Delving into Commit-Issue Correlation to Enhance Commit Message Generation Models

Commit message generation (CMG) is a challenging task in automated software engineering that aims to generate natural language descriptions of code changes for commits. Previous methods all start from the modified code snippets, outputting commit messages through template-based, retrieval-based, or learning-based models. While these methods can summarize what is modified from the perspective of code, they struggle to provide reasons for the commit. The correlation between commits and issues that could be a critical factor for generating rational commit messages is still unexplored. In this work, we delve into the correlation between commits and issues from the perspective of dataset and methodology. We construct the first dataset anchored on combining correlated commits and issues. The dataset consists of an unlabeled commit-issue parallel part and a labeled part in which each example is provided with human-annotated rational information in the issue. Furthermore, we propose \tool (\underline{Ex}traction, \underline{Gro}unding, \underline{Fi}ne-tuning), a novel paradigm that can introduce the correlation between commits and issues into the training phase of models. To evaluate whether it is effective, we perform comprehensive experiments with various state-of-the-art CMG models. The results show that compared with the original models, the performance of \tool-enhanced models is significantly improved.Comment: ASE2023 accepted pape

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Progress in the Application of Biomimetic Mineralization for Tooth Repair

The tooth, including enamel and dentin, is a prominent biomineral that is produced by the biomineralization of living organisms. Although the mechanical performance of the tooth is outstanding, caries easily develop in a complex oral environment. The analysis of the chemical composition and the relationship between the mechanical properties and the structure is of great importance in solving caries. In this review, the multilevel structure and mechanical properties of enamel and dentin are briefly introduced, along with caries formation and the limitations of clinical dental restoration. Furthermore, the progress of the application of a wide range of biomimetic strategies for tooth remineralization is highlighted, including the use of calcium phosphate ionic clusters to construct the mineralization front, ensuring the oriented epitaxial growth of enamel crystals and replicating the complex structure of the enamel. Moreover, compared with the current clinical treatment, in which the resin composite and glass ionomer cement are the main repair materials and the high incidence of secondary caries leads to imperfect restorations, the remineralization tactics could achieve excellent repair effectiveness in reconstructing the complicated structure, restoring mechanical strength and gaining permanent repair. A basic understanding of enamel and dentin, their potential for restoration, and hopeful prospects for tooth repair that can be applied in the clinical setting, not just in the laboratory, is provided by this review

Simultaneous removal of nitrate and sulfate using an up-flow three-dimensional biofilm electrode reactor: Performance and microbial response

Nitrate removal from low carbon water is a problem in the water treatment, especially in the presence of high sulfate. In this work, an up-flow three-dimensional biofilm electrode reactor (3D-BER) was established to remove nitrate and sulfate from low organic carbon water. Results indicated that sulfate negatively affected nitrate removal. Moreover, high electric current and short hydraulic retention time deteriorated the performance of nitrate and sulfate removal. When the influent of SO42- was 150 mg/L, the removal efficiency of NO3 -N and SO42- was 88.49 +/- 4.5% and 29.35 +/- 5.5%, respectively. The high-throughput sequencing revealed that denitrifying bacteria dominated in the lower part of the reactor while sulfate reducing bacteria dominated in the upper part of the reactor. It was speculated that oxidation products of sulfide could serve as supplementary electron donors to enhance nitrate removal in the 3D-BER

Conductive polymer nanocomposites with hierarchical multi-scale structures via self-assembly of carbon-nanotubes on graphene on polymer-microspheress

A novel and highly conductive 3-dimensional (3D) hierarchical multi-scale structure is formed by a new, simple, facile, and water-based method that enables practical production of conductive carbon nanofiller/polymer composites. More specifically, the π–π interaction between CNTs and graphene oxide (GO) is exploited to disperse conductive but non-polar CNTs with amphiphilic GO sheets to form a stable aqueous colloidal solution. Aqueous-dispersible latex–polystyrene microspheres are then added to enable the self-assembly processes of anchoring CNTs on GO and wrapping microspheres with GO-stabilized CNTs for the formation of an intriguing 3D hierarchical multi-scale structure. During this process, GO is reduced to conductive reduced-graphene oxide (RGO). The resultant RGO sheets act as “nano-walls” to prevent CNTs from randomly diffusing into the polymer bulk during thermal pressing of RGO–CNT/microspheres, which results in the formation of a 3D foam-like network of RGO–CNTs with high quality. The resultant composite with such a structure gives an ultra-low percolation threshold (0.03 vol% RGO–CNTs) and a reasonably high conductivity (153 S m−1 at 4 vol% RGO–CNTs), which could satisfy various applications requiring both transparency and electrical conduction characteristics (e.g. transparent antistatic coatings, capacitive touch-screens, and transparent electronic devices)

In situ fabrication of gold nanoparticles into biocathodes enhance chloramphenicol removal

The development of highly conductive biofilms is a key strategy to enhance antibiotic removal in bioelectrochemical systems (BESs) with biocathodes. In this study, Au nanoparticles (Au-NPs) were in situ fabricated in a biocathode (Au biocathode) to enhance the removal of chloramphenicol (CAP) in BESs. The concentration of Au(III) was determined to be 5 mg/L. CAP was effectively removed in the BES containing a Au biocathode with a removal percentage of 94.0% within 48 h; this result was 1.8-fold greater than that obtained using a biocathode without Au-NPs (51.7%). The Au-NPs significantly reduced the charge transfer resistance and promoted the electrochemical activity of the biocathode. In addition, the Au biocathode showed a specifical enrichment of Dokdonella, Bosea, Achromobacter, Bacteroides and Petrimonas, all of which are associated with electron transfer and contaminant degradation. This study provides a new strategy for enhancing CAP removal in BESs through a simple and eco-friendly electrode design. (c) 2021 Elsevier B.V. All rights reserved