Software Supply Chain Development and Application

Motivation: Free Libre Open Source Software (FLOSS) has become a critical componentin numerous devices and applications. Despite its importance, it is not clear why FLOSS ecosystem works so well or if it may cease to function. Majority of existing research is focusedon studying a specific software project or a portion of an ecosystem, but FLOSS has not been investigated in its entirety. Such view is necessary because of the deep and complex technical and social dependencies that go beyond the core of an individual ecosystem and tight inter-dependencies among ecosystems within FLOSS.Aim: We, therefore, aim to discover underlying relations within and across FLOSS projects and developers in open source community, mitigate potential risks induced by the lack of such knowledge and enable systematic analysis over entire open source community through the lens of supply chain (SC).Method: We utilize concepts from an area of supply chains to model risks of FLOSS ecosystem. FLOSS, due to the distributed decision making of software developers, technical dependencies, and copying of the code, has similarities to traditional supply chain. Unlike in traditional supply chain, where data is proprietary and distributed among players, we aim to measure open-source software supply chain (OSSC) by operationalizing supply chain concept in software domain using traces reconstructed from version control data.Results: We create a very large and frequently updated collection of version control data in the entire FLOSS ecosystems named World of Code (WoC), that can completely cross-reference authors, projects, commits, blobs, dependencies, and history of the FLOSS ecosystems, and provide capabilities to efficiently correct, augment, query, and analyze that data. Various researches and applications (e.g., software technology adoption investigation) have been successfully implemented by leveraging the combination of WoC and OSSC.Implications: With a SC perspective in FLOSS development and the increased visibility and transparency in OSSC, our work provides potential opportunities for researchers to conduct wider and deeper studies on OSS over entire FLOSS community, for developers to build more robust software and for students to learn technologies more efficiently and improve programming skills

Coordinating Interdependencies in an Open Source Software Project: A Replication of Lindberg, et al.

The current study is a full replication (conceptual and empirical) of “Coordinating Interdependencies in Online Communities: A Study of an Open Source Software Project” Lindberg et al (2016), which addresses the question of how OSS communities address unresolved interdependencies. Following the original study, we analyze project development data, archived in the GitHub repository, for the OSS project Rubinius. The analysis explores relationships among development and developer interdependencies as well as activity and order variation. Further, we extend the original study by examining the core relationships in the original study and investigating the external generalizability of the results by replicating the analysis on three analogous OSS projects: JRuby, mruby, and RubyMotion. These offer an opportunity to evaluate the generalizability of the original study to projects of different sizes and amount of activity, yet similar otherwise to the project in the original study. Another extension is the use of an additional control variable, length of activity sequence, which proves to have substantial implications of the study’s focal relationships. We find that three out of the four projects we analyze support the findings of the original study as it pertains to four relationships in the original study: order variation and developer interdependencies, activity variation and developer interdependencies, order variation and development interdependencies, and development and developer interdependencies. We also discuss the implications of our findings, especially in cases where the replication results differ from those in the original study and offer suggestions for future research that can help advance this stream of research

An efficient and robust exfoliated bentonite/Ag3PO4/AgBr plasmonic photocatalyst for degradation of parabens

Efficient visible-light-driven heterojunction photocatalysts have attracted broad interest owing to their promising adsorption and degradation performances in the removal of organic pollutants. In this study, a mesoporous exfoliated bentonite (EB)/Ag3PO4/AgBr (30%) photocatalyst was obtained by stripping and exfoliating bentonite as the support for loading Ag3PO4 and AgBr. The particle size ranges of Ag3PO4 and AgBr were about 10-30 nm and 5-10 nm, respectively. The exfoliated bentonite could greatly improve the dispersion and adsorption of Ag3PO4 and AgBr, and significantly enhance the stability of the material during paraben photodegradation. 0.2 g L-1 methylparaben (MPB) was completely decomposed over the EB/Ag3PO4/AgBr (30%) in 40 min under visible light irradiation. In addition, the photocatalytic activity of EB/Ag3PO4/AgBr (30%) remained at about 91% after five recycling runs manifesting that EB/Ag3PO4/AgBr (30%) possessed excellent stability. Radical quenching tests revealed that holes (h+) and hydroxyl radicals (·OH) were the major radicals. They attacked the side chain on the benzene ring of parabens, which were gradually oxidized to the intermediates, such as benzoic acid, 3-hydroxybenzoic acid, 4-hydroxybenzoic acid, azelaic acid, and eventually became CO2 and H2O. The enhancement of photocatalytic activity and photo-stability could be ascribed to the stable structural characteristics, enlarged surface area, high absorption ability, and improved light absorption ability from loading Ag3PO4 onto EB. Meanwhile, the matched energy levels of Ag3PO4 and AgBr made the photoelectron-hole pairs separate and transfer effectively at the interfaces. As a result, the photocatalytic properties of EB/Ag3PO4/AgBr (30%) composites were enhanced. © 2020 The Royal Society of Chemistry

A Dataset and an Approach for Identity Resolution of 38 Million Author IDs extracted from 2B Git Commits

The data collected from open source projects provide means to model large software ecosystems, but often suffer from data quality issues, specifically, multiple author identification strings in code commits might actually be associated with one developer. While many methods have been proposed for addressing this problem, they are either heuristics requiring manual tweaking, or require too much calculation time to do pairwise comparisons for 38M author IDs in, for example, the World of Code collection. In this paper, we propose a method that finds all author IDs belonging to a single developer in this entire dataset, and share the list of all author IDs that were found to have aliases. To do this, we first create blocks of potentially connected author IDs and then use a machine learning model to predict which of these potentially related IDs belong to the same developer. We processed around 38 million author IDs and found around 14.8 million IDs to have an alias, which belong to 5.4 million different developers, with the median number of aliases being 2 per developer. This dataset can be used to create more accurate models of developer behaviour at the entire OSS ecosystem level and can be used to provide a service to rapidly resolve new author IDs

Transgenic Rat Model of Neurodegeneration Caused by Mutation in the TDP Gene

TDP-43 proteinopathies have been observed in a wide range of neurodegenerative diseases. Mutations in the gene encoding TDP-43 (i.e., TDP) have been identified in amyotrophic lateral sclerosis (ALS) and in frontotemporal lobe degeneration associated with motor neuron disease. To study the consequences of TDP mutation in an intact system, we created transgenic rats expressing normal human TDP or a mutant form of human TDP with a M337V substitution. Overexpression of mutant, but not normal, TDP caused widespread neurodegeneration that predominantly affected the motor system. TDP mutation reproduced ALS phenotypes in transgenic rats, as seen by progressive degeneration of motor neurons and denervation atrophy of skeletal muscles. This robust rat model also recapitulated features of TDP-43 proteinopathies including the formation of TDP-43 inclusions, cytoplasmic localization of phosphorylated TDP-43, and fragmentation of TDP-43 protein. TDP transgenic rats will be useful for deciphering the mechanisms underlying TDP-43–related neurodegenerative diseases

Investigating the Survival Benefit of Combining Radiotherapy for Surgery Treated Locally Advanced Esophageal Squamous Cell Carcinoma Patients Aged 65 and Older

PurposeTo evaluate the survival benefit of combining radiotherapy with surgery in locally advanced esophageal squamous cell carcinoma (ESCC) patients aged over 65.MethodsUsing the SEER database, we selected patients age >= 65 years that were diagnosed as locally advanced ESCC during 2004-2013. Cancer-specific survival (CSS) was examined using the Kaplan-Meier analysis and compared by the log-rank test. Univariable and multivariable Cox proportional hazard models were established to identify possible prognostic factors.ResultsA total of 972 cases were included in the study. For surgical patients aged 65-79 years, 74 patients (32.9%) were treated by surgery alone and 122 patients (54.2%) had received additional neoadjuvant radiotherapy (NRT). NRT+surgery was associated with improved CSS comparing with surgery alone (HR, 0.58; 95%CI, 0.39 to 0.85; P=0.005). In subgroup analysis, NRT was associated with improved CSS for patients aged 65-74 years (2-year CSS 56.6% versus 39.6%, P=0.026). No significant differences of progonosis was observed for different treatment groups in 75-79 years patients (P=0.972).ConclusionsIn this SEER-based study, the addition of neoadjuvant radiotherapy before surgery was associated with improved CSS for locally advanced ESCC patients aged 65 to 74 years.Peer reviewe