A Framework for Seamless Variant Management and Incremental Migration to a Software Product-Line

Context: Software systems often need to exist in many variants in order to satisfy varying customer requirements and operate under varying software and hardware environments. These variant-rich systems are most commonly realized using cloning, a convenient approach to create new variants by reusing existing ones. Cloning is readily available, however, the non-systematic reuse leads to difficult maintenance. An alternative strategy is adopting platform-oriented development approaches, such as Software Product-Line Engineering (SPLE). SPLE offers systematic reuse, and provides centralized control, and thus, easier maintenance. However, adopting SPLE is a risky and expensive endeavor, often relying on significant developer intervention. Researchers have attempted to devise strategies to synchronize variants (change propagation) and migrate from clone&own to an SPL, however, they are limited in accuracy and applicability. Additionally, the process models for SPLE in literature, as we will discuss, are obsolete, and only partially reflect how adoption is approached in industry. Despite many agile practices prescribing feature-oriented software development, features are still rarely documented and incorporated during actual development, making SPL-migration risky and error-prone.Objective: The overarching goal of this PhD is to bridge the gap between clone&own and software product-line engineering in a risk-free, smooth, and accurate manner. Consequently, in the first part of the PhD, we focus on the conceptualization, formalization, and implementation of a framework for migrating from a lean architecture to a platform-based one.Method: Our objectives are met by means of (i) understanding the literature relevant to variant-management and product-line migration and determining the research gaps (ii) surveying the dominant process models for SPLE and comparing them against the contemporary industrial practices, (iii) devising a framework for incremental SPL adoption, and (iv) investigating the benefit of using features beyond PL migration; facilitating model comprehension.Results: Four main results emerge from this thesis. First, we present a qualitative analysis of the state-of-the-art frameworks for change propagation and product-line migration. Second, we compare the contemporary industrial practices with the ones prescribed in the process models for SPL adoption, and provide an updated process model that unifies the two to accurately reflect the real practices and guide future practitioners. Third, we devise a framework for incremental migration of variants into a fully integrated platform by exploiting explicitly recorded metadata pertaining to clone and feature-to-asset traceability. Last, we investigate the impact of using different variability mechanisms on the comprehensibility of various model-related tasks.Future work: As ongoing and future work, we aim to integrate our framework with existing IDEs and conduct a developer study to determine the efficiency and effectiveness of using our framework. We also aim to incorporate safe-evolution in our operators

Effects of variability in models: a family of experiments

The ever-growing need for customization creates a need to maintain software systems in many different variants. To avoid having to maintain different copies of the same model, developers of modeling languages and tools have recently started to provide implementation techniques for such variant-rich systems, notably variability mechanisms, which support implementing the differences between model variants. Available mechanisms either follow the annotative or the compositional paradigm, each of which have dedicated benefits and drawbacks. Currently, language and tool designers select the used variability mechanism often solely based on intuition. A better empirical understanding of the comprehension of variability mechanisms would help them in improving support for effective modeling. In this article, we present an empirical assessment of annotative and compositional variability mechanisms for three popular types of models. We report and discuss findings from a family of three experiments with 164 participants in total, in which we studied the impact of different variability mechanisms during model comprehension tasks. We experimented with three model types commonly found in modeling languages: class diagrams, state machine diagrams, and activity diagrams. We find that, in two out of three experiments, annotative technique lead to better developer performance. Use of the compositional mechanism correlated with impaired performance. For all three considered tasks, the annotative mechanism was preferred over the compositional one in all experiments. We present actionable recommendations concerning support of flexible, tasks-specific solutions, and the transfer of established best practices from the code domain to models

Phylogenetic and drug-resistance analysis of HIV-1 sequences from an extensive paediatric HIV-1 outbreak in Larkana, Pakistan

Introduction: In April 2019, an HIV-1 outbreak among children occurred in Larkana, Pakistan, affecting more than a thousand children. It was assumed that the outbreak originated from a single source, namely a doctor at a private health facility. In this study, we performed subtype distribution, phylogenetic and drug-resistance analysis of HIV-1 sequences from 2019 outbreak in Larkana, Pakistan.Methods: A total of 401 blood samples were collected between April-June 2019, from children infected with HIV-1 aged 0-15 years recruited into a case-control study to investigate the risk factors for HIV-1 transmission. Partial HIV-1 pol sequences were generated from 344 blood plasma samples to determine HIV-1 subtype and drug resistance mutations (DRM). Maximum-likelihood phylogenetics based on outbreak and reference sequences was used to identify transmission clusters and assess the relationship between outbreak and key population sequences between and within the determined clusters. Bayesian analysis was employed to identify the time to the most recent common recent ancestor (tMRCA) of the main Pakistani clusters.Results: The HIV-1 circulating recombinant form (CRF) 02_AG and subtype A1 were most common among the outbreak sequences. Of the treatment-naïve participants, the two most common mutations were RT: E138A (8%) and RT: K219Q (8%). Four supported clusters within the outbreak were identified, and the median tMRCAs of the Larkana outbreak sequences were estimated to 2016 for both the CRF02_AG and the subtype A1 clusters. Furthermore, outbreak sequences exhibited no phylogenetic mixing with sequences from other high-risk groups of Pakistan.Conclusion: The presence of multiple clusters indicated a multi-source outbreak, rather than a single source outbreak from a single health practitioner as previously suggested. The multiple introductions were likely a consequence of ongoing transmission within the high-risk groups of Larkana, and it is possible that the so-called Larkana strain was introduced into the general population through poor infection prevention control practices in healthcare settings. The study highlights the need to scale up HIV-1 prevention programmes among key population groups and improving infection prevention control in Pakistan

Basic Hallmarks of Urothelial Cancer Unleashed in Primary Uroepithelium by Interference with the Epigenetic Master Regulator ODC1

Urothelial carcinoma (UC) is a common disease causing significant morbidity and mortality as well as considerable costs for health systems. Extensive aberrant methylation of DNA is broadly documented in early UC, contributing to genetic instability, altered gene expression and tumor progression. However the triggers initiating aberrant methylation are unknown. Recently we discovered that several genes encoding key enzymes of methyl group and polyamine metabolism, including Ornithine Decarboxylase 1 (ODC1), are affected by DNA methylation in early stage UC. In this study, we investigated the hypothesis that these epigenetic alterations act in a feed-forward fashion to promote aberrant DNA methylation in UC. We demonstrate that siRNA-mediated knockdown of ODC1 expression elicits genome-wide LINE-1 demethylation, induction of LINE-1 transcripts and double-strand DNA breaks and decreases viability in primary cultured uroepithelial cells. Similarly, following siRNA-mediated knockdown of ODC1, UC cells undergo double-strand DNA breaks and apoptosis. Collectively, our findings provide evidence that ODC1 gene hypermethylation could be a starting point for the onset of genome-wide epigenetic aberrations in urothelial carcinogenesis. Furthermore, LINE-1 induction enabled by ODC1 interference provides a new experimental model to study mechanisms and consequences of LINE-1 activation in the etiology and progression of UC as well as presumably other cancers

Phylogenetic and Drug-Resistance Analysis of HIV-1 Sequences From an Extensive Paediatric HIV-1 Outbreak in Larkana, Pakistan.

INTRODUCTION: In April 2019, an HIV-1 outbreak among children occurred in Larkana, Pakistan, affecting more than a thousand children. It was assumed that the outbreak originated from a single source, namely a doctor at a private health facility. In this study, we performed subtype distribution, phylogenetic and drug-resistance analysis of HIV-1 sequences from 2019 outbreak in Larkana, Pakistan. METHODS: A total of 401 blood samples were collected between April-June 2019, from children infected with HIV-1 aged 0-15 years recruited into a case-control study to investigate the risk factors for HIV-1 transmission. Partial HIV-1 pol sequences were generated from 344 blood plasma samples to determine HIV-1 subtype and drug resistance mutations (DRM). Maximum-likelihood phylogenetics based on outbreak and reference sequences was used to identify transmission clusters and assess the relationship between outbreak and key population sequences between and within the determined clusters. Bayesian analysis was employed to identify the time to the most recent common recent ancestor (tMRCA) of the main Pakistani clusters. RESULTS: The HIV-1 circulating recombinant form (CRF) 02_AG and subtype A1 were most common among the outbreak sequences. Of the treatment-naïve participants, the two most common mutations were RT: E138A (8%) and RT: K219Q (8%). Four supported clusters within the outbreak were identified, and the median tMRCAs of the Larkana outbreak sequences were estimated to 2016 for both the CRF02_AG and the subtype A1 clusters. Furthermore, outbreak sequences exhibited no phylogenetic mixing with sequences from other high-risk groups of Pakistan. CONCLUSION: The presence of multiple clusters indicated a multi-source outbreak, rather than a single source outbreak from a single health practitioner as previously suggested. The multiple introductions were likely a consequence of ongoing transmission within the high-risk groups of Larkana, and it is possible that the so-called Larkana strain was introduced into the general population through poor infection prevention control practices in healthcare settings. The study highlights the need to scale up HIV-1 prevention programmes among key population groups and improving infection prevention control in Pakistan

CURATION AND MANAGEMENT OF CULTURAL HERITAGE THROUGH LIBRARIES

Libraries, museums and archives hold valuable collections in a variety of media, presenting a vast body of knowledge rooted in the history of human civilisation. These form the repository of the wisdom of great works by thinkers of past and the present. The holdings of these institutions are priceless heritage of the mankind as they preserve documents, ideas, and the oral and written records. To value the cultural heritage and to care for it as a treasure bequeathed to us by our ancestors is the major responsibility of libraries. The past records constitute a natural resource and are indispensable to the present generation as well as to the generations to come. Libraries preserve the documentary heritage resources for which they are primarily responsible. Any loss of such materials is simply irreplaceable. Therefore, preserving this intellectual, cultural heritage becomes not only the academic commitment but also the moral responsibility of the librarians/information scientists, who are in charge of these repositories. The high quality of the papers and the discussion represent the thinking and experience of experts in their particular fields. The contributed papers also relate to the methodology used in libraries in Asia to provide access to manuscripts and cultural heritage. The volume discusses best practices in Knowledge preservation and how to collaborate and preserve the culture. The book also deals with manuscript and archives issues in the digital era. The approach of this book is concise, comprehensively, covering all major aspects of preservation and conservation through libraries. The readership of the book is not just limited to library and information science professionals, but also for those involved in conservation, preservation, restoration or other related disciplines. The book will be useful for librarians, archivists and conservators. We thank the Sunan Kalijaga University, Special Libraries Association- Asian Chapter for their trust and their constant support, all the contributors for their submissions, the members of the Local and International Committee for their reviewing effort for making this publication possible

Investigation of phase evolution and control over phase transformation temperature and thermal hysteresis using stoichiometry and co-doping in VO2 thin films

Structural phase transition temperature and its associated hysteresis in VO2 have been controlled by high valent dopant induced local structural modification which acts as phase nucleation site during phase transformation. Monoclinic phase intensity loops plotted against temperature has been observed to exhibit thermal hysteresis. It is shown that the size, shape and central position of hysteresis loop depend on stoichiometry and doping concentration. Highest reduction in phase transformation temperature and thermal hysteresis width has been observed in case of W+6-Mo+6 co-doping and W+6 doping, respectively. Hence energy barrier associated with the structural phase transition has been successfully manipulated to vary Tc and hysteresis width. These findings have implications for designing the phase switching devices and smart window applications

A Common Notation and Tool Support for Embedded Feature Annotations

Features are typically used to describe the functionalities of software systems. They help understanding systems as well as planning their evolution and managing systems. Especially agile methods foster their use. However, to use features, their locations need to be known. When not documented, they are easily forgotten and then need to be recovered, which is costly. While automated feature-location techniques exist, they are not usable in practice given their inaccuracies. We take a different route and advocate to record locations early using a lightweight annotation system, where feature information is embedded in software assets. However, given the potential design space of annotations, a unified notation and tool support is needed. Extending our prior work, we present a unified, concise notation for embedded annotations, which we implemented in FAXE, a library for parsing and retrieving such annotations, use-able in third-party tooling. We demonstrate its use, especially for an advanced use case of feature-oriented isolated development by automating partial commits

Protein secondary structure prediction using neural networks and deep learning: a review

Literature contains over fifty years of accumulated methods proposed by researchers for predicting the secondary structures of proteins in silico. A large part of this collection is comprised of artificial neural network-based approaches, a field of artificial intelligence and machine learning that is gaining increasing popularity in various application areas. The primary objective of this paper is to put together the summary of works that are important but sparse in time, to help new researchers have a clear view of the domain in a single place. An informative introduction to protein secondary structure and artificial neural networks is also included for context. This review will be valuable in designing future methods to improve protein secondary structure prediction accuracy. The various neural network methods found in this problem domain employ varying architectures and feature spaces, and a handful stand out due to significant improvements in prediction. Neural networks with larger feature scope and higher architecture complexity have been found to produce better protein secondary structure prediction. The current prediction accuracy lies around the 84% marks, leaving much room for further improvement in the prediction of secondary structures in silico. It was found that the estimated limit of 88% prediction accuracy has not been reached yet, hence further research is a timely demand

Causes of merge conflicts: a case study of ElasticSearch

Software branching and merging allows collaborative development and creating software variants, commonly referred to as clone & own. While simple and cheap, a trade-off is the need to merge code and to resolve merge conflicts, which frequently occur in practice. When resolving conflicts, a key challenge for developer is to understand the changes that led to the conflict. While merge conflicts and their characteristics are reasonably well understood, that is not the case for the actual changes that cause them.We present a case study of the changes---on the code and on the project-level (e.g., feature addition, refactoring, feature improvement)---that lead to conflicts. We analyzed the development history of ElasticSearch, a large open-source project that heavily relies on branching (forking) and merging. We inspected 40 merge conflicts in detail, sampled from 534 conflicts not resolvable by a semi-structured merge tool. On a code (structural) level, we classified the semantics of changes made. On a project-level, we categorized the decisions that motivated these changes. We contribute a categorization of code- and project-level changes and a detailed dataset of 40 conflict resolutions with a description of both levels of changes. Similar to prior studies, most of our conflicts are also small; while our categorization of code-level changes surprisingly differs from that of prior work. Refactoring, feature additions and feature enhancements are the most common causes of merge conflicts, most of which could potentially be avoided with better development tooling