ACS Publications最新文献_第3页

Aird-MSI: A High Compression Rate and Decompression Speed Format for Mass Spectrometry Imaging Data. Aird-MSI：质谱成像数据的高压缩率和解压速度格式。

IF 3.6 2区生物学

Journal of Proteome Research Pub Date : 2025-10-17 DOI: 10.1021/acs.jproteome.5c00423

Shuochao Li, Hongping Sheng, Pengyuan Du, Jingying Chen, Xixi Wang, Junjie Tong, Jiahua Hong, Xiaohan Jing, Miaoshan Lu, Changbin Yu

{"title":"Aird-MSI: A High Compression Rate and Decompression Speed Format for Mass Spectrometry Imaging Data.","authors":"Shuochao Li, Hongping Sheng, Pengyuan Du, Jingying Chen, Xixi Wang, Junjie Tong, Jiahua Hong, Xiaohan Jing, Miaoshan Lu, Changbin Yu","doi":"10.1021/acs.jproteome.5c00423","DOIUrl":"https://doi.org/10.1021/acs.jproteome.5c00423","url":null,"abstract":"Mass spectrometry imaging has emerged as a pivotal tool in spatial metabolomics, yet its reliance on the imzML format poses critical challenges in data storage, transmission, and computational efficiency. While imzML ensures cross-platform compatibility, its lower compressed binary architecture results in large file sizes and high parsing overhead, hindering cloud-based analysis and real-time visualization. This study introduces an enhanced Aird compression format optimized for spatial metabolomics through two innovations: (1) a dynamic combinatorial compression algorithm for integer-based encoding of m/z and intensity data; (2) a coordinate-separation storage strategy for rapid spatial indexing. Experimental validation on 47 public data sets demonstrated significant performance gains. Compared to imzML, Aird achieved a 70% reduction in storage footprint (mean compression ratio: 30.89%) while maintaining near-lossless data precision (F1-score = 99.75% at 0.1 ppm m/z tolerance). For high-precision-controlled data sets, Aird accelerated loading speeds by 13-fold in MZmine. The Aird format overcomes crucial bottlenecks in spatial metabolomics by harmonizing storage efficiency, computational speed, and analytical precision, reducing I/O latency for large cohorts. By achieving near-native feature detection accuracy, Aird establishes a robust infrastructure for translational applications, including disease biomarker discovery and pharmacokinetic imaging.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145311986","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Uncrosslinked Thermoresponsive Hybrid Magnetic Nanospheres Directly Prepared from Poly(N-isopropylacrylamide) that Behave as Heating Rate Nanosensors. 由聚n -异丙基丙烯酰胺直接制备的热响应性非交联杂化磁性纳米球作为加热速率纳米传感器。

IF 5.4 2区化学

Biomacromolecules Pub Date : 2025-10-17 DOI: 10.1021/acs.biomac.5c01603

María García-Maestre, Laura Cervera-Gabalda, Eva Natividad

{"title":"Uncrosslinked Thermoresponsive Hybrid Magnetic Nanospheres Directly Prepared from Poly(N-isopropylacrylamide) that Behave as Heating Rate Nanosensors.","authors":"María García-Maestre, Laura Cervera-Gabalda, Eva Natividad","doi":"10.1021/acs.biomac.5c01603","DOIUrl":"https://doi.org/10.1021/acs.biomac.5c01603","url":null,"abstract":"Poly(N-isopropylacrylamide) (PNIPAM) provides thermoresponsiveness to nanoobjects containing magnetic/plasmonic nanoparticles (NPs) for biosensing and biomedicine. Conjugation methods include the grafting of PNIPAM onto NPs or the embedding of NPs in PNIPAM nanogels. Nanoobjects are often obtained simultaneously with monomer (NIPAM) polymerization, and the cytotoxicity of unreacted NIPAM represents a non-negligible concern. Herein, a facile and versatile miniemulsion method employing already polymerized PNIPAM is developed. Miniemulsion is achieved through PNIPAM globulization above the lower critical solution temperature (LCST) and stabilized by poly(vinyl alcohol) (PVA). Aqueous decants, obtained after solvent evaporation, contain thermoresponsive nanospheres with PNIPAM/PVA blends, stable in water for months, monomodal in size at high magnetic NP contents, biocompatible and with hyperthermia capability. Unlike the shrinking/swelling displayed by PNIPAM-based nanogels, these uncrosslinked nanospheres disintegrate/rebuild, with a size after disintegration undoubtedly related to their heating rate across LCST, behaving as unprecedented dual hyperthermia agents and heating rate nanosensors without further sensing molecules.","PeriodicalId":30,"journal":{"name":"Biomacromolecules","volume":" ","pages":""},"PeriodicalIF":5.4,"publicationDate":"2025-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145306338","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Assaying the Gel Cell Size through Fluorescence Anisotropy Measurements. 通过荧光各向异性测量测定凝胶细胞大小。

IF 2.9 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-10-17 DOI: 10.1021/acs.jpcb.5c04744

Yurii B Tsaplev, Ivan D Burtsev, Aleksei V Trofimov

引用次数: 0

Naringenin-Loaded Core-Shell Mg-MOF Nanocomposite Integrated Injectable Hydrogel for Bone Regeneration: Anti-inflammatory, Osteogenic, and Angiogenic. 负载柚皮素核-壳Mg-MOF纳米复合材料集成可注射水凝胶用于骨再生：抗炎、成骨和血管生成。

IF 5.4 2区化学

Biomacromolecules Pub Date : 2025-10-17 DOI: 10.1021/acs.biomac.5c01230

Chaonan He, Peipei Feng, Dingli Xu, Leidong Lian, Jin Li, Kaifeng Gan, Yi Gu, Tingting Pan, Yun Tang, Xiang Wu, Zhaoxiang Peng, Chunhai Ke, Jingyun Ma

{"title":"Naringenin-Loaded Core-Shell Mg-MOF Nanocomposite Integrated Injectable Hydrogel for Bone Regeneration: Anti-inflammatory, Osteogenic, and Angiogenic.","authors":"Chaonan He, Peipei Feng, Dingli Xu, Leidong Lian, Jin Li, Kaifeng Gan, Yi Gu, Tingting Pan, Yun Tang, Xiang Wu, Zhaoxiang Peng, Chunhai Ke, Jingyun Ma","doi":"10.1021/acs.biomac.5c01230","DOIUrl":"https://doi.org/10.1021/acs.biomac.5c01230","url":null,"abstract":"Composite biomaterial systems facilitate regenerative medicine through component synergy. Herein, novel core-shell nanocomposites (N-HMMs) are prepared, with hollow mesoporous silica (HMSNs) as the core and magnesium-gallic acid metal-organic frameworks (Mg-MOFs) as the shell. N-HMMs are loaded with the small-molecule osteoinductive drug naringin (Nar) to form N-HMMs@Nar, which is integrated into methacrylate gelatin/polyethylene glycol diacrylate hydrogels (GelMA/PEGDA, GP) to construct N-HMMs@Nar@GP. N-HMMs@Nar@GP enables sustained release of Nar, bioactive Mg2+, and antioxidant gallic acid for synergistic anti-inflammation, osteogenesis, and angiogenesis of bone regeneration. GP adapts N-HMMs@Nar to the traumatic characteristics of bone defects and facilitates in situ treatments. In vitro studies have confirmed the composite materials' biocompatibility, osteoinductive differentiation, and angiogenesis capabilities. The ability of N-HMMs@Nar@GP to enhance osteogenesis and angiogenesis is demonstrated in an in vivo tibial defect model using micro-CT and histopathological analysis. Therefore, N-HMMs@Nar@GP holds significant potential for application in the repair of bone defects.","PeriodicalId":30,"journal":{"name":"Biomacromolecules","volume":" ","pages":""},"PeriodicalIF":5.4,"publicationDate":"2025-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145306430","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

TorchANI 2.0: An Extensible, High-Performance Library for the Design, Training, and Use of NN-IPs. TorchANI 2.0：一个可扩展的高性能库，用于设计、训练和使用nn - ip。

IF 5.3 2区化学

Journal of Chemical Information and Modeling Pub Date : 2025-10-17 DOI: 10.1021/acs.jcim.5c01853

Ignacio Pickering, Jinze Xue, Kate Huddleston, Nicholas Terrel, Adrian E Roitberg

{"title":"TorchANI 2.0: An Extensible, High-Performance Library for the Design, Training, and Use of NN-IPs.","authors":"Ignacio Pickering, Jinze Xue, Kate Huddleston, Nicholas Terrel, Adrian E Roitberg","doi":"10.1021/acs.jcim.5c01853","DOIUrl":"https://doi.org/10.1021/acs.jcim.5c01853","url":null,"abstract":"In this work, we introduce TorchANI 2.0, a significantly improved version of the free and open source TorchANI software package for training and evaluation of ANI (ANAKIN-ME) deep learning models. TorchANI 2.0 builds upon the foundation of its predecessor, while addressing its limitations and introducing new features. These changes greatly enhance its extensibility, performance, and suitability as a framework for developing models ready for molecular dynamics applications. These improvements include the introduction of a modular system to add arbitrary pairwise potentials to models, CUDA-accelerated optimization for faster and more memory-efficient calculation of local atomic features, and a batched system for better performance of network ensembles, among others. Our benchmarks demonstrate that TorchANI 2.0 achieves significant speedup over previous versions in both training and inference, and the library enhancements allow users to train physically constrained models that better represent important qualities of chemical systems. We demonstrate this by introducing three new ANI models that incorporate these features and evaluating their capabilities.","PeriodicalId":44,"journal":{"name":"Journal of Chemical Information and Modeling ","volume":" ","pages":""},"PeriodicalIF":5.3,"publicationDate":"2025-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145311926","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Lactylation Dynamics and Its Regulatory Roles in Orthopedic Pathologies: A Research Update. 乳酸化动力学及其在骨科病理中的调节作用：最新研究进展。

IF 3.6 2区生物学

Journal of Proteome Research Pub Date : 2025-10-17 DOI: 10.1021/acs.jproteome.5c00714

Zhiqiang Xu, Chengrui Peng, Chenpeng Dong, Guihuo Wei, Chuanhong Zheng, Xianxiong Yin, Hu Qian, Xinghuo Wu, Jun Ao

{"title":"Lactylation Dynamics and Its Regulatory Roles in Orthopedic Pathologies: A Research Update.","authors":"Zhiqiang Xu, Chengrui Peng, Chenpeng Dong, Guihuo Wei, Chuanhong Zheng, Xianxiong Yin, Hu Qian, Xinghuo Wu, Jun Ao","doi":"10.1021/acs.jproteome.5c00714","DOIUrl":"https://doi.org/10.1021/acs.jproteome.5c00714","url":null,"abstract":"Post-translational modifications (PTMs) dynamically regulate cellular processes by modifying protein function. Among these, lactylation, a modification derived from lactate, functions through direct or indirect modification of histones or nonhistone proteins. While glycosylation and phosphorylation have established roles in bone metabolism and joint disorders, the biological significance of lactylation in musculoskeletal diseases remains underexplored. This study synthesizes current evidence investigating lactylation in four major orthopedic diseases: intervertebral disc degeneration (IVDD), osteoporosis (OP), osteoarthritis (OA), and spinal cord injury (SCI). The evidence indicates that lactylation modulates disease progression through dual mechanisms: coordinating cellular metabolism with extracellular matrix remodeling in IVDD and OA and regulating neuroimmune responses during SCI recovery. Notably, lactylation's regulatory patterns differ from classical PTMs by serving as a molecular bridge linking metabolic reprogramming to pathological tissue remodeling. This contrasts with phosphorylation, which primarily dominates signal transduction pathways. These insights reposition lactate from a metabolic byproduct to a disease-modifying signaling molecule, suggesting lactylation could inform therapeutic strategies for inflammatory, degenerative, and regenerative musculoskeletal disorders.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145306356","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Local Potential Functional Embedding Theory of Molecular Systems: Localized Orbital-Based Embedding from an Exact Density-Functional Perspective. 分子系统的局域势泛函嵌入理论：基于精确密度泛函的局域轨道嵌入。

IF 5.5 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-10-17 DOI: 10.1021/acs.jctc.5c01256

Wafa Makhlouf, Bruno Senjean, Emmanuel Fromager

{"title":"Local Potential Functional Embedding Theory of Molecular Systems: Localized Orbital-Based Embedding from an Exact Density-Functional Perspective.","authors":"Wafa Makhlouf, Bruno Senjean, Emmanuel Fromager","doi":"10.1021/acs.jctc.5c01256","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c01256","url":null,"abstract":"Localized orbital-based quantum embedding, as originally formulated in the context of density matrix embedding theory (DMET), is revisited from the perspective of lattice density functional theory (DFT). An in-principle exact (in the sense of full configuration interaction) formulation of the theory, where the occupations of the localized orbitals play the role of the density, is derived for any (model or ab initio) electronic Hamiltonian. From this general formalism we deduce an exact relation between the local Hartree-exchange-correlation (Hxc) potential of the full-size Kohn-Sham (KS) lattice-like system and the embedding chemical potential that is adjusted on each embedded fragment, individually, such that both KS and embedding cluster systems reproduce the exact same local density. When well-identified density-functional approximations (that find their justification in the strongly correlated regime) are applied, a practical self-consistent local potential functional embedding theory (LPFET), where the local Hxc potential becomes the basic variable, naturally emerges from the theory. LPFET differs from previous density embedding approaches by its fragment-dependent embedding chemical potential expression, which is a simple functional of the Hxc potential. Numerical calculations on prototypical systems show the ability of such an ansatz to improve substantially the description of density profiles (localized orbitals occupation numbers in this context) in strongly correlated systems.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145306387","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Heat-Induced Structural Changes in Lactoferrin for Enhanced Mucoadhesion. 热诱导乳铁蛋白结构变化增强黏附。

IF 4.7

ACS Applied Bio Materials Pub Date : 2025-10-17 DOI: 10.1021/acsabm.5c01534

Bianca Hazt, Daniel J Read, Oliver G Harlen, Wilson C K Poon, Adam O'Connell, Simon D Connell, Anwesha Sarkar

{"title":"Heat-Induced Structural Changes in Lactoferrin for Enhanced Mucoadhesion.","authors":"Bianca Hazt, Daniel J Read, Oliver G Harlen, Wilson C K Poon, Adam O'Connell, Simon D Connell, Anwesha Sarkar","doi":"10.1021/acsabm.5c01534","DOIUrl":"https://doi.org/10.1021/acsabm.5c01534","url":null,"abstract":"The development of biocompatible and safe mucoadhesive materials is critical for improving therapeutic strategies, where cationic proteins such as lactoferrin are emerging as promising alternatives to synthetic polymers. Here, we demonstrate how thermal denaturation of lactoferrin can be used as a viable strategy to enhance mucoadhesion. We identify and study in detail the structural changes in lactoferrin upon thermal denaturation using light scattering, circular dichroism spectroscopy, gel-electrophoresis, and atomic force microscopy. Lactoferrin-mucin binding was evaluated using rheology, confocal microscopy, and quartz crystal microbalance with dissipation monitoring. We find that lactoferrin binds to mucin at its native state, heat-treatment at 95 °C enhances its affinity for mucin, and that the adhesion mechanism relies on hydrophobic interactions with no obvious contributions of disulfide bonds. Lactoferrin and its resulting complexes with mucin present high surface activity, which induces an artificial shear-thinning rheological response. While electrostatic interactions have been considered the dominant mucoadhesive mechanism of native lactoferrin up to now, our findings highlight the role of hydrophobic interactions, providing a design route to alter the structural state of the protein to inspire the development of future natural protein-based mucoadhesive systems.","PeriodicalId":2,"journal":{"name":"ACS Applied Bio Materials","volume":" ","pages":""},"PeriodicalIF":4.7,"publicationDate":"2025-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145311921","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A Density Functional Theory and Semiempirical Framework for Trajectory Surface Hopping on Extended Systems. 扩展系统上轨迹表面跳变的密度泛函理论和半经验框架。

IF 5.5 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-10-17 DOI: 10.1021/acs.jctc.5c01082

Jan-Robert Vogt, Michael Schulz, Rafael Souza Mattos, Mario Barbatti, Maurizio Persico, Giovanni Granucci, Jürg Hutter, Anna Hehn

{"title":"A Density Functional Theory and Semiempirical Framework for Trajectory Surface Hopping on Extended Systems.","authors":"Jan-Robert Vogt, Michael Schulz, Rafael Souza Mattos, Mario Barbatti, Maurizio Persico, Giovanni Granucci, Jürg Hutter, Anna Hehn","doi":"10.1021/acs.jctc.5c01082","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c01082","url":null,"abstract":"Nonadiabatic molecular dynamics simulations provide a theoretical understanding of various excited-state processes in photochemistry, offering access to band widths, radiative or nonradiative relaxation and corresponding lifetimes, excited-state energies, and charge transfer. The range of method developments within the framework of time-dependent density functional theory is exceedingly large for molecular quantum chemistry. Still, it shrinks significantly when aiming to treat periodic boundary conditions. To address this gap and complement existing software packages for solid-state nonadiabatic molecular dynamics, we present an interface between the CP2K electronic structure and the NEWTON-X surface hopping codes. The interface features the generation of initial conditions, as well as adiabatic and nonadiabatic molecular dynamics, based on phenomenological or numerical time-derivative couplings. Setups are validated on gas-phase pyrazine, with electronic absorption spectra and excited-state populations for transitions between the lowest singlet states being in agreement with established molecular quantum chemistry methods. Extending the system size to crystalline pyrazine, limitations of approximate couplings are discussed, and the efficiency and applicability of the interface are demonstrated by computing broad spectra over several eV and 100 fs trajectories, considering couplings between all 80th lowest excited states, at low computational cost with a mixed semiempirical density functional theory setup.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145311978","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Fully Analytic Nuclear Gradients for the Bethe-Salpeter Equation. Bethe-Salpeter方程的全解析核梯度。

IF 4.6 2区化学

The Journal of Physical Chemistry Letters Pub Date : 2025-10-17 DOI: 10.1021/acs.jpclett.5c02219

Johannes Tölle, Marios-Petros Kitsaras, Pierre-François Loos

引用次数: 0