13197 research outputs found
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On the Applications of the Recursive Property of the Zero-Suppressed Binary Decision Diagram
Get PDF奈良先端科学技術大学院大学博士（工学）doctoral thesi
Studies on eco-friendly bismuth-based material for lead-free perovskite solar cell applications
Get PDF奈良先端科学技術大学院大学博士（工学）doctoral thesi
CW レーザー ケッショウ カ ニ ヨル テイオン タンケッショウ SOI コウゾウ ノ ケイセイ ト ハクマク トランジスタ トクセイ ニ カンスル ケンキュウ
Get PDF奈良先端科学技術大学院大学博士（工学）doctoral thesi
Co-option and neofunctionalization of stomatal executors for defence against herbivores in Brassicales
No full textCo-option of gene regulatory networks leads to the acquisition of new cell types and tissues. Stomata, valves formed by guard cells (GCs), are present in most land plants and regulate CO2 exchange. The transcription factor (TF) FAMA globally regulates GC differentiation. In the Brassicales, FAMA also promotes the development of idioblast myrosin cells (MCs), another type of specialized cell along the vasculature essential for Brassicales-specific chemical defences. Here we show that in Arabidopsis thaliana, FAMA directly induces the TF gene WASABI MAKER (WSB), which triggers MC differentiation. WSB and STOMATAL CARPENTER 1 (SCAP1, a stomatal lineage-specific direct FAMA target), synergistically promote GC differentiation. wsb mutants lacked MCs and the wsb scap1 double mutant lacked normal GCs. Evolutionary analyses revealed that WSB is conserved across stomatous angiosperms. We propose that the conserved and reduced transcriptional FAMA–WSB module was co-opted before evolving to induce MC differentiation.journal articl
eye2vec: Learning Distributed Representations of Eye Movement for Program Comprehension Analysis
Get PDFThis paper presents eye2vec, an infrastructure for analyzing software developers’ eye movements while reading source code. In common eye-tracking studies in program comprehension, researchers must preselect analysis targets such as control flow or syntactic elements, and then develop analysis methods to extract appropriate metrics from the fixation for source code. Here, researchers can define various levels of AOIs like words, lines, or code blocks, and the difference leads to different results. Moreover, the interpretation of fixation for word/line can vary across the purposes of the analyses. Hence, the eye-tracking analysis is a difficult task that depends on the time-consuming manual work of the researchers. eye2vec represents continuous two fixations as transitions between syntactic elements using distributed representations. The distributed representation facilitates the adoption of diverse data analysis methods with rich semantic interpretations.conference pape
Development of an Automated Classification System for Medication-Related Incident Factors: A Practical Approach to Enhancing Patient Safety Management
No full textAnalyzing medication-related incident reports is crucial for patient safety; however, systematically extracting the underlying factors contributing to incident occurrence remains challenging. We developed a multi-label classifier that automatically identified incident factors from 1,212 drug-related incident reports using the Bidirectional Encoder Representations from Transformers and its derivatives. Based on the P-mSHELL model, a comprehensive framework for incident factor analysis, we established seven distinct factor categories and evaluated various pre-trained models through five-fold cross-validation. Almost all models achieved macro F1 scores exceeding 0.6, with the lightweight A Lite BERT model showing comparable performance to BERT. This study demonstrates the practical feasibility of natural language processing techniques for systematic incident factor analysis, supporting enhanced patient safety management.conference pape
Hydroxyurea modulates thiol–disulfide homeostasis in the yeast endoplasmic reticulum
No full textHydroxyurea (HU) has been extensively used in laboratory settings to induce S-phase arrest and checkpoint activation. Furthermore, it has a history of clinical use as a cost-effective chemotherapeutic agent. Nevertheless, there is still uncertainty regarding its precise pharmacology, side effects, and toxicity, particularly in terms of its impact on organelle homeostasis. Here, we demonstrate that in budding yeast, HU specifically inhibits the endoplasmic reticulum–associated degradation (ERAD) of luminal misfolded proteins (ERAD-L pathway), an effect that is independent of S-phase arrest. In contrast, HU did not affect the degradation of misfolded ER membrane proteins or the degradation of cytosolic proteins. The selective inhibition of ERAD-L by HU is likely attributable to the formation of disulfide bonds in cysteine residues in luminal substrates, which must be reduced before their retrotranslocation to the cytosol. We further demonstrate that HU plays a role in alleviating reductive stress phenotypes observed in cells lacking Ero1, which is essential for oxidative protein folding in the ER. We propose that HU functions as a modulator of thiol–disulfide homeostasis in the ER lumen.journal articl
Phage lysis protein LysM acts as a wedge to block MurJ conformational changes
No full textMany antibiotics target essential cellular processes. To combat multidrug-resistant bacteria, new antibacterial strategies are needed. In the peptidoglycan biogenesis pathway in Escherichia coli, MurJ, the lipid II flippase, is an essential membrane protein. The 37-residue protein M from the Levivirus phage, known as LysM or SglM, targets MurJ and induces cell lysis; however, its molecular mechanism remains unclear. Here, we present the cryo-EM structure of the MurJ/LysM (JM) complex at 3.09-angstrom resolution, revealing that LysM interacts with the crevasse between TM2 and TM7 of MurJ, locking MurJ in an outward-facing conformation, with LysM acting like a wedge. Alanine-scanning mutagenesis and pull-down assays revealed key residues responsible for LysM function, and molecular dynamics simulations showed that LysM stabilizes MurJ’s outward-facing state. These findings demonstrate an unprecedented phage-derived mechanism for blocking lipid II transport, providing a structural framework for designing MurJ-targeted antimicrobial agents.journal articl
Secure Federated Matrix Factorization via Device to Device Model Shuffling
Get PDFLocation-Based Recommendation Systems (LBRS) use device location data to suggest nearby hotels, restaurants, and points of interest. Since directly collecting location data from users can raise privacy concerns, there is growing interest in building recommendation systems based on Federated Learning (FL). Under FL, parameters of recommendation model learned on each user’s device are collected on a single server to build aggregated model. While FL does not raise privacy concerns about data collection since it does not collect user data directly, it may construct unfair models that repeatedly recommend specific locations. Although there are training methods to achieve fair recommendations that prevent such bias, they require more training epochs than usual. In FL, a malicious server can infer the original location data by continuously tracking a specific user’s parameter updates, and the inference accuracy increases proportionally with the number of training epochs. This means that achieving fair location recommendations in FL puts the original data at risk. In this paper, we design a novel parameter aggregation method to build fair and secure FL recommendation models. In the proposed aggregation method, users exchange parameters with each other before model aggregation to prevent malicious servers from inferring the original data. Even if a server (adversary) continuously tracks a specific user’s device, it cannot get parameters from the same user, thus preventing inference of the original location data. An experiment result demonstrated that the proposed method can reduce training time while maintaining the same accuracy as homomorphic encryption approach.journal articl