario: A team of business analysts and users work on a new software system in an organization. The business analysts and users document the business goals, use-case scenarios, system and data requirements in a requirements document. The team of software and system architects studie

DARE to be different? Applying diversity heuristics to the analysis of collaborative research

Growth in collaborative research raises challenges for those tasked with research evaluation, particularly in situations where outcomes are slow to emerge. This article presents the ‘Diversity Approach to Research Evaluation’ (DARE) as a novel way to assess how researchers, engaged in knowledge creation and application, work together as teams. DARE provides two important insights: Firstly it reveals the differences in background and experience between individual team members that can make research collaboration both valuable and challenging; secondly, DARE provides early insights into how these teams are working together. DARE achieves these insights by analysing team diversity and cohesiveness in five dimensions, building on Boschma’s multidimensional concept of proximity. The method we propose combines narratives, maps, and indicators and is broadly applicable to the study of research collaboration. The article introduces the DARE method and pilots a proof-of-concept operationalisation through the study of two grant-funded biomedical research projects led by researchers in the UK. Suggestions for further development of the approach are discussed

DARE to be different? A novel approach for analysing diversity in collaborative research projects

Growth in collaborative research raises difficulties for those tasked with research evaluation, particularly in situations where outcomes are slow to emerge. This article presents the ‘Diversity Approach to Research Evaluation’ (DARE) as a novel way to assess how researchers engaged in knowledge creation and application work together as teams. DARE provides two important insights: first, it reveals the differences in background and experience between individual team members that can make research collaboration both valuable and challenging; second, DARE provides early insights into how team members are working together. DARE achieves these insights by analysing team diversity and cohesiveness in five dimensions, building on Boschma’s multi-dimensional concept of proximity. The method we propose combines narratives, maps, and indicators to facilitate the study of research collaboration. The article introduces the DARE method and pilots an initial operationalization through the study of two grant-funded biomedical research projects led by researchers in the UK. Suggestions for further development of the approach are discussed

Feasibility of shear wave sonoelastography to detect endoleak and evaluate thrombus organization after endovascular repair of abdominal aortic aneurysm

Purpose To investigate the feasibility of shear wave sonoelastography (SWS) for endoleak detection and thrombus characterization of abdominal aortic aneurysm (AAA) after endovascular repair (EVAR). Materials and methods Participants who underwent EVAR were prospectively recruited between November 2014 and March 2016 and followed until March 2019. Elasticity maps of AAA were computed using SWS and compared to computed tomography angiography (CTA) and color Doppler ultrasound (CDUS). Two readers, blinded to the CTA and CDUS results, reviewed elasticity maps and B-mode images to detect endoleaks. Three or more CTAs per participant were analyzed: pre-EVAR, baseline post-EVAR, and follow-ups. The primary endpoint was endoleak detection. Secondary endpoints included correlation between total thrombus elasticity, proportion of fresh thrombus, and aneurysm growth between baseline and reference CTAs. A 3-year follow-up was made to detect missed endoleaks, EVAR complication, and mortality. Data analyses included Cohen’s kappa; sensitivity, specificity, and positive predictive value (PPV); Pearson coefficient; and Student’s t tests. Results Seven endoleaks in 28 participants were detected by the two SWS readers (k = 0.858). Sensitivity of endoleak detection with SWS was 100%; specificity and PPV averaged 67% and 50%, respectively. CDUS sensitivity was estimated at 43%. Aneurysm growth was significantly greater in the endoleak group compared to sealed AAAs. No correlation between growth and thrombus elasticity or proportion of fresh thrombus in AAAs was found. No new endoleaks were observed in participants with SWS negative studies. Conclusion SWS has the potential to detect endoleaks in AAA after EVAR with comparable sensitivity to CTA and superior sensitivity to CDUS

Diamond Dicing

In OLAP, analysts often select an interesting sample of the data. For example, an analyst might focus on products bringing revenues of at least 100 000 dollars, or on shops having sales greater than 400 000 dollars. However, current systems do not allow the application of both of these thresholds simultaneously, selecting products and shops satisfying both thresholds. For such purposes, we introduce the diamond cube operator, filling a gap among existing data warehouse operations. Because of the interaction between dimensions the computation of diamond cubes is challenging. We compare and test various algorithms on large data sets of more than 100 million facts. We find that while it is possible to implement diamonds in SQL, it is inefficient. Indeed, our custom implementation can be a hundred times faster than popular database engines (including a row-store and a column-store).Comment: 29 page

Investigating Class-level Difficulty Factors in Multi-label Classification Problems

This work investigates the use of class-level difficulty factors in multi-label classification problems for the first time. Four class-level difficulty factors are proposed: frequency, visual variation, semantic abstraction, and class co-occurrence. Once computed for a given multi-label classification dataset, these difficulty factors are shown to have several potential applications including the prediction of class-level performance across datasets and the improvement of predictive performance through difficulty weighted optimisation. Significant improvements to mAP and AUC performance are observed for two challenging multi-label datasets (WWW Crowd and Visual Genome) with the inclusion of difficulty weighted optimisation. The proposed technique does not require any additional computational complexity during training or inference and can be extended over time with inclusion of other class-level difficulty factors.Comment: Published in ICME 202

Nickel hyperaccumulation mechanisms: a review on the current state of knowledge

Background: Hyperaccumulator plants are unusual plants that accumulate particular metals or metalloids, such as nickel, zinc, cadmium and arsenic, in their living tissues to concentrations that are hundreds to thousands of times greater than what is normal for most plants. The hyperaccumulation phenomenon is rare (exhibited by less than 0.2% of all angiosperms), with most of the ~500 hyperaccumulator species known globally for nickel. Scope: This review highlights the contemporary understanding of nickel hyperaccumulation processes, which include root uptake and sequestration, xylem loading and transport, leaf compartmentation and phloem translocation processes. Conclusions: Hyperaccumulator plants have evolved highly efficient physiological mechanisms for taking up nickel in their roots followed by rapid translocation and sequestration into the aerial shoots. The uptake of nickel is mainly involved with low affinity transport systems, presumably from the ZIP family. The presence of high concentrations of histidine prevents nickel sequestration in roots. Nickel is efficiently loaded into the xylem, where it mainly presents as Ni. The leaf is the main storage organ, which sequestrates nickel in non-active sites, e.g. vacuoles and apoplast. Recent studies show that phloem translocates high levels of nickel, which has a strong impact on nickel accumulation in young growing tissues