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Single-cell multi-ome regression models identify functional and disease-associated enhancers and enable chromatin potential analysis (vol 56, pg 627, 2024)

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NATURE GENETICS 2024年第6期56卷 1319-1319页

作者： Mitra, Sneha Malik, Rohan Wong, Wilfred Rahman, Afsana Hartemink, Alexander J. Pritykin, Yuri Dey, Kushal K. Leslie, Christina S. Computational and Systems Biology Program Memorial Sloan Kettering Cancer Center New York City NY USA Rye Country Day School Rye NY USA Tri-Institutional Training Program in Computational Biology and Medicine New York City NY USA Hunter College City University of New York New York City NY USA Department of Computer Science Duke University Durham NC USA Program in Computational Biology and Bioinformatics Duke University Durham NC USA Center for Genomic and Computational Biology Duke University Durham NC USA Department of Computer Science Princeton University Princeton NJ USA Lewis-Sigler Institute for Integrative Genomics Princeton University Princeton NJ USA

We present a gene-level regulatory model, single-cell ATAC + RNA linking (SCARlink), which predicts single-cell gene expression and links enhancers to target genes using multi-ome (scRNA-seq and scATAC–seq co-assay) sequencing data. The approach uses regularized Poisson regression on tile-level accessibility data to jointly model all regulatory effects at a gene locus, avoiding the limitations of pairwise gene–peak correlations and dependence on peak calling. SCARlink outperformed existing gene scoring methods for imputing gene expression from chromatin accessibility across high-coverage multi-ome datasets while giving comparable to improved performance on low-coverage datasets. Shapley value analysis on trained models identified cell-type-specific gene enhancers that are validated by promoter capture Hi-C and are 11× to 15× and 5× to 12× enriched in fine-mapped eQTLs and fine-mapped genome-wide association study (GWAS) variants, respectively. We further show that SCARlink-predicted and observed gene expression vectors provide a robust way to compute a chromatin potential vector field to enable developmental trajectory analysis.

关键词： Epigenetics Population genetics Software

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NaviSlim: Adaptive Context-Aware Navigation and Sensing via Dynamic Slimmable Networks

NaviSlim: Adaptive Context-Aware Navigation and Sensing via ...

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IEEE International Conference on Internet-of-Things Design and Implementation (IoTDI)

作者： Timothy K Johnsen Marco Levorato Computational Sciences Joint Doctoral Program University of California Irvine USA San Diego State University USA Computer Science Department University of California Irvine USA

ISBN: (数字)9798350370256

ISBN: (纸本)9798350370263

Small-scale autonomous airborne vehicles, such as micro-drones, are expected to be a central component of a broad spectrum of applications ranging from exploration to surveillance and delivery. This class of vehicles is characterized by severe constraints in computing power and energy reservoir, which impairs their ability to support the complex state-of-the-art neural models needed for autonomous operations. The main contribution of this paper is a new class of neural navigation models – NaviSlim – capable of adapting the amount of resources spent on computing and sensing in response to the current context (i.e., difficulty of the environment, current trajectory, and navigation goals). Specifically, NaviSlim is designed as a gated slimmable neural network architecture that, different from existing slimmable networks, can dynamically select a slimming factor to autonomously scale model complexity, which consequently optimizes execution time and energy consumption. Moreover, different from existing sensor fusion approaches, NaviSlim can dynamically select power levels of onboard sensors to autonomously reduce power and time spent during sensor acquisition, without the need to switch between different neural networks. By means of extensive training and testing on the robust simulation environment Microsoft AirSim, we evaluate our NaviSlim models on scenarios with varying difficulty and a test set that showed a dynamic reduced model complexity on average between 57-92%, and between 61-80% sensor utilization, as compared to static neural networks designed to match computing and sensing of that required by the most difficult scenario.

关键词： Training Adaptation models Navigation computational modeling Atmospheric modeling Neural networks Dynamic scheduling

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Mass transport in a highly immiscible alloy on extended shear deformation

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Journal of Materials science & Technology 2023年第3期134卷 197-208页

作者： Miao Song Jia Liu Xiaolong Ma Qin Pang Matthew J.Olszta Joshua Silverstein Madhusudhan R.Pallaka Peter V.Sushko Suveen N.Mathaudhu Cynthia Powell Arun Devaraj Bharat Gwalani Physical and Computational Sciences Directorate Pacific Northwest National Laboratory902 Battelle BoulevardRichlandWA 99354USA Energy and Environmental Directorate Pacific Northwest National Laboratory902 Battelle BoulevardRichlandWA 99354USA Material Science and Engineering Program University of CaliforniaRiversideCA92521USA Colorado School of Mines 1500 Illinois St.GoldenCO 8040USA Department of Materials Science and Engineering North Carolina State UniversityRaleighNC27695-7907USA State Key Laboratory of Powder Metallurgy Central South Uni-versityChangsha 410083China

Forced mixing to a single-phase or supersaturated solid solution(SSS)and its prerequisite microstructure evolution in immiscible systems has been a focus of research for fundamental science and practical *** the formation of SSS by shear deformation could enable a material design beyond conventional equilibrium microstructure in immiscible ***,a highly immiscible Cu-50 at.%Cr binary alloy(mixing enthalpy of∼20 kJ mol^(−1))was employed to investigate the microstructure evolution and localized tendencies of SSS during severe shear *** results demonstrate the dislocation mediated microstructural refinement process in each phase of the binary alloy and the mechanisms associated with localized solute supersaturation as a function of shear *** grain refinement in the softer Cu phase occurs owing to the strain localization driving the preferential dynamic *** grain refinement of the Cr phase,however,is enabled by the progressive evolution of grain lamination,splitting,and fragmentation as a function of shear *** solute supersaturation is found to be strongly dependent on the local environments that affect the dislocation activity,including the level of microstructure refinement,the interfacial orientation relationship,the mechanical incompatibility,and the localized preferential phase *** initio simulations confirm that it is more favorable to oxidize Cr than Cu at incoherent Cu/Cr interfaces,limiting the mass transport on an incoherent *** results unveil the mechanism underpinning the non-equilibrium mass transport in immiscible systems upon severe deformation that can be applied to produce immiscible alloys with superior mechanical properties.

关键词： Tribology Immiscible alloys Nanostructures Shear deformation Forced mixing Atom probe

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Effect of a pulsating flow on hydrodynamics and fluid catalytic cracking chemical reaction in a circulating fluidized bed riser

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Particuology 2022年第8期20卷 47-56页

作者： Pilaiwan Chaiwang Hannarong Chitcharoenyoo Pornpote Piumsomboon Benjapon Chalermsinsuwan Fuels Rsearch Centerpartment of Chemical Tchnology Faculty of Science Chulalongkon University 254 Phyathai RadWangmaiPathumwan Bangkok 10330Thailand Program in Petrochemistry and Polymer Science Faculty of ScienceChulalongkorn University.254 Phyathai Road WangmaiPathumwanBangok 10330Thailand Centero Eellenceon Perochemicaland Materials Techology Chulalongorn Universy 254 Phyathai Road WangmaiathumwanBangkok 10330.Thailand Advanced Computational Fuidynamics Research Unit Chulalongkom Universy254 Phyathai RoadWangmai Pathumwan Bangkok 10330Thailand

The three-dimensional computational fuid dynamics(3D-CFD)of a pulsating flow applied to the fluid catalytic cracking(FCC)reaction was investigated in the riser of a circulating fluidized bed *** kinetic parameters of the FCC and coke burning reactions for predicting the reactant conversion and product yield percentages were *** increase the reactant conversion level and product *** effect of the pulsating flow operating parameters was considered using a 2k statistical experimental design with four factors(amplitude,frequency,types of the waveform,and amplitude ratio).The 3DCFD simulation was successfully validated from the experimental literature *** frequency and type of the waveform were found to be the significant operating *** expression of the fitted regression model and response surface contour were derived and revealed that the pulsating flow provides a higher reactant conversion level and product yield percentages compared to a non-pulsating or steady flow.

关键词： Fluidcatalytic cracking Circulating fluidized bed riser computationalfluid dynamics Pulsating Statistical experimental design

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A Flow Artist for High-Dimensional Cellular Data 33

A Flow Artist for High-Dimensional Cellular Data

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33rd IEEE International Workshop on Machine Learning for Signal Processing, MLSP 2023

作者： MacDonald, Kincaid Bhaskar, Dhananjay Thampakkul, Guy Nguyen, Nhi Zhang, Joia Perlmutter, Michael Adelstein, Ian Krishnaswamy, Smita Yale University Department of Mathematics United States Pomona College Department of Mathematics United States University of Washington Department of Statistics United States Boise State University Department of Mathematics United States Yale University Department of Computer Science United States Yale University Applied Mathematics Program United States Yale University Computational Biology and Bioinformatics Program United States

ISBN: (纸本)9798350324112

We consider the problem of embedding point cloud data sampled from an underlying manifold with an associated flow or velocity. Such data arises in many contexts where static snapshots of dynamic entities are measured, including in high-throughput biology such as single-cell transcriptomics. Existing embedding techniques either do not utilize velocity information or embed the coordinates and velocities independently, i.e., they either impose velocities on top of an existing point embedding or embed points within a prescribed vector field. Here we present FlowArtist, a neural network that embeds points while jointly learning a vector field around the points. The combination allows FlowArtist to better separate and visualize velocity-informed structures. Our results, on toy datasets and single-cell RNA velocity data, illustrate the value of utilizing coordinate and velocity information in tandem for embedding and visualizing high-dimensional data. © 2023 IEEE.

关键词： RNA

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Unbiased Parameter Estimation for Partially Observed Diffusions

arXiv

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arXiv 2023年

作者： Awadelkarim, Elsiddig Jasra, Ajay Ruzayqat, Hamza Applied Mathematics and Computational Science Program Computer Electrical and Mathematical Sciences and Engineering Division King Abdullah University of Science and Technology Thuwal23955-6900 Saudi Arabia

In this article we consider the estimation of static parameters for partially observed diffusion process with discrete-time observations over a fixed time interval. In particular, we assume that one must time-discretize the partially observed diffusion process and work with the model with bias and consider maximizing the resulting log-likelihood. Using a novel double randomization scheme, based upon Markovian stochastic approximation we develop a new method to unbiasedly estimate the static parameters, that is, to obtain the maximum likelihood estimator with no time discretization bias. Under assumptions we prove that our estimator is unbiased and investigate the method in several numerical examples, showing that it can empirically out-perform existing unbiased *** Codes 60J22, 62M05, 65C40, 62M20 © 2023, CC BY.

关键词： Parameter estimation

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Molecular architecture of mammalian pyruvate dehydrogenase complex

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Protein & Cell 2025年第1期16卷 72-78页

作者： Maofei Chen Yutong Song Sensen Zhang Yitang Zhang Xudong Chen Minghui Zhang Meng Han Xin Gao Sai Li Maojun Yang Tsinghua-Peking Center for Life Sciences Beijing Frontier Research Center for Biological StructureSchool of Life SciencesTsinghua UniversityBeijing 100084China Ministry of Education Key Laboratory of Protein Science Tsinghua UniversityBeijing 100084China State Key Laboratory of Membrane Biology Tsinghua UniversityBeijing 100084China Department of Biochemistry and Molecular Biology School of Basic Medical SciencesShenzhen University Health Science CenterShenzhen 518060China Protein Research Technology Center Protein Chemistry and Omics PlatformSchool of Life SciencesTsinghua UniversityBeijing 100084China Computer Science Program ComputerElectrical and Mathematical Sciences and Engineering DivisionKing Abdullah University of Science and Technology(KAUST)Thuwal 23955-6900Kingdom of Saudi Arabia Computational Bioscience Research Center King Abdullah University of Science and TechnologyThuwal 23955-6900Kingdom of Saudi Arabia Cryo-EM Facility Center Southern University of Science and TechnologyShenzhen 518055China Beijing Life Science Academy Beijing 102209China

Dear Editor,Pyruvate dehydrogenase complex(PDHc) is a large multienzyme assembly(Mr = 4–10 million Daltons) consisting of three essential components: pyruvate dehydrogenase(E1p), dihydrolipoyl transacetylase(E2p), and dihydrolipoyl dehydrogenase(E3). These three enzymes perform distinct functions sequentially to catalyze the oxidative decarboxylation of pyruvate with formation of nicotinamide adenine dinucleotide(NADH) and acetyl-coenzyme A(Patel and Roche, 1990).

关键词： sequentially oxidative Dalton

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Rationally designed antimicrobial peptides with high selectivity and efficiency against phytopathogenic Ralstonia solanecearum

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science of the Total Environment 2025年 976卷 179354页

作者： Manik, Melvalia Cristin Darai, Nitchakan Rungrotmongkol, Thanyada Duan, Lian Harada, Ryuhei Shigeta, Yasuteru Hengphasatporn, Kowit Vangnai, Alisa S. Biotechnology Program Faculty of Science Chulalongkorn University Bangkok10330 Thailand Futuristic Science Research Center School of Science Walailak University Nakhon Si Thammarat80160 Thailand Drug and Cosmetics Excellence Center Walailak University Thasala Nakhon Si Thammarat80160 Thailand Program in Bioinformatics and Computational Biology Chulalongkorn University Bangkok10330 Thailand Center for Computational Sciences University of Tsukuba 1-1-1 Tennodai Ibaraki Tsukuba305-8577 Japan Center of Excellence in Biocatalyst and Sustainable Biotechnology Faculty of Science Chulalongkorn University Bangkok10330 Thailand Department of Biochemistry Faculty of Science Chulalongkorn University Bangkok10330 Thailand

Ralstonia solanacearum, the causative agent of bacterial wilt, poses a global threat to agriculture, necessitating urgent and sustainable solutions as traditional methods lose efficacy. This study developed WRF-13, a synthetic antimicrobial peptide (AMP) designed to mimic natural AMPs, exhibiting potent antibacterial and anti-biofilm activity with high specificity against R. solanacearum. Mechanistic studies, including microscopy and computational analyses, demonstrated that WRF-13 disrupts the bacterial membrane. WRF-13 remained stable across a wide pH (5–8) and temperature (25–50 °C) range, essential for field applications, and showed no detectable toxicity to mammalian or plant cells at elevated concentrations. Greenhouse trials confirmed its efficacy in reducing bacterial wilt severity up to 65 %, highlighting its potential to protect crops from R. solanacearum infection. Overall, this study highlights WRF-13 as a targeted solution for managing bacterial wilt and advancing sustainable agriculture. © 2025 Elsevier B.V.

关键词： Antimicrobial peptides Bacterial wilt Crop protection In silico-peptide design Ralstonia solanacearum

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Multilevel Particle Filters for Partially Observed McKean-Vlasov Stochastic Differential Equations

arXiv

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arXiv 2024年

作者： Awadelkarim, Elsiddig Jasra, Ajay Applied Mathematics and Computational Science Program Computer Electrical and Mathematical Sciences and Engineering Division King Abdullah University of Science and Technology Thuwal23955-6900 Saudi Arabia School of Data Science The Chinese University of Hong Kong Shenzhen China

In this paper we consider the filtering problem associated to partially observed McKean-Vlasov stochastic differential equations (SDEs). The model consists of data that are observed at regular and discrete times and the objective is to compute the conditional expectation of (functionals) of the solutions of the SDE at the current time. This problem, even the ordinary SDE case is challenging and requires numerical approximations. Based upon the ideas in [3, 12] we develop a new particle filter (PF) and multilevel particle filter (MLPF) to approximate the afore-mentioned expectations. We prove under assumptions that, for ϵ > 0, to obtain a mean square error of O(ϵ2) the PF has a cost per-observation time of O(ϵ−5) and the MLPF costs O(ϵ−4) (best case) or O(ϵ−4 log(ϵ)2) (worst case). Our theoretical results are supported by numerical experiments. © 2024, CC BY.

关键词： Mean square error

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Implementation of contact line motion based on the phase-field lattice Boltzmann method

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Physical Review E 2024年第4期109卷 045307-045307页

作者： Long Ju Zhaoli Guo Bicheng Yan Shuyu Sun Computational Transport Phenomena Laboratory (CTPL) King Abdullah University of Science and Technology (KAUST) Thuwal 23955-6900 Kingdom of Saudi Arabia Institute of Interdisciplinary Research for Mathematics and Applied Science Huazhong University of Science and Technology Wuhan 430074 China Energy Resource and Petroleum Engineering Program Physical Science and Engineering Division King Abdullah University of Science and Technology (KAUST) Thuwal 23955-6900 Kingdom of Saudi Arabia

This paper proposes a strategy to implement the free-energy-based wetting boundary condition within the phase-field lattice Boltzmann method. The greatest advantage of the proposed method is that the implementation of contact line motion can be significantly simplified while still maintaining good accuracy. For this purpose, the liquid-solid free energy is treated as a part of the chemical potential instead of the boundary condition, thus avoiding complicated interpolations with irregular geometries. Several numerical testing cases, including droplet spreading processes on the idea flat, inclined, and curved boundaries, are conducted, and the results demonstrate that the proposed method has good ability and satisfactory accuracy to simulate contact line motions.

关键词： Contact line dynamics Wetting Lattice-Boltzmann methods

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