3,905 research outputs found
Cleavage of endogenous gamma ENaC and elevated abundance of alpha ENaC are associated with increased Na+ transport in response to apical fluid volume expansion in human H441 airway epithelial cells
No full textUtilising Deep Learning Models for the Surface Registration Problem in HoloNav
No full textSurface Registration is a registration problem that handles the registration of two similar surfaces. In most research that utilises Deep Learning (DL) models to handle surface registration two theories are investigated; the first being whether surfaces sampled from the same origin can be registered together, and the second theory being whether the models can register Point Clouds with low overlapping data for utilisation in Simultaneous Localisation and Mapping (SLAM) applications. However, the surface registration to be utilised in the HoloNav Augmented Reality (AR) navigation system will utilise Point Clouds sampled from different origins with a high overlap ratio. This research, therefore, aims to determine the viability of DL methods for surface registration in HoloNav data. To determine the viability, rotation and translation errors in the match were used, with the aforementioned metrics later being evaluated manually with the utilisation of a visualiser. The results indicate that the models can generalise on the navigator data for an initial Euler angle difference of 45 degrees, but due to the difference in sampling density on the utilised point clouds can not provide accurate matches. Therefore, the utilisation of DL models can be considered to be viable if the navigator data has a sampling density similar to the pre-operative model.https://github.com/alpcicimen/holonav-dl-registration The link to the github repository containing the utilised dataset, scripts, as well as the modified DL models RPMNet and PREDATOR.CSE3000 Research ProjectComputer Science and Engineerin
The Scent of a Smell: An Extensive Comparison between Textual and Structural Smells
No full textCode smells are symptoms of poor design or implementation choices that have a negative effect on several aspects of software maintenance and evolution, such as program comprehension or change- and fault-proneness. This is why researchers have spent a lot of effort on devising methods that help developers to automatically detect them in source code. Almost all the techniques presented in literature are based on the analysis of structural properties extracted from source code, although alternative sources of information (e.g., textual analysis) for code smell detection have also been recently investigated. Nevertheless, some studies have indicated that code smells detected by existing tools based on the analysis of structural properties are generally ignored (and thus not refactored) by the developers. In this paper, we aim at understanding whether code smells detected using textual analysis are perceived and refactored by developers in the same or different way than code smells detected through structural analysis. To this aim, we set up two different experiments. We have first carried out a software repository mining study to analyze how developers act on textually or structurally detected code smells. Subsequently, we have conducted a user study with industrial developers and quality experts in order to qualitatively analyze how they perceive code smells identified using the two different sources of information. Results indicate that textually detected code smells are easier to identify and for this reason they are considered easier to refactor with respect to code smells detected using structural properties. On the other hand, the latter are often perceived as more severe, but more difficult to exactly identify and remove.Accepted Author ManuscriptSoftware Engineerin
Apical and basolateral localisation of GLUT2 transporters in human lung epithelial cells
No full textGlucose concentrations of normal human airway surface liquid are approximately 12.5 times lower than blood glucose concentrations indicating that glucose uptake by epithelial cells may play a role in maintaining lung glucose homeostasis. We have therefore investigated potential glucose uptake mechanisms in non-polarised and polarised H441 human airway epithelial cells and bronchial biopsies. We detected mRNA and protein for glucose transporter type 2 (GLUT2) and glucose transporter type 4 (GLUT4) in non-polarised cells but GLUT4 was not detected in the plasma membrane. In polarised cells, GLUT2 protein was detected in both apical and basolateral membranes. Furthermore, GLUT2 protein was localised to epithelial cells of human bronchial mucosa biopsies. In non-polarised H441 cells, uptake of D: -glucose and deoxyglucose was similar. Uptake of both was inhibited by phloretin indicating that glucose uptake was via GLUT-mediated transport. Phloretin-sensitive transport remained the predominant route for glucose uptake across apical and basolateral membranes of polarised cells and was maximal at 5-10 mM glucose. We could not conclusively demonstrate sodium/glucose transporter-mediated transport in non-polarised or polarised cells. Our study provides the first evidence that glucose transport in human airway epithelial cells in vitro and in vivo utilises GLUT2 transporters. We speculate that these transporters could contribute to glucose uptake/homeostasis in the human airway
Fructose transport-deficient Staphylococcus aureus reveals important role of epithelial glucose transporters in limiting sugar-driven bacterial growth in airway surface liquid.
No full textHyperglycaemia as a result of diabetes mellitus or acute illness is associated with increased susceptibility to respiratory infection with Staphylococcus aureus. Hyperglycaemia increases the concentration of glucose in airway surface liquid (ASL) and promotes the growth of S. aureus in vitro and in vivo. Whether elevation of other sugars in the blood, such as fructose, also results in increased concentrations in ASL is unknown and whether sugars in ASL are directly utilised by S. aureus for growth has not been investigated. We obtained mutant S. aureus JE2 strains with transposon disrupted sugar transport genes. NE768(fruA) exhibited restricted growth in 10 mM fructose. In H441 airway epithelial-bacterial co-culture, elevation of basolateral sugar concentration (5-20 mM) increased the apical growth of JE2. However, sugar-induced growth of NE768(fruA) was significantly less when basolateral fructose rather than glucose was elevated. This is the first experimental evidence to show that S. aureus directly utilises sugars present in the ASL for growth. Interestingly, JE2 growth was promoted less by glucose than fructose. Net transepithelial flux of D-glucose was lower than D-fructose. However, uptake of D-glucose was higher than D-fructose across both apical and basolateral membranes consistent with the presence of GLUT1/10 in the airway epithelium. Therefore, we propose that the preferential uptake of glucose (compared to fructose) limits its accumulation in ASL. Pre-treatment with metformin increased transepithelial resistance and reduced the sugar-dependent growth of S. aureus. Thus, epithelial paracellular permeability and glucose transport mechanisms are vital to maintain low glucose concentration in ASL and limit bacterial nutrient sources as a defence against infection
March dl: Adding Adaptive Heuristics and a New Branching Strategy
No full textWe introduce the march dl satisability (SAT) solver, a successor of march eq. The latter was awarded state-of-the-art in two categories during the Sat 2004 competition. The focus lies on presenting those features that are new in march dl. Besides a description, each of these features is illustrated with some experimental results. By extending the pre-processor, using adaptive heuristics, and by using a new branching strategy, march dl is able to solve nearly all benchmarks faster than its predecessor. Moreover, various instances which were beyond the reach of march eq, can now be solved - relatively easily - due to these new features.Software TechnologyElectrical Engineering, Mathematics and Computer Scienc
Crash Reproduction Using Helper Objectives
No full textEvolutionary-based crash reproduction techniques aid developers in their debugging practices by generating a test case that reproduces a crash given its stack trace. In these techniques, the search process is typically guided by a single search objective called Crash Distance. Previous studies have shown that current approaches could only reproduce a limited number of crashes due to a lack of diversity in the population during the search. In this study, we address this issue by applying Multi-Objectivization using Helper-Objectives (MO-HO) on crash reproduction. In particular, we add two helper-objectives to the Crash Distance to improve the diversity of the generated test cases and consequently enhance the guidance of the search process. We assessed MO-HO against the single-objective crash reproduction. Our results show that MO-HO can reproduce two additional crashes that were not previously reproducible by the single-objective approach.Virtual/online event due to COVID-19 Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.Software EngineeringSoftware Technolog
A General Formulation to Describe Empirical Rainfall Thresholds for Landslides
No full textAbstractIn this paper, a brief description of the Generalized FLaIR Model (GFM, De Luca and Versace, 2016) is provided, that is able to reproduce all the empirical thresholds proposed in literature, aimed to forecast landslides triggered by rainfall. In particular, this paper focuses on Antecedent Precipitation (AP) schemes. The paper demonstrates that these are particular solutions of the GFM and will exemplify this using AP schemes for NE Italy1, Seattle2 and Nicaragua - El Salvador3
Lipopolysaccharide modifies amiloride-sensitive Na+ transport processes across human airway cells: role of mitogen-activated protein kinases ERK 1/2 and 5
No full textBacterial lipopolysaccharides (LPS) are potent inducers of proinflammatory signaling pathways via the activation of nuclear factor-kappa B (NF-KB) and mitogenactivated protein kinase (MAPK), causing changes in the processes that control lung fluid homeostasis and contributing to the pathogenesis of lung disease. In human H441 airway epithelial cells, incubation of cells with 15 ng ml-1 LPS caused a significant reduction in amiloride-sensitive / sc from 15±2 to 8±2 uA cm-2 (p=0.01, n=13) and a shift in IC50 amiloride of currents from 6.8 × 10 -7 to 6.4×10-6 M. This effect was associated with a decrease in the activity of 5 pS, highly Na+ selective, amiloride-sensitive 10 uM cation channels (NSC) in the apical membrane. LPS decreased aENaC mRNA and protein abundance, inferring that LPS inhibited aENaC gene expression. This correlated with the decrease in HSC activity, indicating that these channels, but not NSCs, were comprised of at least aENaC protein. LPS increased NF- KB DNA binding activity and phosphorylation of extracellular signal-related kinase (ERK) 1/2, but decreased phosphorylation of ERKS in H.441 cells. Pretreatment of monolayers with PD98059 (20 uM) inhibited ERK1/2 phosphorylation, promoted phosphorylation of ERK5, increased aENaC protein abundance, and reversed the effect of LPS on I80 and the shift in amiloride sensitivity. Inhibitors of NF-KB activation were without effect. Taken together, our data indicate that LPS acts via ERK signaling pathways to decrease ccENaC transcription, reducing HSC/ ENaC channel abundance, activity, and transepithelial Na+ transport in H441 airway epithelial cells
Releasing Fast and Slow: An Exploratory Case Study at ING
No full textThe appeal of delivering new features faster has led many software projects to adopt rapid releases. However, it is not well understood what the effects of this practice are. This paper presents an exploratory case study of rapid releases at ING, a large banking company that develops software solutions in-house, to characterize rapid releases. Since 2011, ING has shifted to a rapid release model. This switch has resulted in a mixed environment of 611 teams releasing relatively fast and slow. We followed a mixed-methods approach in which we conducted a survey with 461 participants and corroborated their perceptions with 2 years of code quality data and 1 year of release delay data. Our research shows that: rapid releases are more commonly delayed than their non-rapid counterparts, however, rapid releases have shorter delays; rapid releases can be beneficial in terms of reviewing and user-perceived quality; rapidly released software tends to have a higher code churn, a higher test coverage and a lower average complexity; challenges in rapid releases are related to managing dependencies and certain code aspects, e.g. design debt.Software EngineeringSoftware Technolog
- …
