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Decomposition of dynamic transcriptomic responses during effector-triggered immunity reveals conserved responses in two distinct plant cell populations

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Plant Communications 2024年第8期5卷 1-17页

作者： Xiaotong Liu Daisuke Igarashi Rachel A.Hillmer Thomas Stoddard You Lu Kenichi Tsuda Chad L.Myers Fumiaki Katagiri Department of Plant and Microbial Biology University of Minnesota-Twin CitiesSt PaulMN 55108USA Department of Computer Science and Engineering University of Minnesota-Twin CitiesMinneapolisMN 55455USA Bioinformatics and Computational Biology Graduate Program University of Minnesota-Twin CitiesMinneapolisMN 55455USA Institute for Innovation Ajinomoto Co.Inc.KawasakiJapan State Key Laboratory of Agricultural Microbiology Hubei Hongshan LaboratoryHubei Key Lab of Plant PathologyCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhan 430070China Present address:225 S 6th St MinneapolisMN 55402USA Present address:Biotalys Inc.2520 Meridian Parkway Suite 480DurhamNC 27713USA Present address:Life Sciences Institute and Department of Cell and Developmental Biology University of Michigan Medical SchoolAnn ArborMI 48109USA

Rapid plant immune responses in the appropriate cells are needed for effective defense against *** transcriptome analysis is often used to describe overall immune responses,collection of transcriptome data with sufficient resolution in both space and time is *** reanalyzed public Arabidopsis time-course transcriptome data obtained after low-dose inoculation with a Pseudomonas syringae strain expressing the effector AvrRpt2,which induces effector-triggered immunity in ***-peak time-course patterns are prevalent among thousands of upregulated *** implemented a multicompartment modeling approach to decompose the double-peak pattern into two single-peak patterns for each *** decomposed peaks reveal an“echoing”pattern:the peak times of the first and second peaks correlate well across most upregulated *** demonstrated that the two peaks likely represent responses of two distinct cell populations that respond either cell autonomously or indirectly to ***,the peak decomposition has extracted spatial information from the time-course *** echoing pattern also indicates a conserved transcriptome response with different initiation times between the two cell populations despite different elicitor types.A gene set highly overlapping with the conserved gene set is also upregulated with similar kinetics during pattern-triggered *** of a WRKY network via different entry-point WRKYs can explain the similar but not identical transcriptome responses elicited by different elicitor *** discuss potential benefits of the properties of the WRKY activation network as an immune signaling network in light of pressure from rapidly evolving pathogens.

关键词： Arabidopsis Pseudomonas syringae plant immune response multi-compartment model WRKY transcription factors resilient immune signaling network

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To Trust or Not to Trust: Evolutionary Dynamics of an Asymmetric N-player Trust Game

arXiv

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arXiv 2023年

作者： Soo Lim, Ik. Masuda, Naoki School of Computing and Mathematical Sciences University of Greenwich LondonSE10 9LS United Kingdom Department of Mathematics and Computational and Data-Enabled Science and Engineering Program State University of New York Buffalo United States

Trusting others and reciprocating the received trust with trustworthy actions are fundaments of economic and social interactions. The trust game (TG) is widely used for studying trust and trustworthiness and entails a sequential interaction between two players, an investor and a trustee. It requires at least two strategies or options for an investor (e.g. to trust versus not to trust a trustee). According to the evolutionary game theory, the antisocial strategies (e.g. not to trust) evolve such that the investor and trustee end up with lower payoffs than those that they would get with the prosocial strategies (e.g. to trust). A generalisation of the TG to a multiplayer (i.e. more than two players) TG was recently proposed. However, its outcomes hinge upon two assumptions that various real situations may substantially deviate from: (i) investors are forced to trust trustees and (ii) investors can turn into trustees by imitation and vice versa. We propose an asymmetric multiplayer TG that allows investors not to trust and prohibits the imitation between players of different roles;instead, investors learn from other investors and the same for trustees. We show that the evolutionary game dynamics of the proposed TG qualitatively depends on the nonlinearity of the payoff function and the amount of incentives collected from and distributed to players through an institution. We also show that incentives given to trustees can be useful and sufficient to cost-effectively promote trust and trustworthiness among self-interested players. © 2023, CC BY.

关键词： Dynamics

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Heterogeneous quantization regularizes spiking neural network activity

arXiv

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arXiv 2024年

作者： Moyal, Roy Mama, Kyrus R. Einhorn, Matthew Borthakur, Ayon Cleland, Thomas A. Computational Physiology Lab Department of Psychology Cornell University IthacaNY14853 United States AI for Science Institute Cornell University IthacaNY14853 United States Neurosciences Graduate Program Stanford University StanfordCA94305 United States Mehta Family School of Data Science and Artificial Intelligence IIT Guwahati Assam Guwahati781039 India

The learning and recognition of object features from unregulated input has been a longstanding challenge for artificial intelligence systems. Brains are adept at learning stable representations given small samples of noisy observations;across sensory modalities, this capacity is aided by a cascade of signal conditioning steps informed by domain knowledge. The olfactory system, in particular, solves a source separation and denoising problem compounded by concentration variability, environmental interference, and unpredictably correlated sensor affinities. To function optimally, its plastic network requires statistically well-behaved input. We present a data-blind neuromorphic signal conditioning strategy whereby analog data are normalized and quantized into spike phase representations. Input is delivered to a column of duplicated spiking principal neurons via heterogeneous synaptic weights;this regularizes layer utilization, yoking total activity to the network’s operating range and rendering internal representations robust to uncontrolled open-set stimulus variance. We extend this mechanism by adding a data-aware calibration step whereby the range and density of the quantization weights adapt to accumulated input statistics, optimizing resource utilization by balancing activity regularization and information retention. Copyright © 2024, The Authors. All rights reserved.

关键词： Quantization (signal)

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Near-Optimal Pilot Assignment in Cell-Free Massive MIMO

arXiv

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arXiv 2023年

作者： Guedes, Raphael M. de Rezende, José F. Barbosa, Valmir C. Informatics and Computer Science Department State University of Rio de Janeiro RJ Rio de Janeiro20550-900 Brazil Systems Engineering and Computer Science Program Federal University of Rio de Janeiro RJ Rio de Janeiro21941-914 Brazil Graduate Program in Computational Sciences State University of Rio de Janeiro RJ Rio de Janeiro20550-900 Brazil

Cell-free massive MIMO systems are currently being considered as potential enablers of future (6G) technologies for wireless communications. By combining distributed processing and massive MIMO, they are expected to deliver improved user coverage and efficiency. A possible source of performance degradation in such systems is pilot contamination, which contributes to causing interference during uplink training and affects channel estimation negatively. Contamination occurs when the same pilot sequence is assigned to more than one user. This is in general inevitable, as the number of mutually orthogonal pilot sequences corresponds to only a fraction of the coherence interval. We introduce a new algorithm for pilot assignment and analyze its performance both from a theoretical perspective and in computational experiments. We show that it has an approximation ratio close to 1 for a plausibly large number of orthogonal pilot sequences, as well as low computational complexity under massive parallelism. We also show that, on average, it outperforms other methods in terms of per-user SINR and throughput on the uplink. Copyright © 2023, The Authors. All rights reserved.

关键词： Channel estimation

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Temporal Motifs for Financial Networks: A Study on Mercari, JPMC, and Venmo Platforms

arXiv

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arXiv 2023年

作者： Liu, Penghang Acharyya, Rupam Tillman, Robert E. Kimura, Shunya Masuda, Naoki Sarıyüce, Ahmet Erdem Department of Computer Science and Engineering University at Buffalo United States Amazon Web Services United States Optum Labs United States Mercari Inc. Japan Department of Mathematics University at Buffalo United States Computational and Data-Enabled Science and Engineering Program University at Buffalo United States

Understanding the dynamics of financial transactions among people is critically important for various applications such as fraud detection. One important aspect of financial transaction networks is temporality. The order and repetition of transactions can offer new insights when considered within the graph structure. Temporal motifs, defined as a set of nodes that interact with each other in a short time period, are a promising tool in this context. In this work, we study three unique temporal financial networks: transactions in Mercari, an online marketplace, payments in a synthetic network generated by J.P. Morgan Chase, and payments and friendships among Venmo users. We consider the fraud detection problem on the Mercari and J.P. Morgan Chase networks, for which the ground truth is available. We show that temporal motifs offer superior performance than a previous method that considers simple graph features. For the Venmo network, we investigate the interplay between financial and social relations on three tasks: friendship prediction, vendor identification, and analysis of temporal cycles. For friendship prediction, temporal motifs yield better results than general heuristics, such as Jaccard and Adamic-Adar measures. We are also able to identify vendors with high accuracy and observe interesting patterns in rare motifs, like temporal cycles. We believe that the analysis, datasets, and lessons from this work will be beneficial for future research on financial transaction networks. Copyright © 2023, The Authors. All rights reserved.

关键词： Finance

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PepTune: De Novo Generation of Therapeutic Peptides with Multi-Objective-Guided Discrete Diffusion

arXiv

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arXiv 2024年

作者： Tang, Sophia Zhang, Yinuo Chatterjee, Pranam Department of Biomedical Engineering Duke University United States Management and Technology Program University of Pennsylvania United States Center of Computational Biology Duke-NUS Medical School Singapore Department of Computer Science Duke University United States Department of Biostatistics and Bioinformatics Duke University United States

Peptide therapeutics, a major class of medicines, have achieved remarkable success across diseases such as diabetes and cancer, with landmark examples such as GLP-1 receptor agonists revolutionizing the treatment of type-2 diabetes and obesity. Despite their success, designing peptides that satisfy multiple conflicting objectives, such as target binding affinity, solubility, and membrane permeability, remains a major challenge. Classical drug development and target structure-based design are ineffective for such tasks, as they fail to optimize global functional properties critical for therapeutic efficacy. Existing generative frameworks are largely limited to continuous spaces, unconditioned outputs, or single-objective guidance, making them unsuitable for discrete sequence optimization across multiple properties. To address this, we present PepTune, a multi-objective discrete diffusion model for the simultaneous generation and optimization of therapeutic peptide SMILES. Built on the Masked Discrete Language Model (MDLM) framework, PepTune ensures valid peptide structures with bond-dependent masking schedules and penalty-based objectives. To guide the diffusion process, we propose a Monte Carlo Tree Search (MCTS)-based strategy that balances exploration and exploitation to iteratively refine Pareto-optimal sequences. MCTS integrates classifier-based rewards with search-tree expansion, overcoming gradient estimation challenges and data sparsity. Using PepTune, we generate diverse, chemically modified peptides optimized for multiple therapeutic properties, including target binding affinity, membrane permeability, solubility, hemolysis, and non-fouling for various disease-relevant targets. In total, our results demonstrate that MCTS-guided masked discrete diffusion is a powerful and modular approach for multi-objective sequence design in discrete state spaces. © 2024, CC BY-NC-ND.

关键词： Trees (mathematics)

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What affects the performance of POD for the simulation of heat transfer through building component? 8

What affects the performance of POD for the simulation of he...

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8th International Building Physics Conference, IBPC 2021

作者： Hou, Tianfeng Roels, Staf Janssen, Hans KU Leuven Department of Civil Engineering Building Physics Section Leuven3001 Belgium Data Assimilation Research Team RIKEN Center for Computational Science Kobe Japan RIKEN Prediction Science Laboratory Kobe Japan RIKEN Interdisciplinary Theoretical and Mathematical Sciences Program Kobe Japan

The capability of the proper orthogonal decomposition for the simulation of heat transfer in building components is investigated via three applications: linear heat transfer (not coupled to mass transfer), mildly non-linear heat transfer (coupled to air and moisture transfer (hygroscopic)) and highly non-linear heat transfer (coupled to moisture transfer (capillary)). It is shown that increasing non-linearity leads to an increasing number of required construction modes. To further investigate the reason for this degrading performance of POD, the singular values' decay progress from the different training snapshots is addressed in this paper. The results confirm that a fast decay of the singular values implies a high interrelation of the snapshots and a better performance of the POD method. © 2021 Institute of Physics Publishing. All rights reserved.

关键词： Heat transfer

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Characterization of Chromogenic Bacteria Using Agro-Waste Extracts as Substrate for Pigments Production

SSRN

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SSRN 2024年

作者： Zeleke, Birhanu Muleta, Diriba Dinka, Hunduma Tsegaye, Dereje Ali, Jemal Hassen Department of Applied Biology School of Applied Natural Science Adama Science and Technology University Adama Ethiopia Environmental Biotechnology Unit Institute of Biotechnology Addis Ababa University Addis Ababa Ethiopia College of Natural and Computational Sciences Ethiopia Department of Applied Chemistry School of Applied Natural Science Adama Science andTechnology University Adama Ethiopia Adama Public Health Research Referral Laboratory Center Adama895067 Ethiopia Ethiopian Field Epidemiology Training Program Ethiopia

Background: Microbial pigments are becoming one of the important research areas to explore their potential as eco-friendly substitute to synthetic chemicals. Therefore, this research aims at exploring pigment producing bacteria as potential substitute to synthetic dyes by culturing on agro-waste ***: The study was conducted by collecting environmental samples from various sites in Ethiopia. The samples were serially diluted and inoculated on nutrient agar using streak plate technique for colony detection and isolation. Screenings for eco-physiological tolerance were conducted using one-variable-at-a-time-method on agro-waste extracts that were prepared by decoction method. Morphological, biochemical and MALDI-TOF techniques were used for identification of the pigment producing isolates. Solvent extraction method was employed for pigment extraction. The extracted pigments were characterized using ATR-FTIR, UV-Vis spectroscopy and LC-MS techniques. Results: A total of 1321 isolates were retrieved from the samples. The pigmented isolates were tolerant to incubation temperature between 28oC-45oC, pH 6-10, culture agitation between 60 rpm-120 rpm, salt concentration from 1% -5%, and glucose and yeast extract at 1% and 0.1%, respectively. The retrieved potent pigment producing isolates were identified as Kocuria rosea, Micrococcus luteus and Exiguobacterium auranticum. Among the isolates, Micrococcus luteus was found the major pigment producing from which 1.47 g/L of pigment produced using orange waste extract as substrate. The FTIR spectral analysis of the pigment demonstrated the presence of hydroxyl, alkane and alkene groups. Moreover, analysis of UV-Vis and LC-MS revealed that the organic species responsible for the pigmentation was carotenoid compound. The pigment was found temperature and pH sensitive compared to other factors. Conclusion: The study indicates the potential of Micrococcus luteus isolated from hot environment as a promising candidate for

关键词： Textile industry

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Generative AI-Driven Data Augmentation for Robust Virtual Metrology: GANs, VAEs, and Diffusion Models

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IEEE Transactions on Semiconductor Manufacturing 2025年

作者： Lin, Chin-Yi Tseng, Tzu-Liang Emon, Solayman Hossain Tsai, Tsung-Han Department of Industrial Manufacturing and Systems Engineering University of Texas at El Paso El PasoTX79968 United States Computational Science Program University of Texas at El Paso El PasoTX79968 United States Institute of Information and Decision Sciences National Taipei University of Business Taipei10051 Taiwan

Advanced semiconductor manufacturing increasingly depends on Virtual Metrology (VM) for real-time quality monitoring, yet conventional data-driven models rarely capture the scarce or extreme process conditions critical for robust predictions. We propose a Multi-Stage Constrained Data Generative Augmentation (MSC-DGA) framework that integrates Variational Autoencoders (VAE), Normalizing Flows, and Constrained Diffusion to systematically expand coverage of seldom-seen regimes. By embedding strict engineering constraints during generation and applying a two-stage quality filter, MSCDGA ensures physically plausible synthetic samples. We further present theoretical proofs showing that multi-stage generation can approximate complex sensor distributions while enforcing domain validity, thereby improving coverage and preserving essential process physics. Empirically, we demonstrate the approach on real WBG SiC data, incorporating these curated samples into a Generative Foundation Model (GFA-VM) with few-shot finetuning and uncertainty-based active sampling, yielding significant accuracy gains for rarely observed conditions. Experiments confirm notable performance improvements over single-stage augmentation and naive oversampling. By rigorously balancing distribution realism with engineering feasibility, MSC-DGA offers a practical and theoretically grounded advancement for VM, enhancing adaptive control and product quality in next-generation power semiconductor manufacturing. © 2024 IEEE.

关键词： Computer control

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Quantifying gender imbalance in East Asian academia: Research career and citation practice

arXiv

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arXiv 2023年

作者： Nakajima, Kazuki Liu, Ruodan Shudo, Kazuyuki Masuda, Naoki Department of Mathematical and Computing Science Tokyo Institute of Technology Meguro-ku Tokyo152-8552 Japan Department of Mathematics State University of New York at Buffalo Buffalo14260 United States Academic Center for Computing and Media Studies Kyoto University Sakyo-ku Kyoto606-8501 Japan Computational and Data-Enabled Science and Engineering Program State University of New York at Buffalo Buffalo14260 United States Center for Computational Social Science Kobe University Kobe657-8501 Japan

Gender imbalance in academia has been confirmed in terms of a variety of indicators, and its magnitude often varies from country to country. Europe and North America, which cover a large fraction of research workforce in the world, have been the main geographical regions for research on gender imbalance in academia. However, the academia in East Asia, which accounts for a substantial fraction of research, may be exposed to strong gender imbalance because Asia has been facing persistent and stronger gender imbalance in society at large than Europe and North America. Here we use publication data between 1950 and 2020 to analyze gender imbalance in academia in China, Japan, and South Korea in terms of the number of researchers, their career, and citation practice. We found that, compared to the average of the other countries, gender imbalance is larger in these three East Asian countries in terms of the number of researchers and their citation practice and additionally in Japan in terms of research career. Moreover, we found that Japan has been exposed to the larger gender imbalance than China and South Korea in terms of research career and citation practice. Copyright © 2023, The Authors. All rights reserved.

关键词： Geographical regions

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