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Molecular profiling of adult C. elegans glia across sexes by single-nuclear RNA-seq

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Developmental cell 2025年

作者： Maria D Purice Elgene J A Quitevis R Sean Manning Liza J Severs Nina-Tuyen Tran Violet Sorrentino Connor Finkbeiner Feinan Wu Michael Zager Manu Setty Aakanksha Singhvi Division of Basic Sciences Fred Hutchinson Cancer Center Seattle WA 98109 USA. Division of Basic Sciences Fred Hutchinson Cancer Center Seattle WA 98109 USA Herbold Computational Biology Program Public Health Sciences Division Fred Hutchinson Cancer Center Seattle WA 98109 USA. Molecular and Cell Biology Graduate Program Fred Hutchinson Cancer Center and University of Washington Seattle WA 98109 USA. Herbold Computational Biology Program Public Health Sciences Division Fred Hutchinson Cancer Center Seattle WA 98109 USA Department of Genome Sciences University of Washington Seattle WA 98109 USA. Genomics and Bioinformatics Shared Resource Fred Hutchinson Cancer Center Seattle WA 98109 USA. Data Visualization Core Fred Hutchinson Cancer Center Seattle WA 98109 USA. Translational Data Science IRC Fred Hutchinson Cancer Center Seattle WA 98109 USA. Electronic address: msetty@***. Department of Neurobiology and Biophysics University of Washington School of Medicine Seattle WA 98195 USA. Electronic address: asinghvi@***.

A comprehensive understanding of nervous system function requires molecular insight into the diversity and sex dimorphism of both its component cell types, glia and neurons. Here, we present a single-nuclear RNA sequencing (RNA-seq) census of all neuroectoderm-derived glia in the adult C. elegans nervous system, across sexes. By iteratively coupling computational modeling and custom analytics with in vivo validations, we uncovered molecular markers for all glia, as well as class-specific and pan-glial molecular signatures. These identified that each glia is functionally heterogeneous across the nervous system and variably sex dimorphic between sexes. Thus, this glial transcriptome (***) offers deep mechanistic insights into glial biology brain wide. Complementing the existing C. elegans neuronal transcriptome and mapped connectome, it also enables single-cell and molecular resolution insight into the entire nervous system of an adult metazoan.

关键词： C. elegans glia cell-type classification cellular heterogeneity dense core vesicles glia glial transcriptome sexual dimorphism snRNA-seq

Homoharringtonine as a PHGDH inhibitor: Unraveling metabolic dependencies and developing a potent therapeutic strategy for high-risk neuroblastoma

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Biomedicine and Pharmacotherapy 2023年 166卷 115429-115429页

作者： Hsieh, Chiao-Hui Huang, Chen-Tsung Cheng, Yi-Sheng Hsu, Chun-Hua Hsu, Wen-Ming Chung, Yun-Hsien Liu, Yen-Lin Yang, Tsai-Shan Chien, Chia-Yu Lee, Yu-Hsuan Huang, Hsuan-Cheng Juan, Hsueh-Fen Department of Life Science National Taiwan University Taipei Taiwan Center for Computational and Systems Biology National Taiwan University Taipei Taiwan Graduate Institute of Biomedical Electronics and Bioinformatics National Taiwan University Taipei Taiwan Institute of Plant Biology National Taiwan University Taipei Taiwan Genome and Systems Biology Degree Program National Taiwan University and Academia Sinica Taipei Taiwan Department of Agricultural Chemistry National Taiwan University Taipei Taiwan Department of Surgery National Taiwan University Hospital and National Taiwan University College of Medicine Taipei Taiwan Department of Pediatrics School of Medicine College of Medicine Taipei Medical University Taipei Taiwan Institute of Biomedical Informatics National Yang Ming Chiao Tung University Taipei Taiwan Center for Advanced Computing and Imaging in Biomedicine Taipei Taiwan

Neuroblastoma, a childhood cancer affecting the sympathetic nervous system, continues to challenge the development of potent treatments due to the limited availability of druggable targets for this aggressive illness. Recent investigations have uncovered that phosphoglycerate dehydrogenase (PHGDH), an essential enzyme for de novo serine synthesis, serves as a non-oncogene dependency in high-risk neuroblastoma. In this study, we show that homoharringtonine (HHT) acts as a PHGDH inhibitor, inducing intricate alterations in cellular metabolism, and thus providing an efficient treatment for neuroblastoma. We have experimentally verified the reliance of neuroblastoma on PHGDH and employed molecular docking, thermodynamic evaluations, and X-ray crystallography techniques to determine the bond interactions between HHT and PHGDH. Administering HHT to treat neuroblastoma resulted in effective cell elimination in vitro and tumor reduction in vivo. Metabolite and functional assessments additionally disclosed that HHT treatment suppressed de novo serine synthesis, initiating intricate metabolic reconfiguration and oxidative stress in neuroblastoma. Collectively, these discoveries highlight the potential of targeting PHGDH using HHT as a potent approach for managing high-risk neuroblastoma. © 2023 The Authors

关键词： computational molecular docking Drug discovery High-risk neuroblastoma Metabolic reprogramming Molecular target therapy Phosphoglycerate dehydrogenase

DeePMD-kit v2: A software package for Deep Potential models

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arXiv 2023年

作者： Zeng, Jinzhe Zhang, Duo Lu, Denghui Mo, Pinghui Li, Zeyu Chen, Yixiao Rynik, Marián Huang, Li'ang Li, Ziyao Shi, Shaochen Wang, Yingze Ye, Haotian Tuo, Ping Yang, Jiabin Ding, Ye Li, Yifan Tisi, Davide Zeng, Qiyu Bao, Han Xia, Yu Huang, Jiameng Muraoka, Koki Wang, Yibo Chang, Junhan Yuan, Fengbo Bore, Sigbjørn Løland Cai, Chun Lin, Yinnian Wang, Bo Xu, Jiayan Zhu, Jia-Xin Luo, Chenxing Zhang, Yuzhi Goodall, Rhys E.A. Liang, Wenshuo Singh, Anurag Kumar Yao, Sikai Zhang, Jingchao Wentzcovitch, Renata Han, Jiequn Liu, Jie Jia, Weile York, Darrin M. Weinan, E. Car, Roberto Zhang, Linfeng Wang, Han Laboratory for Biomolecular Simulation Research Institute for Quantitative Biomedicine Department of Chemistry and Chemical Biology Rutgers University PiscatawayNJ08854 United States AI for Science Institute Beijing100080 China DP Technology Beijing100080 China Academy for Advanced Interdisciplinary Studies Peking University Beijing100871 China HEDPS CAPT College of Engineering Peking University Beijing100871 China College of Electrical and Information Engineering Hunan University Changsha China Yuanpei College Peking University Beijing100871 China Program in Applied and Computational Mathematics Princeton University PrincetonNJ08540 United States Department of Experimental Physics Comenius University Mlynská Dolina F2 Bratislava842 48 Slovakia Center for Quantum Information Institute for Interdisciplinary Information Sciences Tsinghua University Beijing100084 China Center for Data Science Peking University Beijing100871 China ByteDance Research Zhonghang Plaza No. 43 North 3rd Ring West Road Haidian District Beijing China College of Chemistry and Molecular Engineering Peking University Beijing100871 China Baidu Inc. Beijing China Key Laboratory of Structural Biology of Zhejiang Province School of Life Sciences Westlake University Zhejiang Hangzhou China Westlake AI Therapeutics Lab Westlake Laboratory of Life Sciences and Biomedicine Zhejiang Hangzhou China Department of Chemistry Princeton University PrincetonNJ08544 United States SISSA Scuola Internazionale Superiore di Studi Avanzati Trieste34136 Italy Laboratory of Computational Science and Modeling Institute of Materials École Polytechnique Fédérale de Lausanne Lausanne1015 Switzerland Department of Physics National University of Defense Technology Hunan Changsha410073 China State Key Lab of Processors Institute of Computing Technology Chinese Academy of Sciences Beijing China University of Chinese Academy of Sciences Beijing China School of Electronics Engineerin

DeePMD-kit is a powerful open-source software package that facilitates molecular dynamics simulations using machine learning potentials (MLP) known as Deep Potential (DP) models. This package, which was released in 2017, has been widely used in the fields of physics, chemistry, biology, and material science for studying atomistic systems. The current version of DeePMD-kit offers numerous advanced features such as DeepPot-SE, attention-based and hybrid descriptors, the ability to fit tensile properties, type embedding, model deviation, Deep Potential - Range Correction (DPRc), Deep Potential Long Range (DPLR), GPU support for customized operators, model compression, non-von Neumann molecular dynamics (NVNMD), and improved usability, including documentation, compiled binary packages, graphical user interfaces (GUI), and application programming interfaces (API). This article presents an overview of the current major version of the DeePMD-kit package, highlighting its features and technical details. Additionally, the article benchmarks the accuracy and efficiency of different models and discusses ongoing developments. © 2023, CC BY-NC-ND.

关键词： Molecular dynamics

Theoretical study on adsorption and reaction of polymeric formic acid on the Cu(111) surface

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Physical Review Materials 2021年第7期5卷 075801-075801页

作者： Septia Eka Marsha Putra Fahdzi Muttaqien Yuji Hamamoto Kouji Inagaki Akitoshi Shiotari Jun Yoshinobu Yoshitada Morikawa Ikutaro Hamada Department of Precision Engineering Graduate School of Engineering Osaka University 2-1 Yamada-oka Suita Osaka 565-0871 Japan Department of Engineering Physics Institut Teknologi Sumatera Jalan Terusan Ryacudu Way Hui Jati Agung South Lampung 35365 Indonesia Instrumentation and Computational Physics Research Group Faculty of Mathematics and Natural Sciences Institut Teknologi Bandung Jalan Ganesha 10 Bandung West Java 40132 Indonesia Master Program in Computational Science Faculty of Mathematics and Natural Sciences Institut Teknologi Bandung Jalan Ganesha 10 Bandung West Java 40132 Indonesia Elements Strategy Initiative for Catalysts and Batteries (ESICB) Kyoto University Goryo-Ohara Nishikyou-ku Katsura Kyoto 615-8245 Japan Department of Advanced Materials Science The University of Tokyo 5-1-5 Kashiwanoha Kashiwa Chiba 277-8561 Japan The Institute for Solid State Physics The University of Tokyo 5-1-5 Kashiwanoha Kashiwa Chiba 277-8581 Japan Research Center for Precision Engineering Graduate School of Engineering Osaka University 2-1 Yamada-oka Suita Osaka 565-0871 Japan

We investigate the polymeric adsorption of formic acid (HCOOH) on the Cu(111) surface by means of density functional theory. We present structural models for the polymeric form of HCOOH on Cu(111) and characterize their stability, electronic, and vibrational properties. Based on the energetics and dynamics, as well as simulated scanning tunneling microscopy and atomic force microscopy images, we propose that the α polymorph is likely to be formed on the Cu(111) surface and can explain the experimental findings. We also study the initial step of the catalytic dehydrogenation of HCOOH and find that the O-H bond dissociation at the edge of the polymer is facilitated, rather than that forming hydrogen bonding, agreeing well with the experiments.

关键词： Adsorption Chemical bonding Chemical kinetics, dynamics & catalysis Electronic structure Surface & interfacial phenomena Surfaces Density functional theory First-principles calculations

Effective Elastic Wave Characteristics of Composite Media

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arXiv 2020年

作者： Kim, Jaeuk Torquato, S. Department of Physics Princeton University PrincetonNJ08544 United States Department of Chemistry Princeton University PrincetonNJ08544 United States Princeton Institute for the Science and Technology of Materials Princeton University PrincetonNJ08544 United States Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States

We derive exact expressions for effective elastodynamic properties of two-phase composites in the long-wavelength (quasistatic) regime via homogenized constitutive relations that are local in space. This is accomplished by extending the "strong-contrast" expansion formalism that was previously applied to the static problem. These strong-contrast expansions explicitly incorporate complete microstructural information of the composite via an infinite set of n-point correlation functions. Utilizing the rapid-convergence properties of these series expansions (even for extreme contrast ratios), we extract accurate approximations that depend on the microstructure via the spectral density, which is easy to compute or measure for any composite. We also investigate the predictive power of modifications of such approximation formulas postulated elsewhere [J. Kim and S. Torquato, Proc. Nat. Acad. Sci. 117, 8764 (2020)] to extend their applicability beyond the quasistatic regime. The accuracy of these nonlocal microstructure-dependent approximations is validated by comparison to full-waveform simulation results for certain models of dispersions. We apply our formulas to a variety of models of nonhyperuniform and hyperuniform disordered composites. We demonstrate that hyperuniform systems are less lossy than their nonhyperuniform counterparts in the quasistatic regime, and stealthy hyperuniform media can be perfectly transparent for a wide range of wavenumbers. Finally, we discuss how to utilize our approximations for engineering composites with prescribed elastic wave characteristics. Copyright © 2020, The Authors. All rights reserved.

关键词： Microstructure

Concurrency measures in the era of temporal network epidemiology: A review

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arXiv 2020年

作者： Masuda, Naoki Miller, Joel C. Holme, Petter Department of Mathematics State University of New York Buffalo United States Computational and Data-Enabled Science and Engineering Program State University of New York Buffalo United States School of Engineering and Mathematical Sciences La Trobe University Australia Institute of Innovative Research Tokyo Institute of Technology Yokohama226-8503 Japan

Diseases spread over temporal networks of interaction events between individuals. Structures of these temporal networks hold the keys to understanding epidemic propagation. One early concept of the literature to aid in discussing these structures is concurrency-quantifying individuals' tendency to form time-overlapping "partnerships". Although conflicting evaluations and an overabundance of operational definitions have marred the history of concurrency, it remains important, especially in the area of sexually transmitted infections. Today, much of theoretical epidemiology uses more direct models of contact patterns, and there is an emerging body of literature trying to connect methods to the concurrency literature. In this review, we will cover the development of the concept of concurrency and these new approaches. © 2020, CC BY.

关键词： Epidemiology

Quantum phase transitions in long-range interacting hyperuniform spin chains in a transverse field

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arXiv 2020年

作者： Bose, Amartya Torquato, Salvatore Department of Chemistry Princeton University PrincetonNJ08544 United States Department of Physics Princeton University PrincetonNJ08544 United States Princeton Institute for the Science and Technology of Materials Princeton University PrincetonNJ08544 United States Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States

Hyperuniform states of matter are characterized by anomalous suppression of long-wavelength density fluctuations. While most of the interesting cases of disordered hyperuniformity are provided by complex many-body systems like liquids or amorphous solids, classical spin chains with certain long-range interactions have been shown to demonstrate the same phenomenon. Such systems involving spin chains are ideal models for exploring the effects of quantum mechanics on hyperuniformity. It is well-known that the transverse field Ising model shows a quantum phase transition (QPT) at zero temperature. Under the quantum effects of a transverse magnetic field, classical hyperuniform spin chains are expected to lose their hyperuniformity. High-precision simulations of these cases are complicated because of the presence of highly nontrivial long-range interactions. We perform extensive analysis of these systems using density matrix renormalization group (DMRG) to study the possibilities of phase transitions and the mechanism by which they lose hyperuniformity. Even for a spin chain of length 30, we see discontinuous changes in properties like the "τ order metric" of the ground state, the measure of hyperuniformity and the second cumulant of the total magnetization along the x-direction, all suggestive of first-order QPTs. An interesting feature of the phase transitions in these disordered hyperuniform spin chains is that, depending on the parameter values, the presence of transverse magnetic field may remarkably lead to increase in the order of the ground state as measured by the "τ order metric," even if hyperuniformity is lost. Therefore, it would be possible to design materials to target specific novel quantum behaviors in the presence of a transverse magnetic field. Our numerical investigations suggest that these spin chains can show no more than two QPTs. We further analyze the long-range interacting spin chains via the Jordan-Wigner mapping on to a system of spinless ferm

关键词： Phase transitions

Characterizing the hyperuniformity of ordered and disordered two-phase media

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arXiv 2020年

作者： Kim, Jaeuk Torquato, Salvatore Department of Physics Princeton University PrincetonNJ08544 United States Department of Chemistry Princeton University PrincetonNJ08544 United States Princeton Institute for the Science and Technology of Materials Princeton University PrincetonNJ08544 United States Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States

The hyperuniformity concept provides a unified means to classify all perfect crystals, perfect quasicrystals, and exotic amorphous states of matter according to their capacity to suppress large-scale density fluctuations. While the classification of hyperuniform point configurations has received considerable attention, much less is known about the classification of hyperuniform heterogeneous two-phase media, which include composites, porous media, foams, cellular solids, colloidal suspensions and polymer blends. The purpose of this article is to begin such a program for certain two-dimensional models of hyperuniform two-phase media by ascertaining their local volume-fraction variances σV2 (R) and the associated hyperuniformity order metrics BV . This is a highly challenging task because the geometries and topologies of the phases are generally much richer and more complex than point-configuration arrangements and one must ascertain a broadly applicable length scale to make key quantities dimensionless. Therefore, we purposely restrict ourselves to a certain class of two-dimensional periodic cellular networks as well as periodic and disordered/irregular packings, some of which maximize their effective transport and elastic properties. Among the cellular networks considered, the honeycomb networks have the minimal value of the hyperuniformity order metrics BV across all volume fractions. On the other hand, among all packings considered, the triangular-lattice packings have the smallest values of BV for the possible range of volume fractions. Among all structures studied here, the triangular-lattice packing has the minimal order metric for almost all volume fractions. Our study provides a theoretical foundation for the establishment of hyperuniformity order metrics for general two-phase media and a basis to discover new hyperuniform two-phase systems by inverse design procedures. Copyright © 2020, The Authors. All rights reserved.

关键词： Wireless networks

Nonlocal effective electromagnetic wave characteristics of composite media: Beyond the quasistatic regime

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arXiv 2020年

作者： Torquato, Salvatore Kim, Jaeuk Department of Physics Princeton University PrincetonNJ08544 United States Department of Chemistry Princeton University PrincetonNJ08544 United States Princeton Institute Science and Technology of Materials Princeton University PrincetonNJ08544 United States Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States

We derive exact nonlocal homogenized constitutive relations for the effective electromagnetic wave properties of disordered two-phase composites and metamaterials from first principles. This exact formalism enables us to extend the long-wavelength limitations of conventional homogenization estimates of the effective dynamic dielectric constant tensor Εe(kI, ω) for arbitrary microstructures so that it can capture spatial dispersion well beyond the quasistatic regime (where ω and kI are the frequency and wave vector of the incident radiation). We accomplish this task by deriving nonlocal strong-contrast expansions that exactly account for complete microstructural information (infinite set of n-point correlation functions) and hence multiple scattering to all orders for the range of wave numbers for which our extended homogenization theory applies, i.e., 0 ≤ |kI|. 1 (where is a characteristic heterogeneity length scale). Because of the fast-convergence properties of such expansions, their lower-order truncations yield accurate closed-form approximate formulas for Εe(kI, ω) that apply for a wide class of microstructures. These nonlocal formulas are resummed representations of the strong-contrast expansions that still accurately capture multiple scattering to all orders via the microstructural information embodied in the spectral density, which is easy to compute for any composite. The accuracy of these microstructure-dependent approximations is validated by comparison to full-waveform simulation computations for both 2D and 3D ordered and disordered models of composite media. Thus, our closed-form formulas enable one to predict accurately and efficiently the effective wave characteristics well beyond the quasistatic regime for a wide class of composite microstructures without having to perform full-blown simulations. We find that disordered hyperuniform media are generally less lossy than their nonhyperuniform counterparts. We also show that certain disordered hyperunif

关键词： Microstructure