arXiv subjects

Luis Cruz

Publications and source records attributed to Luis Cruz.

28 records · Page 2Linked to original sources

arXiv2021

Fixing Vulnerabilities Potentially Hinders Maintainability

Security is a requirement of utmost importance to produce high-quality software. However, there is still a considerable amount of vulnerabilities being discovered and fixed almost weekly. We hypothesize that developers affect the maintainability of their codebases when patching vulnerabilities. This paper evaluates the impact of patches to improve security on the maintainability of open-source software. Maintainability is measured based on the Better Code Hub's model of 10 guidelines on a dataset, including 1300 security-related commits. Results show evidence of a trade-off between security and maintainability for 41.90% of the cases, i.e., developers may hinder software maintainability. Our analysis shows that 38.29% of patches increased software complexity and 37.87% of patches increased the percentage of LOCs per unit. The implications of our study are that changes to codebases while patching vulnerabilities need to be performed with extra care; tools for patch risk assessment should be integrated into the CI/CD pipeline; computer science curricula needs to be updated; and, more secure programming languages are necessary.

cs.SE↗

arXiv2020

QUALINET White Paper on Definitions of Immersive Media Experience (IMEx)

With the coming of age of virtual/augmented reality and interactive media, numerous definitions, frameworks, and models of immersion have emerged across different fields ranging from computer graphics to literary works. Immersion is oftentimes used interchangeably with presence as both concepts are closely related. However, there are noticeable interdisciplinary differences regarding definitions, scope, and constituents that are required to be addressed so that a coherent understanding of the concepts can be achieved. Such consensus is vital for paving the directionality of the future of immersive media experiences (IMEx) and all related matters. The aim of this white paper is to provide a survey of definitions of immersion and presence which leads to a definition of immersive media experience (IMEx). The Quality of Experience (QoE) for immersive media is described by establishing a relationship between the concepts of QoE and IMEx followed by application areas of immersive media experience. Influencing factors on immersive media experience are elaborated as well as the assessment of immersive media experience. Finally, standardization activities related to IMEx are highlighted and the white paper is concluded with an outlook related to future developments.

cs.MM↗

arXiv2019

Do Energy-oriented Changes Hinder Maintainability?

Energy efficiency is a crucial quality requirement for mobile applications. However, improving energy efficiency is far from trivial as developers lack the knowledge and tools to aid in this activity. In this paper we study the impact of changes to improve energy efficiency on the maintainability of Android applications. Using a dataset containing 539 energy efficiency-oriented commits, we measure maintainability -- as computed by the Software Improvement Group's web-based source code analysis service Better Code Hub (BCH) -- before and after energy efficiency-related code changes. Results show that in general improving energy efficiency comes with a significant decrease in maintainability. This is particularly evident in code changes to accommodate the Power Save Mode and Wakelock Addition energy patterns. In addition, we perform manual analysis to assess how real examples of energy-oriented changes affect maintainability. Our results help mobile app developers to 1) avoid common maintainability issues when improving the energy efficiency of their apps; and 2) adopt development processes to build maintainable and energy-efficient code. We also support researchers by identifying challenges in mobile app development that still need to be addressed.

cs.SE↗

arXiv2019

EMaaS: Energy Measurements as a Service for Mobile Applications

Measuring energy consumption is a challenging task faced by developers when building mobile apps. This paper presents EMaaS: a system that provides reliable energy measurements for mobile applications, without requiring a complex setup. It combines estimations from an energy model with --- typically more reliable, but also expensive --- hardware-based measurements. On a per scenario basis, it decides whether the energy model is able to provide a reliable estimation of energy consumption. Otherwise, hardware-based measurements are provided. In addition, the system is accessible to the community of mobile software practitioners/researchers in the form of a Software as a Service. With this service, we aim at solving current problems in the field of energy efficiency in mobile software engineering: the complexity of hardware-based power monitor tools, the reliability of energy models, and the continuous need of data to build energy models.

cs.SE↗

arXiv2019

To the Attention of Mobile Software Developers: Guess What, Test your App!

Software testing is an important phase in the software development life-cycle because it helps in identifying bugs in a software system before it is shipped into the hand of its end users. There are numerous studies on how developers test general-purpose software applications. The idiosyncrasies of mobile software applications, however, set mobile apps apart from general-purpose systems (e.g., desktop, stand-alone applications, web services). This paper investigates working habits and challenges of mobile software developers with respect to testing. A key finding of our exhaustive study, using 1000 Android apps, demonstrates that mobile apps are still tested in a very ad hoc way, if tested at all. However, we show that, as in other types of software, testing increases the quality of apps (demonstrated in user ratings and number of code issues). Furthermore, we find evidence that tests are essential when it comes to engaging the community to contribute to mobile open source software. We discuss reasons and potential directions to address our findings. Yet another relevant finding of our study is that Continuous Integration and Continuous Deployment (CI/CD) pipelines are rare in the mobile apps world (only 26% of the apps are developed in projects employing CI/CD) --- we argue that one of the main reasons is due to the lack of exhaustive and automatic testing.

cs.SE↗

arXiv2019

Catalog of Energy Patterns for Mobile Applications

Software engineers make use of design patterns for reasons that range from performance to code comprehensibility. Several design patterns capturing the body of knowledge of best practices have been proposed in the past, namely creational, structural and behavioral patterns. However, with the advent of mobile devices, it becomes a necessity a catalog of design patterns for energy efficiency. In this work, we inspect commits, issues and pull requests of 1027 Android and 756 iOS apps to identify common practices when improving energy efficiency. This analysis yielded a catalog, available online, with 22 design patterns related to improving the energy efficiency of mobile apps. We argue that this catalog might be of relevance to other domains such as Cyber-Physical Systems and Internet of Things. As a side contribution, an analysis of the differences between Android and iOS devices shows that the Android community is more energy-aware.

cs.SE↗

arXiv2018

Using Automatic Refactoring to Improve Energy Efficiency of Android Apps

The ever-growing popularity of mobile phones has brought additional challenges to the software development lifecycle. Mobile applications (apps, for short) ought to provide the same set of features as conventional software, with limited resources: such as, limited processing capabilities, storage, screen and, not less important, power source. Although energy efficiency is a valuable requirement, developers often lack knowledge of best practices. In this paper, we study whether or not automatic refactoring can aid developers ship energy efficient apps. We leverage a tool, Leafactor, with five energy code smells that tend to go unnoticed. We use Leafactor to analyze code smells in 140 free and open source apps. As a result, we detected and fixed code smells in 45 apps, from which 40% have successfully merged our changes into the official repository.

cs.SE↗

arXiv2008

Automated identification of neurons and their locations

Individual locations of many neuronal cell bodies (>10^4) are needed to enable statistically significant measurements of spatial organization within the brain such as nearest-neighbor and microcolumnarity measurements. In this paper, we introduce an Automated Neuron Recognition Algorithm (ANRA) which obtains the (x,y) location of individual neurons within digitized images of Nissl-stained, 30 micron thick, frozen sections of the cerebral cortex of the Rhesus monkey. Identification of neurons within such Nissl-stained sections is inherently difficult due to the variability in neuron staining, the overlap of neurons, the presence of partial or damaged neurons at tissue surfaces, and the presence of non-neuron objects, such as glial cells, blood vessels, and random artifacts. To overcome these challenges and identify neurons, ANRA applies a combination of image segmentation and machine learning. The steps involve active contour segmentation to find outlines of potential neuron cell bodies followed by artificial neural network training using the segmentation properties (size, optical density, gyration, etc.) to distinguish between neuron and non-neuron segmentations. ANRA positively identifies 86[5]% neurons with 15[8]% error (mean[st.dev.]) on a wide range of Nissl-stained images, whereas semi-automatic methods obtain 80[7]%/17[12]%. A further advantage of ANRA is that it affords an unlimited increase in speed from semi-automatic methods, and is computationally efficient, with the ability to recognize ~100 neurons per minute using a standard personal computer. ANRA is amenable to analysis of huge photo-montages of Nissl-stained tissue, thereby opening the door to fast, efficient and quantitative analysis of vast stores of archival material that exist in laboratories and research collections around the world.

physics.bio-ph↗

arXiv2007

Role of electrostatic interactions in amyloid beta-protein (Abeta) oligomer formation: A discrete molecular dynamics study

Pathological folding and oligomer formation of the amyloid beta-protein (Abeta) are widely perceived as central to Alzheimer's disease (AD). Experimental approaches to study Abeta self-assembly are problematic, because most relevant aggregates are quasi-stable and inhomogeneous. We apply a discrete molecular dynamics (DMD) approach combined with a four-bead protein model to study oligomer formation of the amyloid beta-protein (Abeta). We address the differences between the two most common Abeta alloforms, Abeta40 and Abeta42, which oligomerize differently in vitro. We study how the presence of electrostatic interactions (EIs) between pairs of charged amino acids affects Abeta40 and Abeta42 oligomer formation. Our results indicate that EIs promote formation of larger oligomers in both Abeta40 and Abeta42. The Abeta40 size distribution remains unimodal, whereas the Abeta42 distribution is trimodal, as observed experimentally. Abeta42 folded structure is characterized by a turn in the C-terminus that is not present in Abeta40. We show that the same C-terminal region is also responsible for the strongest intermolecular contacts in Abeta42 pentamers and larger oligomers. Our results suggest that this C-terminal region plays a key role in the formation of Abeta42 oligomers and the relative importance of this region increases in the presence of EIs. These results suggest that inhibitors targeting the C-terminal region of Abeta42 oligomers may be able to prevent oligomer formation or structurally modify the assemblies to reduce their toxicity.

q-bio.BM↗

arXiv2005

Solvent and mutation effects on the nucleation of amyloid $β$-protein folding

Experimental evidence suggests that the folding and aggregation of the amyloid $β$-protein (A$β$) into oligomers is a key pathogenetic event in Alzheimer's disease (AD). Inhibiting the pathologic folding and oligomerization of A$β$ could be effective in the prevention and treatment of AD. Here, using all-atom molecular dynamics simulations in explicit solvent, we probe the initial stages of folding of a decapeptide segment of A$β$, A$β_{21-30}$, shown experimentally to nucleate the folding process. In addition, we examine the folding of a homologous decapeptide containing an amino acid substitution linked to hereditary cerebral hemorrhage with amyloidosis--Dutch type, [Gln22]A$β_{21-30}$. We find that: (i) when the decapeptide is in water, hydrophobic interactions and transient salt bridges between Lys28 and either Glu22 or Asp23 are important in the formation of a loop in the Val24--Lys28 region of the wild type decapeptide; (ii) in the presence of salt ions, salt bridges play a more prominent role in the stabilization of the loop; (iii) in water with a reduced density, the decapeptide forms a helix, indicating the sensitivity of folding to different aqueous environments; (iv) the ``Dutch'' peptide in water, in contrast to the wild type peptide, fails to form a long-lived Val24--Lys28 loop, suggesting that loop stability is a critical factor in determining whether A$β$ folds into pathologic structures. Our results are relevant to understand the mechanism of A$β$ peptide folding in different environments, such as intra- and extracellular milieus or cell membranes, and how amino acid substitutions linked to familial forms of amyloidosis cause disease.

q-bio.BM↗