Papers¶
Neural cellular automata: Applications to biology and beyond classical AI
Neural Cellular Automata: From Cells to Pixels
Solving Heterogeneous Agent Models with Physics-informed Neural Networks
本文提出 ABH-PINN solver，将 PINNs 应用于宏观经济学中的 Aiyagari-Bewley-Huggett（ABH）异质代理人模型，通过将 Hamilton-Jacobi-Bellman 和 Kolmogorov Forward 方程嵌入神经网络训练目标，替代传统网格求解器，初步结果与有限差分求解器匹配。
→ 暂不继续；若未来需要探索 PINNs 在耦合 PDE 系统上的应用方法，可重新评估
Fiber recruitment drives a phase transition of cell polarization at a critical cell spacing in matrix-mediated tissue remodeling
Engineering a serum response factor superactivator of smooth muscle gene expression with a condensate-forming domain
Discovering governing equations in discrete systems using PINNs
Endothelium calls macrophages for destruction
Towards multimodal foundation models in molecular cell biology
Quantitative characterization of cell niches in spatially resolved omics data
Decoding Macrophage Heterogeneity to Unravel Vascular Inflammation as a Path to Precision Medicine
The nonequilibrium mechanism of noise-enhanced drug synergy in HIV latency reactivation
Stochastic Phenotype Transition of a Single Cell in an Intermediate Region of Gene State Switching
Modeling stochastic phenotype switching and bet-hedging in bacteria: stochastic nonlinear dynamics and critical state identification
Stochastic theory of nonequilibrium steady states. Part II: Applications in chemical biophysics
Stochastic theory of nonequilibrium steady states and its applications. Part I
Cholesterol-Inflammation Fusion Hypothesis in Atherosclerosis: An Evolving Paradigm in Pathogenesis and Therapy
MultiCell: geometric learning in multicellular development
Calibrating tissue level PDE models of ligand dynamics using single cell and spatial transcriptomics data
Parameter Identifiability Under Limited Experimental Data in Age-Structured Models of the Cell Cycle
Modelling cerebrovascular pathology and the spread of amyloid beta in Alzheimer's disease
Atherosclerotic progression at sites of low shear stress is attenuated by myeloid-PlexinD1 deficiency through suppression of classical macrophage polarization
The mechanics and physics of tofu: understanding hydrated soft solids through feature networks
Smooth muscle cell phenotypic modulation during atherosclerosis
GeoPT: Scaling Physics Simulation via Lifted Geometric Pre-Training
From reductionism to realism: Holistic mathematical modelling for complex biological systems
The future of machine learning for small-molecule drug discovery will be driven by data
Applying Spatiotemporal Modeling of Cell Dynamics to Accelerate Drug Development
Physics-informed machine learning
Chemoinformatics in the New Era: From Molecular Dynamics to Systems Dynamics
Multilingual Translation for Zero-Shot Biomedical Classification Using BioTranslator
Explicit physics-informed neural networks for nonlinear closure: The case of transport in tissues
Physics-informed neural networks: A deep learning framework for solving forward and inverse problems involving nonlinear partial differential equations
Topological model selection: a case-study in tumour-induced angiogenesis
Roadmap on the use of artificial intelligence for imaging of vulnerable atherosclerotic plaque in coronary arteries
Spatial distribution and network morphology of epicardial, endocardial, interstitial, and Purkinje cell-associated elastin fibers in porcine left ventricle
Noninvasive Detection of Smooth Muscle Cell-Derived Hot Spots to Study Atherosclerosis by PET/MRI in Mice
Translational opportunities of single-cell biology in atherosclerosis
Stiffness sensing by smooth muscle cells: Continuum mechanics modeling of the acto-myosin role
Bayesian optimisation for efficient parameter inference in a cardiac mechanics model of the left ventricle
A novel numerical and artificial intelligence based approach to study anti-angiogenic drugs: Endostatin
Multi-omics single-cell data integration and regulatory inference with graph-linked embedding
Computational model of damage-induced growth in soft biological tissues considering the mechanobiology of healing
Phenotypic Modulation of Macrophages and Vascular Smooth Muscle Cells in Atherosclerosis—Nitro-Redox Interconnections
Moving towards reproducible machine learning
Smart wearable devices in cardiovascular care: where we are and how to move forward
A Comparison of Two LDL Cholesterol Targets after Ischemic Stroke
Approximate Bayesian model inversion for PDEs with heterogeneous and state-dependent coefficients
Integrating machine learning and multiscale modeling—perspectives, challenges, and opportunities in the biological, biomedical, and behavioral sciences
Multi-Layer Mechanical Model of Glagov Remodeling in Coronary Arteries: Differences between In-Vivo and Ex-Vivo Measurements
Remodelling the extracellular matrix in development and disease
Open problems in computational vascular biomechanics: Hemodynamics and arterial wall mechanics
Ponatinib, But Not the New Abl-Kinase Inhibitor Asciminib, Activates Platelets, Leukocytes, and Endothelial Cell TNF Signaling to Induce Atherosclerotic Plaque Inflammation, Myocardial Infarction, and Stroke
The role of hemodynamics in the formation of atherosclerotic plaques
Advances in Atherosclerosis Theranostics Harnessing Iron Oxide-Based Nanoparticles
Atherosclerotic plaque stabilization and regression: a review of clinical evidence
Designing nanotheranostics with machine learning
A wearable cardiac ultrasound imager
World Heart Report 2023: Confronting the World's Number One Killer
Apolipoproteins in vascular biology and atherosclerotic disease
COCOMO-ACS Trial Statistical Analysis Plan
Multi-organ imaging demonstrates the heart-brain-liver axis in UK Biobank participants
A proteomic surrogate for cardiovascular outcomes that is sensitive to multiple mechanisms of change in risk
Genetically predicted on-statin LDL response is associated with higher intracerebral haemorrhage risk
Generative Adversarial Networks and Its Applications in Biomedical Informatics
Loss-of-function genomic variants highlight potential therapeutic targets for cardiovascular disease
Machine learning in cardiovascular flows modeling: Predicting arterial blood pressure from non-invasive 4D flow MRI data using physics-informed neural networks
Single-Cell Genomics Reveals a Novel Cell State During Smooth Muscle Cell Phenotypic Switching and Potential Therapeutic Targets for Atherosclerosis in Mouse and Human
Artificial intelligence in cardiovascular imaging: state of the art and implications for the imaging cardiologist
Emerging Role of Precision Medicine in Cardiovascular Disease
In vivo assessment of the relationship between shear stress and necrotic core in early and advanced coronary artery disease
Cholesterol Efflux and Atheroprotection: Advancing the Concept of Reverse Cholesterol Transport
Associations of Long-Term and Early Adult Atherosclerosis Risk Factors With Aortic and Mitral Valve Calcium
In Vivo Validation of a Catheter-Based Near-Infrared Spectroscopy System for Detection of Lipid Core Coronary Plaques: Initial Results of the SPECTACL Study
Vascular Lipid Accumulation, Lipoprotein Oxidation, and Macrophage Lipid Uptake in Hypercholesterolemic Zebrafish
Early Human Atherosclerosis: Accumulation of Lipid and Proteoglycans in Intimal Thickenings Followed by Macrophage Infiltration
High-density lipoprotein protects macrophages from oxidized low-density lipoprotein-induced apoptosis by promoting efflux of 7-ketocholesterol via ABCG1
Oxidized LDL Regulates Macrophage Gene Expression through Ligand Activation of PPARγ
Do Plaques Grow Upstream or Downstream? An Angiographic Study in the Femoral Artery
Hemodynamics of coronary artery with systolic luminal narrowing
Role of biomechanical factors in plaque rupture and erosion: insight from intravascular imaging based computational modeling
Biomechanics of soft biological tissues and organs, mechanobiology, homeostasis and modelling
Role of vascular smooth muscle cell clonality in atherosclerosis
Vascular Mechanotransduction
Sulfide regulation of cardiovascular function in health and disease
Mechanical programming of arterial smooth muscle cells in health and ageing
Coronary Microvascular Disease: Pathogenic Mechanisms and Therapeutic Options
Vascular Smooth Muscle Cells and Arterial Stiffening: Relevance in Development, Aging, and Disease
Vascular Extracellular Matrix and Arterial Mechanics
A mechano-immunological framework for lymph node remodeling during inflammation and homeostasis
本文针对淋巴结（LN）在炎症-稳态循环中的几何结构、细胞组分与力学性质耦合演化问题，提出了一套基于连续介质力学的 mechano-chemo-biological 耦合理论，将 LN 视为由 supportive phase（SC 网络与 ECM）和 primary phase（免疫细胞流）组成的孔隙介质，刻画其生长、变形与细胞迁移的协同机制。
→ 保留参考；仅在当前问题需要其完整方法或定量证据时升级为 deep note。
PerSiVal: deep neural networks for pervasive simulation of an activation-driven continuum-mechanical upper limb model
本文提出一种密集连接的深度神经网络架构（PerSiVal），用于在资源受限设备（如 AR/移动端）上实现基于连续介质力学的肌肉骨骼系统仿真的实时可视化。
→ 保留参考；仅在当前问题需要其完整方法或定量证据时升级为 deep note。
Challenges and Strategies for Deep Learning in Cardiovascular Imaging: Ejection Fraction and Heart Failure Management
A multiscale theory for network advection-reaction-diffusion
本文针对网络上的对流-反应-扩散（advection-reaction-diffusion）过程提出一种多尺度理论：在微观尺度上将每条边视为一维细长管道，其中物质遵循对流-反应-扩散偏微分方程；在宏观尺度上节点密度由常微分方程组（含反应项与图拉普拉斯算子）刻画。
→ 保留参考；仅在当前问题需要其完整方法或定量证据时升级为 deep note。
Smooth muscle cell-specific CD47 deletion suppresses atherosclerosis
Discrete and continuous mathematical models of sharp-fronted collective cell migration and invasion
本文针对细胞群体迁移实验中常见的"尖锐前缘"（sharp front）现象，指出传统基于线性扩散的反应-扩散 PDE 模型无法预测这种紧支撑前沿，而非线性退化扩散（porous medium 形式）又缺乏清晰的生物学机制解释。
→ 保留参考；仅在当前问题需要其完整方法或定量证据时升级为 deep note。
Inflammation, Cholesterol, Lipoprotein(a) and 30-Year Cardiovascular Outcomes in Women
In-Vivo Left Atrial Surface Motion and Strain Measurement Using Novel Mesh Regularized Image Block Matching Method with 4D-CTA
首次引入网格正则化图像块匹配方法（MR-BM）用于 4D CTA 的左心房 3D 表面应变测量，在体模和体内数据上验证了可靠性和一致性，结果可作为左心房血流动力学计算的边界条件。
→ 保留参考；若需要图像应变测量方法，再升级为 deep note。
Lipoprotein(a) levels in a population with clinical atherosclerotic cardiovascular disease in the United States: A subanalysis from the Lp(a)HERITAGE study
Mechanochemical Dynamics of Collective Cells and Hierarchical Topological Defects in Multicellular Lumens
建立了 3D 化学-力学顶点模型，揭示了多细胞管腔中化学信号与力学反馈的相互作用可触发叉形或 Hopf 分岔，产生静态化学-力学图案和多种振荡模式，并发现了从细胞级六角缺陷到组织级取向缺陷的分层拓扑缺陷演化。
→ 保留参考；若需要顶点模型或分层缺陷分析方法，再升级为 deep note。
Nanomedicine-Based Strategies for the Treatment of Vein Graft Disease
综述了纳米医学在静脉移植疾病（VGD）治疗中的最新进展，涵盖针对 VGD 各阶段（早期内皮功能障碍、中期内膜增生、晚期加速动脉粥样硬化）的纳米颗粒设计和纳米制造生物材料策略。
→ 保留参考；若需要 VGD 病理生理机制作为 G&R 模型输入，再升级为 deep note。
Nanoparticle-Directed Antioxidant Therapy Can Ameliorate Disease Progression in a Novel, Diet-Inducible Model of Coronary Artery Disease
Novel Therapeutics and Upcoming Clinical Trials Targeting Inflammation in Cardiovascular Diseases
Optical coherence tomography assessment of the impact of colchicine on non-culprit coronary plaque composition after myocardial infarction
Targeting Unc5b in macrophages drives atherosclerosis regression and pro-resolving immune cell function
Artificial intelligence in diabetic retinopathy: Bibliometric analysis
Biochemomechanical Tensegrity Model of Cytoskeletons
本文建立了一个细胞骨架的生物化学-力学耦合张拉整体（tensegrity）模型，将肌动蛋白皮层与应力纤维建模为受预张力的弦单元，将微管与交联肌动蛋白束建模为承压杆单元，并通过节点连接形成张拉整体结构。
→ 保留参考；仅在当前问题需要其完整方法或定量证据时升级为 deep note。
A cell model about symmetric and asymmetric stem cell division
本文构建了一个包含干细胞自我更新、凋亡、细胞运动及对称/不对称分裂的多阶段细胞谱系反应扩散模型，解析了不对称分裂对细胞群体动态和传播波速的影响。
→ 保留 quick_note.md 作为参考，若未来涉及干细胞动力学或集体迁移建模时再升级 deep。
Coronary Flow Reserve, Inflammation, and Myocardial Strain: The CIRT-CFR Trial
Liraglutide Lowers Endothelial Vascular Cell Adhesion Molecule-1 in Murine Atherosclerosis Independent of Glucose Levels
Macrophages in Cardiac Remodelling After Myocardial Infarction
综述了心肌梗死后巨噬细胞在心脏重塑中的多重角色，重点介绍了驻留心脏巨噬细胞（RCM）的心脏保护功能及其与其他细胞类型（心肌细胞、成纤维细胞、内皮细胞）的交互机制。
→ 暂不继续；不纳入当前阅读队列。
Minimal Morphoelastic Models of Solid Tumour Spheroids: A Tutorial
本教程以 morphoelasticity（结合固体力学与生长的理论）为基础，系统构建了一组复杂度递增的肿瘤球体（tumour spheroid）生长模型，旨在探究力学因素对生长动力学的调控作用。
→ 保留参考；仅在当前问题需要其完整方法或定量证据时升级为 deep note。
NCCT-CECT image synthesizers and their application to pulmonary vessel segmentation
Nanomedicines for cardiovascular disease
Radial Wall Strain and Plato's Cave: Are Shadows Enough to Get the Truth?
Rational nanoparticle design: Optimization using insights from experiments and mathematical models
Short-Term Risk Stratification of Non–Flow-Limiting Coronary Stenosis by Angiographically Derived Radial Wall Strain
A target-cell limited model can reproduce influenza infection dynamics in hosts with differing immune responses
Prevention of atherosclerosis from childhood
Blood M2-like Monocyte Polarization Is Associated with Calcific Plaque Phenotype in Stable Coronary Artery Disease: A Sub-Study of SMARTool Clinical Trial
Chiral Topographic Instability in Shrinking Spheres
报道了收缩核-壳球体中的手性褶皱形貌（从 buckyball 模式到手性模式再到二次对称性破缺），建立了核-壳模型和普适标度律，并展示了基于手性定位的自适应抓取应用。
→ 暂不继续；不纳入当前阅读队列。
Coronary Artery Calcium for Risk Stratification of Sudden Cardiac Death
Irish National Diabetic RetinaScreen Programme: report on five rounds of retinopathy screening and screen-positive referrals (INDEAR study report no. 1)
Dynamic Multiscale Regulation of Perfusion Recovery in Experimental Peripheral Arterial Disease: A Mechanistic Computational Model
建立了首个描述外周动脉疾病（PAD）中灌注恢复多尺度调控的系统生物学计算模型，通过模型预测并实验验证了抑制细胞坏死作为改善灌注恢复的治疗策略。
→ 保留参考；若需要多尺度系统生物学建模方法学，再升级为 deep note。
Effects of Cuisine-Based Chinese Heart-Healthy Diet in Lowering Blood Pressure Among Adults in China: Multicenter, Single-Blind, Randomized, Parallel Controlled Feeding Trial
Energy landscape decomposition for cell differentiation with proliferation effect
本文针对带有细胞增殖（birth-death）效应的细胞分化过程建立了一套能量景观（energy landscape）理论。
→ 保留参考；仅在当前问题需要其完整方法或定量证据时升级为 deep note。
An Energy Method for the Bifurcation Analysis of Necking
基于最小能量势垒准则结合 Monte Carlo 模拟，提出了预测材料颈缩失稳和分岔后行为的理论方法，揭示了表面张力对软材料颈缩形态（位置和波数）的关键调控作用。
→ 保留参考；若需要失稳分析方法学细节，再升级为 deep note。
Gender medicine: effects of sex and gender on cardiovascular disease manifestation and outcomes
Haemodynamic Wall Shear Stress, Endothelial Permeability and Atherosclerosis—A Triad of Controversy
本文是一篇综述，系统梳理了围绕动脉粥样硬化局部定位的三方争议——壁面剪应力（WSS）、内皮通透性与病灶分布之间的关系。
→ 保留参考；仅在当前问题需要其完整方法或定量证据时升级为 deep note。
Identifying patterns in amyotrophic lateral sclerosis progression from sparse longitudinal data
Large-Scale Microbiome Data Integration Enables Robust Biomarker Identification
提出了 NetMoss 算法，通过网络模块偏移（module shift）评估跨队列微生物组数据中细菌的重要性，实现去除批次效应和鲁棒的疾病生物标志物识别。
→ 暂不继续；不纳入当前阅读队列。
Mathematical models of neuronal growth
本文是 Oxford 的 Oliveri 与 Goriely 撰写的一篇综述 (review paper)，系统梳理了过去约三十年间关于神经元 neurite（包括 axon 与 dendrite）生长与 morphogenesis 的数学建模工作。
→ 保留参考；仅在当前问题需要其完整方法或定量证据时升级为 deep note。
Mechanical-Electrochemical Coupling Theory of Bacterial Cells
建立了细菌细胞的力学-电化学耦合理论模型（双层结构：带负电多糖荚膜 + 弹性包膜），揭示了静电双层力、渗透压在细菌纳米压痕三阶段响应中的调控机制。
→ 保留参考；若需要力学-电化学耦合建模方法，再升级为 deep note。
Toward the Cellular-Scale Simulation of Motor-Driven Cytoskeletal Assemblies
开发了 aLENS（a Living Ensemble Simulator）计算框架，通过隐式马达力计算和几何约束硬体排斥方法，实现了数万至数十万细胞骨架细丝和交联马达的大规模并行模拟。
→ 暂不继续；不纳入当前队列，未来需要颗粒或纤维模拟方法时再重新评估。
Pathway Trajectory Analysis with Tensor Imputation Reveals Drug-Induced Single-Cell Transcriptomic Landscape
提出了 TIGERS 算法，利用张量补全预测药物诱导的单细胞基因表达数据，并识别受调控通路的轨迹，揭示细胞类型特异性的药物转录组响应。
→ 暂不继续；不纳入当前阅读队列。
Predictors of Left Main Coronary Artery Disease in the ISCHEMIA Trial
Race-Dependent Association of High-Density Lipoprotein Cholesterol Levels With Incident Coronary Artery Disease
Three-Dimensional Chiral Morphodynamics of Chemomechanical Active Shells
建立了化学-力学耦合活性壳理论，揭示了细胞皮层中活性驱动的手性形态动力学——包括脉冲螺旋波、行波、驻波及伴随的3D大变形，阐明了力学反馈对螺旋模式稳定性的关键调控作用。
→ 保留参考；若需要活性壳耦合建模方法，再升级为 deep note。
The Universal Program of Nonlinear Hyperelasticity
系统发展了非均匀各向异性超弹性材料的通用变形理论，推导了可压缩和不可压缩横观各向同性、正交各向异性及单斜材料的通用变形、通用材料优选方向和通用非均匀性。
→ 保留参考；若需要解析血管壁的通用变形族，再升级为 deep note。
Well-Posedness of a Mathematical Model of Diabetic Atherosclerosis
提出了糖尿病动脉粥样硬化的 PDE 模型（含自由边界），利用 Hanzawa 变换将自由边界固定化并简化为 Banach 空间中的抽象演化方程，证明了局部解的存在唯一性。
→ 保留参考；若需要糖尿病动脉粥样硬化建模的具体 PDE 形式，再升级为 deep note。
Angiographic Quantitative Flow Ratio-Guided Coronary Intervention (FAVOR III China): A Multicentre, Randomised, Sham-Controlled Trial
BMP9 and BMP10 Act Directly on Vascular Smooth Muscle Cells for Generation and Maintenance of the Contractile State
Chitinase 3 like 1 is a regulator of smooth muscle cell physiology and atherosclerotic lesion stability
Effects of the Haemodynamic Stimulus on the Location of Carotid Plaques Based on a Patient-Specific Mechanobiological Plaque Atheroma Formation Model
Cellular and molecular pathobiology of heart failure with preserved ejection fraction
High-density lipoproteins, reverse cholesterol transport and atherogenesis
An in-silico Investigation Into the Role of Strain and Structure on Vascular Smooth Muscle Cell Growth
本文构建了一个 2D agent-based model (ABM) 来模拟大鼠主动脉平滑肌细胞 (RASMC) 在不同循环应变幅度 (0–10%、2–8%、4–6%) 下、分别种植于非结构化 (PDMS) 与结构化 (脱细胞胶原组织) 基质上的集体响应。
→ 保留参考；仅在需要 VSMC 取向或 agent-based 规则时升级为 deep note。
Targeting inflammation in atherosclerosis — from experimental insights to the clinic
Interpretable predictions of cellular behavior
本篇是发表在 *Nature Computational Science* 上的研究亮点（research highlight），由 Ananya Rastogi 撰写，介绍了 Sander 课题组提出的 CellBox 框架（原始论文发表于 *Cell Systems* 12, 128–140, 2021）。
→ 保留参考；仅在当前问题需要其完整方法或定量证据时升级为 deep note。
Management of Antithrombotic Therapy After Acute Coronary Syndromes
Targeted delivery of therapeutic agents to the heart
Cardiac and Renal Function Interactions in Heart Failure with Reduced Ejection Fraction: A Mathematical Modeling Analysis
建立了心-肾耦合数学模型（含毛细血管液体交换），模拟了射血分数降低的心衰（HF-rEF）进展，并用 SOLVD 临床试验数据校准和验证，预测了 SGLT2 抑制剂通过降低前负荷减缓心脏重塑的机制。
→ 保留参考；若需要耦合模型方法论，再升级为 deep note。
Evinacumab in Patients with Refractory Hypercholesterolemia
Evolocumab reduces LDL-cholesterol levels in FH
Switching Behaviour in Vascular Smooth Muscle Cell-Matrix Adhesion During Oscillatory Loading
结合 AFM 实验和弹簧系统数学模型，发现振荡加载下 SMC 整合素粘附在"牢固粘附"和"完全脱离"两态间存在双稳态切换行为，力学协同性和细胞形变决定初始条件依赖的最终状态。
→ 保留参考；若需要 SMC-ECM 粘附双稳态建模方法，再升级为 deep note。
A Multiscale Model to Predict Neuronal Cell Deformation with Varying Extracellular Matrix Stiffness and Topography
建立了从分子层面（integrin/NCAM 受体的 steered MD）到微米尺度（neo-Hookean 细胞 + 粘弹性 ECM 的 FEA）的多尺度神经元变形模型，揭示了 ECM 刚度阈值（~500 Pa）和厚度临界值（1 μm）对力学传感的影响。
→ 保留参考；若需要多尺度耦合方法学细节，再升级为 deep note。
Regulation of Vascular Calcification by Reactive Oxygen Species
A review study on blood in human coronary artery: Numerical approach
Role of Vascular Smooth Muscle Cell Plasticity and Interactions in Vessel Wall Inflammation
scIGANs: single-cell RNA-seq imputation using generative adversarial networks
scIGANs 将生成对抗网络应用于 scRNA-seq 数据插补，用生成细胞替代观测细胞以减少过度平滑，并在多种模拟与真实数据集上表现为有竞争力且可扩展至十万细胞级数据的方法。
→ 方法学标签保留参考；若未来涉及单细胞组学数据降噪或预处理，可返回评估 scIGANs 在相关场景下的适用性。
Switching of vascular cells towards atherogenesis, and other factors contributing to atherosclerosis: a systematic review
本文是一篇系统性综述，从"血管细胞向动脉粥样硬化发生(atherogenesis)切换"的角度，整合 PubMed/MEDLINE/Google Scholar 文献，阐述动脉粥样硬化起病、发展与进展的多步骤、序贯性机制。
→ 保留参考；仅在当前问题需要其完整方法或定量证据时升级为 deep note。
Systems biology informed deep learning for inferring parameters and hidden dynamics
提出 SBINNs（systems-biology-informed neural networks），将 ODE 系统作为约束嵌入神经网络，从而从少量稀疏含噪测量中推断未知参数和隐藏动力学；在三个合成基准上验证有效。
→ 保留参考；需要处理基于 ODE 的参数推断任务时，再升级 deep 并检查开源实现。
Coronary Disease-Associated Gene TCF21 Inhibits Smooth Muscle Cell Differentiation by Blocking the Myocardin-Serum Response Factor Pathway
本文揭示冠心病风险基因 TCF21 (transcription factor 21) 通过多重机制拮抗 SMC (smooth muscle cell) 分化的核心调控通路 MYOCD-SRF。
→ 保留参考；仅在当前问题需要其完整方法或定量证据时升级为 deep note。
Near-infrared spectroscopy-derived lipid core burden index predicts adverse cardiovascular outcome in patients with coronary artery disease during long-term follow-up
Applications and Limitations of Mouse Models for Understanding Human Atherosclerosis
本文系统综述了小鼠模型在理解人类冠状动脉疾病（CAD）/动脉粥样硬化中的应用与局限，基于对 9000 余篇文献的梳理，构建了 827 个小鼠动脉粥样硬化相关基因的数据库，并与人类 GWAS 结果进行三层面比较：风险因素、基因重叠和通路一致性。
→ 保留参考；仅在当前问题需要其完整方法或定量证据时升级为 deep note。
Diagnostic Accuracy of Angiography-Based Quantitative Flow Ratio Measurements for Online Assessment of Coronary Stenosis
Evolocumab and Clinical Outcomes in Patients with Cardiovascular Disease
Simulating muscular thin films using thermal contraction capabilities in finite element analysis tools
本文研究了使用 Finite Element Analysis (FEA) 中的热收缩(thermal contraction)能力来近似模拟 biohybrid 器件中细胞收缩性质的新技术。
→ 保留参考；仅在当前问题需要其完整方法或定量证据时升级为 deep note。
Coronary artery disease associated transcription factor TCF21 regulates smooth muscle precursor cells that contribute to the fibrous cap
Does low and oscillatory wall shear stress correlate spatially with early atherosclerosis? A systematic review
本文对"低且振荡的壁面剪切应力(WSS)导致早期动脉粥样硬化"这一广泛共识进行了系统综述,检索 PubMed 并筛选出 27 篇将 CFD 计算的血流动力学指标与病灶分布进行对比的原创研究。
→ 保留参考；仅在当前问题需要其完整方法或定量证据时升级为 deep note。
Parameter Estimation of Partial Differential Equation Models
提出了两种基于基函数展开的 PDE 参数估计方法——参数级联法和贝叶斯方法，无需反复数值求解 PDE，在估计精度上优于传统的两阶段方法。
→ 保留参考；若需要 PDE 参数估计的具体统计方法，再升级为 deep note。
Atherosclerosis Screening by Noninvasive Imaging for Cardiovascular Prevention: A Systematic Review
Rarefaction and blood pressure in systemic and pulmonary arteries
Computed high concentrations of low-density lipoprotein correlate with plaque locations in human coronary arteries
本文针对 60 名冠状动脉疾病（CAD）患者，利用 dual-source CT angiography 重建左、右冠状动脉（LCA/RCA）几何结构，并通过"虚拟去除斑块"的方式近似还原动脉的健康态解剖。
→ 保留参考；仅在当前问题需要其完整方法或定量证据时升级为 deep note。
Coronary Artery Wall Shear Stress Is Associated With Progression and Transformation of Atherosclerotic Plaque and Arterial Remodeling in Patients With Coronary Artery Disease
Numerical simulations of haemodynamic factors and hyperelastic Circumferential Strain/Stress in the ideal and healthy-patient-specific carotid bifurcations for different rheological models
本文采用计算流体力学(CFD)方法研究颈动脉分叉处血流动力学因素在动脉粥样硬化起始与发展中的作用,并对比了四种流变学模型(Newtonian 与非 Newtonian)对速度场和壁面剪切应力(WSS)的影响。
→ 保留参考；仅在当前问题需要其完整方法或定量证据时升级为 deep note。
Smooth Muscle Cell Differentiation In Vitro: Models and Underlying Molecular Mechanisms
本文综述体外 SMC 分化模型及其调控机制，核心判断是模型选择必须匹配 SMC 的胚胎来源和具体研究问题，而且体外发现需要体内实验支持。
→ 保留为模型选择的背景参考；只有需要比较具体诱导方案时再升级 deep。
3D Critical Plaque Wall Stress Is a Better Predictor of Carotid Plaque Rupture Sites Than Flow Shear Stress: An In Vivo MRI-Based 3D FSI Study
Arterial spin labeling in neuroimaging
Crucial Role of Nrf3 in Smooth Muscle Cell Differentiation From Stem Cells
本文研究了转录因子 Nrf3（nuclear factor erythroid 2-related factor 3）在胚胎干细胞（ESC）向平滑肌细胞（SMC）分化中的功能角色。
→ 保留参考；仅在当前问题需要其完整方法或定量证据时升级为 deep note。
The ATHEROMA (Atorvastatin Therapy: Effects on Reduction of Macrophage Activity) Study — Evaluation Using Ultrasmall Superparamagnetic Iron Oxide-Enhanced Magnetic Resonance Imaging in Carotid Disease
Phagocytosis in atherosclerosis: Molecular mechanisms and implications for plaque progression and stability
Mechanical, biochemical, and extracellular matrix effects on vascular smooth muscle cell phenotype
本文综述了机械、生化和细胞外基质（ECM）三类环境因素对血管平滑肌细胞（VSMC）表型调控的作用，强调三者之间的相互依存关系。
→ 保留参考；仅在当前问题需要其完整方法或定量证据时升级为 deep note。
The role of shear stress in the destabilization of vulnerable plaques and related therapeutic implications
Human IL-23-producing type 1 macrophages promote but IL-10-producing type 2 macrophages subvert immunity to (myco)bacteria
本文通过 GM-CSF 与 M-CSF 分别诱导人单核细胞分化为促炎型 Mφ-1 和抗炎型 Mφ-2 两种巨噬细胞亚群，系统比较二者在抗分枝杆菌免疫中的功能差异。
→ 保留参考；仅在当前问题需要其完整方法或定量证据时升级为 deep note。
Arterial Remodeling and Coronary Artery Disease: The Concept of 'Dilated' Versus 'Obstructive' Coronary Atherosclerosis
Influence of stenosis morphology on flow through severely stenotic vessels: implications for plaque rupture
Signal Transduction in Arteriosclerosis: Mechanical Stress-Activated MAP Kinases in Vascular Smooth Muscle Cells (Review)
综述了力学应激（高血压、剪切应力、周期性牵张）通过 MAP 激酶通路在血管平滑肌细胞中传导信号的分子机制，展示了力学刺激可直接磷酸化 PDGF 受体并激活通常由生长因子使用的信号通路。
→ 保留参考；若需要 MAPK 通路细节，优先查找更新综述而不是升级本文 deep note。
In vivo Wall Shear Stress Measured by Magnetic Resonance Velocity Mapping in the Normal Human Abdominal Aorta
Differentiation, Maturation, and Proliferation of Macrophages in the Mouse Yolk Sac: A Light-Microscopic, Enzyme-Cytochemical, Immunohistochemical, and Ultrastructural Study
本文通过光镜、酶细胞化学、免疫组化及超微结构技术，系统研究了小鼠卵黄囊中巨噬细胞的分化、成熟与增殖过程。
→ 保留参考；仅在当前问题需要其完整方法或定量证据时升级为 deep note。
Multiscale Kinematic Growth Coupled With Mechanosensitive Systems Biology in Open-Source Software
Active hole formation in epithelioid tissues
Atherosclerosis on a Chip: A 3-Dimensional Microfluidic Model of Early Arterial Events in Human Plaques
Biomechanics-mediated endocytosis in atherosclerosis
Management of Coronary Vulnerable Plaque With Medical Therapy or Local Preventive Percutaneous Coronary Intervention
The Distance Between: An Algorithmic Approach to Comparing Stochastic Models to Time-Series Data
The age of bone marrow dictates the clonality of smooth muscle-derived cells in atherosclerotic plaques
CRAT links cholesterol metabolism to innate immune responses in the heart
Fir(e)ing the Rhythm: Inflammatory Cytokines and Cardiac Arrhythmias
A high-salt diet promotes atherosclerosis by altering haematopoiesis
Physiological and pathological roles of lipogenesis
A role for lipophagy in atherosclerosis
Programming multicellular assembly with synthetic cell adhesion molecules
A stochastic mathematical model of 4D tumour spheroids with real-time fluorescent cell cycle labelling
Bidirectional, unlike unidirectional transport, allows transporting axonal cargos against their concentration gradient
Deep learning artificial intelligence framework for multiclass coronary artery disease prediction using combination of conventional risk factors, carotid ultrasound, and intraplaque neovascularization
Cardiorespiratory Fitness and Carotid Intima–Media Thickness in Physically Active Young Adults: CHIEF Atherosclerosis Study
Improving cardio-mechanic inference by combining in vivo strain data with ex vivo volume-pressure data
The Impact of Phenotypic Heterogeneity on Chemotactic Self-Organisation
Coupled reaction-diffusion transport into a core-shell geometry
Forced and spontaneous symmetry breaking in cell polarization
A mathematical model of immunomodulatory treatment in myocardial infarction
Receptor-independent fluid-phase macropinocytosis promotes arterial foam cell formation and atherosclerosis
NeuroMechFly, a neuromechanical model of adult Drosophila melanogaster
OxLDL induces membrane structure rearrangement leading to biomechanics alteration and migration deficiency in macrophage
Reviving a failed network through microscopic interventions
The changing landscape of atherosclerosis
Association of Coronary Artery Atherosclerosis With Brain White Matter Hyperintensity
A general principle for spontaneous genetic symmetry breaking and pattern formation within cell populations
Longitudinal histomechanical heterogeneity of the internal thoracic artery
Two-year plaque level outcomes involving the left anterior descending artery: insights from the Lipid-Rich Plaque study
Processing and reprocessing liquid crystal elastomer actuators
Nonlinear multiscale analysis of coronary atherosclerotic vulnerable plaque artery: fluid-structural modeling with micromechanics
Remodeling of the small caliber coronary vessels in experimental atherosclerosis
SIRT6 slows VSMC senescence and atherogenesis
The role of single-cell mechanical behaviour and polarity in driving collective cell migration
Emerging roles of fibroblasts in cardiovascular calcification
Flocking with a q-fold discrete symmetry: Band-to-lane transition in the active Potts model
Information transmission from NFkB signaling dynamics to gene expression
Strong intracellular signal inactivation produces sharper and more robust signaling from cell membrane to nucleus
Atherosclerosis
Identification of High-Risk Plaques Destined to Cause Acute Coronary Syndrome Using Coronary Computed Tomographic Angiography and Computational Fluid Dynamics
Single-cell analysis of fate-mapped macrophages reveals heterogeneity, including stem-like properties, during atherosclerosis progression and regression
The structure of binding curves and practical identifiability of equilibrium ligand-binding parameters
Structural identifiability of equilibrium ligand-binding parameters
Pim1 Kinase Overexpression Enhances ckit+ Cardiac Stem Cell Cardiac Repair Following Myocardial Infarction in Swine
Biomechanical regulation of vascular smooth muscle cell functions: from in vitro to in vivo understanding
Th1/Th2 paradigm extended: macrophage polarization as an unappreciated pathogen-driven escape mechanism?
Tissue-Specific Signals Control Reversible Program of Localization and Functional Polarization of Macrophages
Optimal homeostasis necessitates bistable control
Cholesterol Efflux Capacity, High-Density Lipoprotein Function, and Atherosclerosis
Macrophages in the Pathogenesis of Atherosclerosis
Modeling cardiac β-adrenergic signaling with normalized-Hill differential equations: comparison with a biochemical model
Multimodality Imaging of Carotid Artery Plaques: 18F-Fluoro-2-Deoxyglucose Positron Emission Tomography, Computed Tomography, and Magnetic Resonance Imaging
A methodology for performing global uncertainty and sensitivity analysis in systems biology
A Computational Study on Axisymmetric Abdominal Aortic Aneurysm Models Using Fluid-Structure Interactions Under Pulsatile Flow Conditions
Numerical investigation of physiologically realistic pulsatile flow through arterial stenosis
Signaling Networks: The Origins of Cellular Multitasking
Convective mass transfer at the carotid bifurcation
Morphometry of pig coronary venous system
Morphometry of pig coronary arterial trees
The Flowering of Applied Mathematics in America
Parametric Empirical Bayes Inference: Theory and Applications
Combination therapy and drug co-delivery systems for atherosclerosis
Modeling the biomechanical properties of soft biological tissues: Constitutive theories
Role of Antibodies and Their Specificities in Atherosclerotic Cardiovascular Disease
Multiscale computational modeling of arterial micromechanics: A review
LIANA+ provides an all-in-one framework for cell–cell communication inference
Management of Acute Coronary Syndrome in the Older Adult Population: A Scientific Statement From the American Heart Association
Current concepts and novel targets for antiplatelet therapy
Full-scale scaffold model of the human hippocampus CA1 area
Therapeutic strategies targeting inflammation and immunity in atherosclerosis: how to proceed?
The emergence of spontaneous coordinated epithelial rotation on cylindrical curved surfaces
The nonequilibrium mechanism of noise-enhanced drug synergy in HIV latency reactivation
Dynamic Mechanism of Phase Variations in Bacteria Based on Multistable Gene Regulatory Networks
Transforming growth factor-β in myocardial disease
Modeling Transport Regulation in Gene Regulatory Networks
Macrophage-produced VEGFC is induced by efferocytosis to ameliorate cardiac injury and inflammation
Evolving concepts of the vulnerable atherosclerotic plaque and the vulnerable patient: implications for patient care and future research
A mathematical modelling portrait of Wnt signalling in early vertebrate embryogenesis
Tutorial: Understanding the transport, deposition, and translocation of particles in human respiratory systems using Computational Fluid-Particle Dynamics and Physiologically Based Toxicokinetic models
Interleukin-1β suppression dampens inflammatory leukocyte production and uptake in atherosclerosis
Immune cell profiling in atherosclerosis: role in research and precision medicine
Identification of vulnerable plaques and patients by intracoronary near-infrared spectroscopy and ultrasound (PROSPECT II): a prospective natural history study
SMC-Derived Hyaluronan Modulates Vascular SMC Phenotype in Murine Atherosclerosis
Sex-Stratified Gene Regulatory Networks Reveal Female Key Driver Genes of Atherosclerosis Involved in Smooth Muscle Cell Phenotype Switching
Chemical signals from eggs facilitate cryptic female choice in humans
Microanatomy of the Human Atherosclerotic Plaque by Single-Cell Transcriptomics
Well-posedness and invariant measures for a class of stochastic 3D Navier-Stokes equations with damping driven by jump noise
Perivascular cell-specific knockout of the stem cell pluripotency gene Oct4 inhibits angiogenesis
Nanoparticle Therapy for Vascular Diseases
Margination and adhesion of micro- and nanoparticles in the coronary circulation: a step towards optimised drug carrier design
PCSK9 Inhibitors: Mechanisms of Action, Metabolic Effects, and Clinical Outcomes
Vascular Adaptation: Pattern Formation and Cross Validation between an Agent Based Model and a Dynamical System
Comprehensive Assessment of Coronary Plaque Progression With Advanced Intravascular Imaging, Physiological Measures, and Wall Shear Stress: A Pilot Double-Blinded Randomized Controlled Clinical Trial of Nebivolol Versus Atenolol in Nonobstructive Coronary Artery Disease
Stem cell-based therapies to promote angiogenesis in ischemic cardiovascular disease
Epigenetic Control of Smooth Muscle Cell Identity and Lineage Memory
Determination of parameter identifiability in nonlinear biophysical models: A Bayesian approach
Origin and Functions of Tissue Macrophages
Atherosclerotic coronary plaque regression and the risk of adverse cardiovascular events: A meta-regression of randomized clinical trials
Association of Coronary Wall Shear Stress With Atherosclerotic Plaque Burden, Composition, and Distribution in Patients With Coronary Artery Disease
Gene-expression profiles and transcriptional regulatory pathways that underlie the identity and diversity of mouse tissue macrophages
An Immune Response Network Associated with Blood Lipid Levels
Reconstruction of potential energy profiles from multiple rupture time distributions
Simulation of the human intracranial arterial tree
Modelling evolutionary cell behaviour using neural networks: Application to tumour growth
Mechanisms of Vascular Smooth Muscle Cell Migration
The role of shear stress in the pathogenesis of atherosclerosis
Lost in transdifferentiation
One-dimensional models for blood flow in arteries
Bistability in cell signaling: How to make continuous processes discontinuous, and reversible processes irreversible
Advection–diffusion equations for generalized tactic searching behaviors
Ultrasensitivity in the mitogen-activated protein kinase cascade
A quantitative model for the emergent population dynamics of the melanoma MITF rheostat
Personalized multiscale modeling of coronary plaque progression: the interaction between low-density-lipoprotein transport and cellular dynamics
Bioinspired Strategy for Controlling Crack Network Morphology on Curved Films
Smooth muscle cells in atherosclerosis: essential but overlooked translational perspectives
Constructing custom thermodynamics using deep learning
Mechanics of elliptical interlocking sutures in biological interfaces
Coronary microvascular function and atherosclerotic plaque burden in ischaemia and no obstructive coronary arteries: a secondary analysis of the CorMicA trial
Validation and Reproducibility of Total Plaque Thickness in Carotid and Femoral Arteries Using Ultrasound
Structural identifiability analysis of linear reaction–advection–diffusion processes in mathematical biology
Systems immunology-based drug repurposing framework to target inflammation in atherosclerosis
Novel and future lipid-modulating therapies for the prevention of cardiovascular disease
A stochastic lipid structured model for macrophage dynamics in atherosclerotic plaques
Atherosclerosis: Recent developments
Pathophysiology of Coronary Microvascular Dysfunction
A DNA-structured mathematical model of cell-cycle progression in cyclic hypoxia
Mathematical investigation into the role of macrophage heterogeneity on the temporal and spatio-temporal dynamics of non-small cell lung cancers
Macrophage-targeted nanomedicine for the diagnosis and treatment of atherosclerosis
Randomized, Placebo-Controlled Phase 2b Study to Evaluate the Safety and Efficacy of Recombinant Human Lecithin Cholesterol Acyltransferase in Acute ST-Segment–Elevation Myocardial Infarction: Results of REAL-TIMI 63B
Effect of statin therapy on muscle symptoms: an individual participant data meta-analysis of large-scale, randomised, double-blind trials
Stress-free morphing by means of compatible distortions
BioDynaMo: a modular platform for high-performance agent-based simulation
Atherosclerotic Carotid Plaque Composition and Incident Stroke and Coronary Events
Macroevolutionary stability predicts interaction patterns of species in seed dispersal networks
Mathematical modeling of plaque progression and associated microenvironment: How far from predicting the fate of atherosclerosis?
Probabilistic Inference on Noisy Time Series (PINTS)
Size control in mammalian cells involves modulation of both growth rate and cell cycle duration
Cellular uptake of nanoparticles: journey inside the cell
Probabilistic numerical methods for PDE-constrained Bayesian inverse problems
Well-posedness and large deviations for a class of SPDEs with Lévy noise
Role of biomechanical forces in the natural history of coronary atherosclerosis
A morphoelastic model for dermal wound closure
Activation of the pluripotency factor OCT4 in smooth muscle cells is atheroprotective
Precision medicine in cardiology
Anti-inflammatory therapies for atherosclerosis
Dividing Cells Regulate Their Lipid Composition and Localization
In vivo detection of high-risk coronary plaques by radiofrequency intravascular ultrasound and cardiovascular outcome: results of the ATHEROREMO-IVUS study
Mechanisms of Plaque Formation and Rupture
Oxygen mass transfer in a model three-dimensional artery
Aging and immortality in a cell proliferation model
Inflammatory monocytes recruited after skeletal muscle injury switch into antiinflammatory macrophages to support myogenesis
Multi-scale modeling of a wound-healing cell migration assay
Carotid Plaque Ultrasonic Heterogeneity and Severity of Stenosis
Lipid Lowering and Plaque Regression: New Insights Into Prevention of Plaque Disruption and Clinical Events in Coronary Disease
Chemo-orientation
Patterns of Cell Division and Cell Movement in the Formation of the Imaginal Nervous System in Drosophila melanogaster