Gitor: Scalable Code Clone Detection by Building Global Sample Graph

Code clone detection is about finding out similar code fragments, which has drawn much attention in software engineering since it is important for software maintenance and evolution. Researchers have proposed many techniques and tools for source code clone detection, but current detection methods concentrate on analyzing or processing code samples individually without exploring the underlying connections among code samples. In this paper, we propose Gitor to capture the underlying connections among different code samples. Specifically, given a source code database, we first tokenize all code samples to extract the pre-defined individual information. After obtaining all samples individual information, we leverage them to build a large global sample graph where each node is a code sample or a type of individual information. Then we apply a node embedding technique on the global sample graph to extract all the samples vector representations. After collecting all code samples vectors, we can simply compare the similarity between any two samples to detect possible clone pairs. More importantly, since the obtained vector of a sample is from a global sample graph, we can combine it with its own code features to improve the code clone detection performance. To demonstrate the effectiveness of Gitor, we evaluate it on a widely used dataset namely BigCloneBench. Our experimental results show that Gitor has higher accuracy in terms of code clone detection and excellent execution time for inputs of various sizes compared to existing state-of-the-art tools. Moreover, we also evaluate the combination of Gitor with other traditional vector-based clone detection methods, the results show that the use of Gitor enables them detect more code clones with higher F1.Comment: 12 pages, 5 figure

Towards Understanding the Capability of Large Language Models on Code Clone Detection: A Survey

Code cloning, the duplication of code fragments, is common in software development. While some reuse aids productivity, excessive cloning hurts maintainability and introduces bugs. Hence, automatic code clone detection is vital. Meanwhile, large language models (LLMs) possess diverse code-related knowledge, making them versatile for various software engineering challenges. However, LLMs' performance in code clone detection is unclear and needs more study for accurate assessment. In this paper, we provide the first comprehensive evaluation of LLMs for clone detection, covering different clone types, languages, and prompts. We find advanced LLMs excel in detecting complex semantic clones, surpassing existing methods. Adding intermediate reasoning steps via chain-of-thought prompts noticeably enhances performance. Additionally, representing code as vector embeddings, especially with text encoders, effectively aids clone detection.Lastly, the ability of LLMs to detect code clones differs among various programming languages. Our study suggests that LLMs have potential for clone detection due to their language capabilities, offering insights for developing robust LLM-based methods to enhance software engineering.Comment: 13 pages, 3 figure

Messenger RNA Oxidation Occurs Early in Disease Pathogenesis and Promotes Motor Neuron Degeneration in ALS

BACKGROUND: Accumulating evidence indicates that RNA oxidation is involved in a wide variety of neurological diseases and may be associated with neuronal deterioration during the process of neurodegeneration. However, previous studies were done in postmortem tissues or cultured neurons. Here, we used transgenic mice to demonstrate the role of RNA oxidation in the process of neurodegeneration. METHODOLOGY/PRINCIPAL FINDINGS: We demonstrated that messenger RNA (mRNA) oxidation is a common feature in amyotrophic lateral sclerosis (ALS) patients as well as in many different transgenic mice expressing familial ALS-linked mutant copper-zinc superoxide dismutase (SOD1). In mutant SOD1 mice, increased mRNA oxidation primarily occurs in the motor neurons and oligodendrocytes of the spinal cord at an early, pre-symptomatic stage. Identification of oxidized mRNA species revealed that some species are more vulnerable to oxidative damage, and importantly, many oxidized mRNA species have been implicated in the pathogenesis of ALS. Oxidative modification of mRNA causes reduced protein expression. Reduced mRNA oxidation by vitamin E restores protein expression and partially protects motor neurons. CONCLUSION/SIGNIFICANCE: These findings suggest that mRNA oxidation is an early event associated with motor neuron deterioration in ALS, and may be also a common early event preceding neuron degeneration in other neurological diseases

AMS measurement of 53Mn and its initial application at CIAE

The determination of cosmogenic 53Mn in terrestrial archives has important applications, such as burial ages, exposure age and erosion rates. Accelerator mass spectrometry (AMS) is the most sensitive technique to detect minute amounts of 53Mn. 53Mn measurements were developed at the China Institute of Atomic nergy (CIAE) using the DE-Q3D equipped AMS system. This approach was recently optimized with the goal to reach the sensitivity required for AMS measurements of 53Mn in deep-sea ferromanganese crust (DSFC) samples. Based on these improvements of sample preparation, current beam transmission and so on, 53Mn in two samples of DSFC was measured by AMS. The ratios of 53Mn/Mn corresponding to an age of 3.77 ± 0.42 and 13.73 ± 2.74 Ma by 129I dating method are (5.01 ± 2.15) 10 13 and (1.90 ± 0.96) 10 13. The ratios are close to the experimental reference values, deduced from the previous research. The experimental progress, performances and results are presented in this contribution.This work was mainly supported by the National Natural Science Foundations of China (NSFC), under Grant No. 11075221, and a partly supported by the National Natural Science Foundation of China under Grant Nos. 10705054, 41073044 and 11265005

Silencing Dicer-Like Genes Reduces Virulence and sRNA Generation in Penicillium italicum, the Cause of Citrus Blue Mold

The Dicer protein is one of the most important components of RNAi machinery because it regulates the production of small RNAs (sRNAs) in eukaryotes. Here, Dicer1-like gene (Pit-DCL1) and Dicer2-like gene (Pit-DCL2) RNAi transformants were generated via pSilent-1 in Penicillium italicum (Pit), which is the causal agent of citrus blue mold. Neither transformant showed a change in mycelial growth or sporulation ability, but the pathogenicity of the Pit-DCL2 RNAi transformant to citrus fruits was severely impaired, compared to that of the Pit-DCL1 RNAi transformant and the wild type. We further developed a citrus wound-mediated RNAi approach with a double-stranded fragment of Pit-DCL2 generated in vitro, which achieved an efficiency in reducing Pi-Dcl2 expression and virulence that was similar to that of protoplast-mediated RNAi in P. italicum, suggesting that this approach is promising in the exogenous application of dsRNA to control pathogens on the surface of citrus fruits. In addition, sRNA sequencing revealed a total of 69.88 million potential sRNAs and 12 novel microRNA-like small RNAs (milRNAs), four of which have been predicated on target innate immunity or biotic stress-related genes in Valencia orange. These data suggest that both the Pit-DCL1 and Pit-DCL2 RNAi transformants severely disrupted the biogenesis of the potential milRNAs, which was further confirmed for some milRNAs by qRT-PCR or Northern blot analysis. These data suggest the sRNAs in P. italicum that may be involved in a molecular virulence mechanism termed cross-kingdom RNAi (ck-RNAi) by trafficking sRNA from P. italicum to citrus fruits

Hydrocarbon accumulation of Sinian natural gas reservoirs, Leshan-Longnüsi paleohigh, Sichuan Basin, SW China

The old Sinian carbonate reservoir in the Leshan-Longnüsi paleohigh was taken as a research object to study the process of gas accumulation in the Sinian reservoir through analysis of gas reservoir characteristics, gas composition, gas reservoir types, accumulation condition and evolution. The results show that the reservoir lithology and type are almost the same in the six gas pools discovered in the Leshan-Longnüsi paleohigh. All the gas reservoirs are characterized by high temperature, ordinary pressure, and intense heterogeneity. The gas reservoir type in different layers and the gas compositions and carbon isotopes in different locations vary obviously. The gas of Sinian Dengying Formation, originated from oil cracking, is mixed gas mainly from source rocks of Sinian Dengying Formation as well as Cambrian Qiongzhusi Formation. The source and reservoir condition, their combination and fluid transporting conditions are favorable, which can determine the gas accumulation and preservation in Dengying Formation. The Sinian gas reservoirs are believed to have been accumulated by the following processes: paleo-oil accumulation, paleo-oil cracking, and gas reservoir adjustment and finalization. There are three processes of gas accumulation in the reservoir, which are influenced by the formation of paleohigh and differential structural evolution in different positions. Key words: Sichuan Basin, Leshan-Longnüsi paleohigh, Sinian System, Dengying Formation, natural gas, accumulation condition, accumulation proces

The unmediated choline sensor based on layered double hydroxides in hydrogen peroxide detection mode

International audienc

Microbiota of a seepage face at the mouth of a subterranean estuary: diversity, distribution and substrate dependence

11 pages, 2 tables, 7 figuresSubterranean estuaries, i.e., the mixing zone between terrestrial groundwater and recirculated seawater, host a wide range of microbiota. Here, field campaigns were conducted at the mouth of the subterranean estuary at the Sanggou Bay (Shandong Province, China) over four consecutive seasons at a seepage face (0–20 cm depth). The diversity of benthic microbiome was characterized via 16S rRNA gene sequencing and metagenomics, combined with physic-chemical parameters, e.g., organic carbon, total nitrogen and sulfate contents in sediments. During spring, the dominant species were assigned to the phylum Proteobacteria. Important opportunistic species was assigned to Acidobacteria, Actinobacteria and Bacteroidetes. The key components were identified to be species of the genera Pseudoalteromonas, Colwellia and Sphingobium, indicating the involvement of sediment microbiota in the degradation of sedimentary organic carbon, particularly that of pelagic origin, e.g., phytoplankton detritus and bivalve pseudo-feces. During spring, the microbial community was statistically similar along the depth profiles and among the three sampled stations. Similar spatial distributions were obtained in the remaining seasons. By contrast, the dominant species assemblages varied significantly among seasons, with key genera being Thioprofundum and Nitrosopumilus during summer and autumn and Thioprofundum and Ilumatobacter during winter. Network analysis revealed a seasonal shift in benthic nitrogen and sulfur metabolism associated with these variations in microbial community composition. Overall, our findings suggested that macro elements derived from pelagic inputs, particularly detrital phytoplankton, shaped the microbial community compositions at the seepage face, resulting in significant seasonal variations, while the influence of terrestrial materials transported by groundwater on the sediment microbiota at the seepage face found to be minorPeer reviewe

Cultivable gut bacteria of scarabs (Coleoptera: Scarabaeidae) inhibit Bacillus thuringiensis multiplication

The entomopathogen Bacillus thuringiensis is used to control various pest species of scarab beetle but is not particularly effective. Gut bacteria have diverse ecological and evolutionary effects on their hosts, but whether gut bacteria can protect scarabs from B. thuringiensis infection remains poorly understood. To investigate this, we isolated 32 cultivable gut bacteria from Holotrichia oblita Faldermann, Holotrichia parallela Motschulsky, and Anomala corpulenta Motschulsky, and analyzed their effect on B. thuringiensis multiplication and Cry toxin stability. 16S rDNA analysis indicated that these gut bacteria belong to the Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes phyla. A confrontation culture analyses of the 32 isolates against three scarab-specific B. thuringiensis strains showed that the majority of the scarab gut bacteria had antibacterial activity against the B. thuringiensis strains. The Cry toxin stability analysis results showed that while several strains produced proteases capable of processing the scarab-specific toxin Cry8Ea, none were able to completely degrade it. These results suggest that gut bacteria can potentially affect the susceptibility of scarabs to B. thuringiensis and that this should be considered when considering future control measures