13197 research outputs found
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The role of fibroblast growth factors during sensory nerve development in zebrafish lateral line
Get PDF奈良先端科学技術大学院大学博士（ﾊﾞｲｵｻｲｴﾝｽ）doctoral thesi
Chinese-English Code-Switching Speech Data Construction and Prompt-Enhanced ASR for Medical Dialogues
Get PDF奈良先端科学技術大学院大学修士（工学）master thesi
Quantitative analysis of the spatiotemporal expression patterns of the clock genes in A. thaliana roots
Get PDF奈良先端科学技術大学院大学博士（理学）doctoral thesi
Genome-wide association study identifies candidate genes contributing to flowering time variation in Lotus japonicus in Japan
Get PDFFlowering time is an important factor in plant fitness and local adaptation. Genome-wide association (GWA) studies have allowed the identification of candidate genes in certain plant species for various traits, including flowering time. Lotus japonicus is widely found throughout the Japanese archipelago. To obtain flowering time data with more prominent difference as more suitable indicator of environmental adaptation, flowering time data were collected for 132 wild accessions originating from various points across this region under shorter day length conditions than in previous studies. The results showed latitudinal variations in flowering time, with southern accessions flowering earlier. Comparing data from four flowering times with varying conditions revealed greater differences under a shorter day length. It is likely that day length significantly affects flowering time in this species. GWA analyses were conducted on flowering time variation measured in this study and the ratios between flowering time under different conditions. Candidate genes different from previous study were detected, including orthologues of known flowering time genes in each analysis. Correlation tests between flowering time and strongly detected single-nucleotide polymorphisms (SNPs) in the GWA analysis suggested that approximately 60% of flowering time variation can be explained by the two main SNPs. This result suggests that the majority of the variation could be explained by a small number of genetic factors. Considering the strong association with flowering time variation, these candidates may be responsible for these differences and therefore can be related to local adaptation in this species.journal articl
Structural basis of lipopolysaccharide translocon assembly mediated by the small lipoprotein LptM
No full textGram-negative bacteria possess an outer membrane (OM) that acts as a barrier against toxic compounds. Lipopolysaccharide (LPS) in the outer leaflet of the OM is crucial for barrier function. After its synthesis in the cytoplasm and translocation to the periplasm, LPS is transported to the OM by the LPS transport system. The LPS translocon, composed of an OM protein LptD and a lipoprotein LptE, mediates LPS assembly into the OM. Recently, the small lipoprotein LptM (YifL) was identified as a novel LptD/E-interactor that facilitates LptD maturation. However, its mechanism remains unclear. Here, we investigated the detailed interaction between LptM and LptD. We found that LptM interacts with the folded LptD intermediate at the late stage of its maturation. Mutational analyses demonstrated that the N-terminal conserved region (C20GLKGPLYF28) of LptM is essential for its function. Cryo-EM structural analysis of the E. coli LptD/E/M complex, combined with biochemical analyses, revealed the molecular basis of the LptM–LptD interaction and its functional importance. Thus, we propose that LptM functions as a “barrel-rivet,” stabilizing LptD for its proper assembly.journal articl
Do Developers Depend on Deprecated Library Versions? A Mining Study of Log4j
No full textLog4j has become a widely adopted logging library for Java programs due to its long history and high reliability. Its widespread use is notable not only because of its maturity but also due to the complexity and depth of its features, which have made it an essential tool for many developers. However, Log4j 1.x, which reached its end of support (deprecated), poses significant security risks and has numerous deprecated features that can be exploited by attackers. Despite this, some clients may still rely on this library. We aim to understand whether clients are still using Log4j 1.x despite its official support ending. We utilized the Mining Software Repositories 2025 challenge dataset, which provides a large and representative sample of open-source software projects. We analyzed over 10,000 log entries from the Mining Software Repositories 2025 challenge dataset using the Goblin framework to identify trends in usage rates for both Log4j 1.x and Log4j-core 2.x. Specifically, our study addressed two key issues: (1) We examined the usage rates and trends for these two libraries, highlighting any notable differences or patterns in their adoption. (2) We demonstrate that projects initiated after a deprecated library has reached the end of its support lifecycle can still maintain significant popularity. These findings highlight how deprecated are still popular, with the next step being to understand the reasoning behind these adoptions.conference pape
eBPF-Based Ordered Proof of Transit for Trustworthy Service Function Chaining
No full textService function chaining (SFC) establishes a service path where a sequence of functions is executed according to service requirements. However, SFC lacks a mechanism to ensure proper traversal of relay nodes in the data plane. Misconfigurations and the presence of attackers can lead to forwarding anomalies and path deviation, potentially allowing packets to bypass security network functions in the service path. To mitigate potential security breaches, ordered proof of transit (OPoT) has been proposed as a mechanism to verify whether traffic adheres to the designated path. In this paper, we realize lightweight OPoT-based path verification based on extended Berkeley Packet Filter (eBPF) for trustworthy SFC. Furthermore, by integrating it with the existing SFC proxy, we extend the proposed approach to accommodate both SFC-aware and SFC-unaware virtual network functions (VNFs) in the segment routing over IPv6 data plane (SRv6) domain. Through experiments, we demonstrate the capability of the proposed approach to detect path deviations. Additionally, we reveal the performance limitations of the proposed approach.journal articl
