TEASMA: A Practical Approach for the Test Assessment of Deep Neural Networks using Mutation Analysis

Successful deployment of Deep Neural Networks (DNNs), particularly in safety-critical systems, requires their validation with an adequate test set to ensure a sufficient degree of confidence in test outcomes. Mutation analysis, one of the main techniques for measuring test adequacy in traditional software, has been adapted to DNNs in recent years. This technique is based on generating mutants that aim to be representative of actual faults and thus can be used for test adequacy assessment. In this paper, we investigate for the first time whether mutation operators that directly modify the trained DNN model (i.e., post-training) can be used for reliably assessing the test inputs of DNNs. We propose and evaluate TEASMA, an approach based on post-training mutation for assessing the adequacy of DNN's test sets. In practice, TEASMA allows engineers to decide whether they will be able to trust test results and thus validate the DNN before its deployment. Based on a DNN model's training set, TEASMA provides a methodology to build accurate prediction models of the Fault Detection Rate (FDR) of a test set from its mutation score, thus enabling its assessment. Our large empirical evaluation, across multiple DNN models, shows that predicted FDR values have a strong linear correlation (R2 >= 0.94) with actual values. Consequently, empirical evidence suggests that TEASMA provides a reliable basis for confidently deciding whether to trust test results or improve the test set

Recruitment of cyanobacteria from the sediments in the eutrophic Shanzi Reservoir

This study investigated the impact of four environmental factors on the recruitment of cyanobacteria from bottom sediments in the eutrophic Shanzi Reservoir. Temperature and light were identified as the key determinants for the recruitment of Microcystis and Oscillatoria. Cyanobacteria became dominant at higher temperature (20°C) and light intensity (2000 lx) and Microcystis and Oscillatoria were the major species. Detailed recruitment simulation undertaken with the respective gradients of temperature and light suggested that both Microcystis and Oscillatoria are temperature sensitive and that their critical temperature point was 10°C. However, distinct light impacts were observed only on Microcystis. The recruitment of Oscillatoria was light independent, whereas Microcystis had a positive relationship with light intensity. Physical disturbance promoted Microcystis recruitment and also affected the structure of the recruited cyanobacterial community at the water–sediment interface, based on quantitative polymerase chain reaction (qPCR) and phylogenetic analysis

Enhancing pentachlorophenol degradation by vermicomposting associated bioremediation

Vermicomposting is an effective and environmentally friendly approach for soil organic contamination clean-up. This study investigated the roles and mechanisms of earthworm (Eisenia foetida) on soil pentachlorophenol (PCP) degradation with sterile and non-sterile soil-compost treatment. Limited soil PCP degradation was observed in the control and sterile compost treatments, whereas the synergetic effects of earthworm and compost contributed to the PCP biodegradation acceleration by significantly improving microbial biomass and activities. Sequence analysis and phylogentic classification of soil bacterial and fungal community structure after 42 days treatment identified the dominancy of indigenous bacterial families Pseudomonadaceae, Sphingobacteriaceae and Xanthomonadaceae, and fungal family Trichocomaceae, which were responsible for PCP biodegradation and stimulated by vermicomposting. Further investigation revealed the dominant roles of sterile compost during PCP biodegradation as the formation of humus-PCP in soil rather than neutralizing soil pH and increasing PCP availability. The mechanisms of vermicomposting include humus-PCP complex degradation, humus consumption and soil pH neutralization. This study provides a comprehensive understanding of the synergetic effect of vermicomposting on microbial community functions and PCP degradation enhancement in soils

The impact on the soil microbial community and enzyme activity of two earthworm species during the bioremediation of pentachlorophenol-contaminated soils

The ecological effect of earthworms on the fate of soil pentachlorophenol (PCP) differs with species. This study addressed the roles and mechanisms by which two earthworm species (epigeic Eisenia fetida and endogeic Amynthas robustus E. Perrier) affect the soil microbial community and enzyme activity during the bioremediation of PCP-contaminated soils. A. robustus removed more soil PCP than did E. foetida. A. robustus improved nitrogen utilisation efficiency and soil oxidation more than did E. foetida, whereas the latter promoted the organic matter cycle in the soil. Both earthworm species significantly increased the amount of cultivable bacteria and actinomyces in soils, enhancing the utilisation rate of the carbon source (i.e. carbohydrates, carboxyl acids, and amino acids) and improving the richness and evenness of the soil microbial community. Additionally, earthworm treatment optimized the soil microbial community and increased the amount of the PCP-4-monooxygenase gene. Phylogenic classification revealed stimulation of indigenous PCP bacterial degraders, as assigned to the families Flavobacteriaceae, Pseudomonadaceae and Sphingobacteriacea, by both earthworms. A. robustus and E. foetida specifically promoted Comamonadaceae and Moraxellaceae PCP degraders, respectively

Effects of two ecological earthworm species on atrazine degradation performance and bacterial community structure in red soil

Vermicomposting is an effective and environmentally friendly approach for eliminating soil organic contamination. Atrazine is one of the most commonly applied triazinic herbicides and frequently detected in agricultural soils. This study investigated the roles and mechanisms of two earthworm species (epigeic Eisenia foetida and endogeic Amynthas robustus) in microbial degradation of atrazine. Both earthworms accelerated atrazine degradation performance from 39.0% in sterile soils to 94.9%–95.7%, via neutralizing soil pH, consuming soil humus, altering bacterial community structure, enriching indigenous atrazine degraders and excreting the intestinal atrazine-degrading bacteria. Rhodoplanes and Kaistobacter were identified as soil indigenous degraders for atrazine mineralization and stimulated by both earthworm species. A. robustus excreted the intestinal Cupriavidus and Pseudomonas, whereas Flavobacterium was released by E. foetida. This study provides a comprehensive understanding of the distinct effects of two earthworm species on soil microbial community and atrazine degradation, offering technical supports to apply vermicomposting in effective soil bioremediation

Interrogating cadmium and lead biosorption mechanisms by Simplicillium chinense via infrared spectroscopy

Fungi-associated phytoremediation is an environmentally friendly and cost-efficient approach to remove potential toxic elements (PTEs) from contaminated soils. Many fungal strains have been reported to possess PTE-biosorption behaviour which benefits phytoremediation performance. Nevertheless, most studies are limited in rich or defined medium, far away from the real-world scenarios where nutrients are deficient. Understanding fungal PTE-biosorption performance and influential factors in soil environment can expand their application potential and is urgently needed. This study applied attenuated total reflection Fourier-transform infrared (ATR-FTIR) coupled with phenotypic microarrays to study the biospectral alterations of a fungal strain Simplicillium chinense QD10 and explore the mechanisms of Cd and Pb biosorption. Both Cd and Pb were efficiently adsorbed by S. chinense QD10 cultivated with 48 different carbon sources and the biosorption efficiency achieved >90%. As the first study using spectroscopic tools to analyse PTE-biosorption by fungal cells in a high-throughput manner, our results indicated that spectral biomarkers associated with phosphor-lipids and proteins (1745 cm−1, 1456 cm−1 and 1396 cm−1) were significantly correlated with Cd biosorption, suggesting the cell wall components of S. chinense QD10 as the primary interactive targets. In contrast, there was no any spectral biomarker associated with Pb biosorption. Addtionally, adsorption isotherms evidenced a Langmuir model for Cd biosorption but a Freundlich model for Pb biosorption. Accordingly, Pb and Cd biosorption by S. chinense QD10 followed discriminating mechanisms, specific adsorption on cell membrane for Cd and unspecific extracellular precipitation for Pb. This work lends new insights into the mechanisms of PTE-biosorption via IR spectrochemical tools, which provide more comprehensive clues for biosorption behaviour with a nondestructive and high-throughput manner solving the traditional technical barrier regarding the real-world scenarios

Circ_0003645 serves as miR-335-5p sponge to promote the biological process of diffuse large B-cell lymphoma by upregulating NFIB

Background Circular RNAs (circRNAs) are critical regulators for the development of many tumours, including diffuse large B-cell lymphoma (DLBCL). However, the role and mechanism of circ_0003645 in DLBCL progression remains obscure. Methods Quantitative real-time PCR was performed to measure the expression of circ_0003645, microRNA (miR)-335-5p and nuclear factor I/B (NFIB). Cell viability, apoptosis and cell cycle were measured by cell counting kit 8 assay and flow cytometry. Protein expression was assessed using western blot analysis, and cell glycolysis was evaluated by detecting glucose consumption and ATP/ADP ratios. Besides, dual-luciferase reporter assay and RIP assay were used to confirm RNA interaction. Results Our data showed that circ_0003645 expression was significantly upregulated in DLBCL tumour tissues. After circ_0003645 knockdown, the viability, cell cycle and glycolysis of DLBCL cells were inhibited, while cell apoptosis was promoted. MiR-335-5p could be sponged by circ_0003645, and NFIB was confirmed to be a downstream target of miR-335-5p. Function analysis revealed that anti-miR-335-5p reversed the regulation of si-circ_0003645 on DLBCL cell progression, and NFIB overexpression also abolished miR-335-5p-mediated the biological functions of DLBCL cells. Conclusion The present study revealed that circ_0003645 promoted the proliferation and glycolysis of DLBCL cells by the miR-335-5p/NFIB axis, which might provide a novel insight for DLBCL treatment

Molecular Dynamics Characteristics and Model of Vehicle-Following Behavior

The vehicle-following behavior is a self-organizing behavior that restores dynamic balance under the stimulation of external environmental factors. In fact, there are asymmetric problems in the process of acceleration and deceleration of drivers. The existing traditional models ignored the differences between acceleration and deceleration of vehicles. In order to solve this problem, the vehicles driving on the road are compared to interacting molecules. Vehicle-following characteristics are studied, and the molecular following model is established based on molecular dynamics. The model parameters under different conditions are calibrated considering the required safety distance by the vehicle and the reaction time of the driver. With the help of the vehicle running track graphs, speed, and acceleration graphs, the numerical simulations of the molecular following model and the classical optimal speed vehicle-following model are carried out. The results of the comparative analysis show that the acceleration in the process of acceleration and deceleration is not constant but more sensitive to the deceleration of the preceding vehicle than to the acceleration and more sensitive to the acceleration/deceleration of the short-distance vehicle than to the acceleration/deceleration of the long-distance vehicle. Therefore, the molecular following model can better describe the vehicle-following behavior, and the research results can provide a theoretical basis and a technical reference for the analysis of traffic flow dynamic characteristics and adaptive cruise control technology

Games and Software Engineering: Engineering fun, inspiration, and motivation

Games are a popular form of entertainment and, due to their nature (i.e., interactive, immersive, etc.), strongly lend themselves for use beyond this original intent. Serious games, or games with a purpose, have been introduced to integrate the entertainment value games with domain specific objectives on important topics within education, health, and the environment to mention a few. In addition, gamification has been used to enhance nonentertainment applications with game elements; it aspires to foster behavioral changes, engagement, motivation, and participation in activities. In this context, the actions performed have meaning/value in the game experience in order to improve workplace performance or learn something in real life. The growing adoption of gameful experiences in all of the previous contexts make their design and development increasingly complex due to, for example, the number and variety of users, and their potential mission criticality. This complexity is nurtured, among the other factors, by a lack of theoretical grounding and adequate frameworks to engineer the intended solutions. In this paper, we report the outcomes of the 6th International Workshop on Games and Software Engineering: Engineering fun, inspiration, and motivation (GAS 2023 ) 1, which was held as part of the 44th International Conference on Software Engineering (ICSE 2022) in Pittsburgh, PA, USA on May 20, 2022. The workshop program includes two exciting keynotes discussing topics related to training and learning, and fulfilling the promise and potential of gamification. The two paper sessions examined gamification from the perspectives of software project, testing, and, design. The conclusion of the workshop is anchored by a panel of four highly qualified researchers and practitioners discussing lessons learned and the future of gamification