Ray Luo
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View article: Myeloid-driven immunosuppression in head and neck cancer: single-cell ATAC/RNA and spatial transcriptomic perspectives
Myeloid-driven immunosuppression in head and neck cancer: single-cell ATAC/RNA and spatial transcriptomic perspectives Open
Head and neck squamous cell carcinoma (HNSCC) remains a prevalent epithelial malignancy. Immune-checkpoint inhibitors have reshaped first-line therapy for recurrent/metastatic disease; yet durable benefit is confined to a subset, reflectin…
View article: HMRM: A Hybrid Motion and Region-Fused Mamba Network for Micro-Expression Recognition
HMRM: A Hybrid Motion and Region-Fused Mamba Network for Micro-Expression Recognition Open
Micro-expression recognition (MER), as an important branch of intelligent visual sensing, enables the analysis of subtle facial movements for applications in emotion understanding, human–computer interaction and security monitoring. Howeve…
View article: DEGAUSS: A Novel Softcore Force Field Using Double Exponential van der Waals and Gaussian Charge for Molecular Dynamics Simulations I: Theory and Validation
DEGAUSS: A Novel Softcore Force Field Using Double Exponential van der Waals and Gaussian Charge for Molecular Dynamics Simulations I: Theory and Validation Open
Classical molecular force fields contain singularities in Lennard-Jones and Coulombic potentials that cause numerical challenges under extreme conditions, including transition states, high temperatures and pressures, and alchemical free en…
View article: Amino Acid Transporter CsBAT Links GABA Accumulation to Flavonoid Metabolism in <i>Camellia sinensis</i>
Amino Acid Transporter CsBAT Links GABA Accumulation to Flavonoid Metabolism in <i>Camellia sinensis</i> Open
γ-Aminobutyric acid (GABA), a signature bioactive compound in tea, plays a crucial role in determining both flavor profile and health-promoting properties. Despite its importance, the molecular regulation of GABA accumulation in tea plants…
View article: Engineered Fusion Enzyme‐Mediated Non‐Consecutive Cyclization‐Glycosylation Enables Heterologous Synthesis of Antifungal Enfumafungin
Engineered Fusion Enzyme‐Mediated Non‐Consecutive Cyclization‐Glycosylation Enables Heterologous Synthesis of Antifungal Enfumafungin Open
Enfumafungin‐type antibiotics, represented by enfumafungin and fuscoatroside, constitute a distinct class of fungi‐derived fernane‐type triterpenoids renowned for their potent antifungal activity. Notably, ibrexafungerp, a semi‐chemically …
View article: Conformal Thresholded Intervals for Efficient Regression
Conformal Thresholded Intervals for Efficient Regression Open
This paper introduces Conformal Thresholded Intervals (CTI), a novel conformal regression method that aims to produce the smallest possible prediction set with guaranteed coverage. Unlike existing methods that rely on nested conformal fram…
View article: Extending the MMPBSA method to membrane proteins: Addressing conformational changes upon ligand binding to P2Y12R
Extending the MMPBSA method to membrane proteins: Addressing conformational changes upon ligand binding to P2Y12R Open
Membrane proteins play crucial roles in biological signaling and represent key targets in drug discovery, garnering significant experimental and computational attention. Recent advances in computational screening techniques have enabled th…
View article: Refinement of Atomic Polarizabilities for a Polarizable Gaussian Multipole Force Field with Simultaneous Considerations of Both Molecular Polarizability Tensors and In-Solution Electrostatic Potentials
Refinement of Atomic Polarizabilities for a Polarizable Gaussian Multipole Force Field with Simultaneous Considerations of Both Molecular Polarizability Tensors and In-Solution Electrostatic Potentials Open
Atomic polarizabilities are considered to be fundamental parameters in polarizable molecular mechanical force fields that play pivotal roles in determining model transferability across different electrostatic environments. In an earlier wo…
View article: Extending the MMPBSA method to membrane proteins: Addressing conformational changes upon ligand binding to P2Y12R
Extending the MMPBSA method to membrane proteins: Addressing conformational changes upon ligand binding to P2Y12R Open
Membrane proteins play crucial roles in biological signaling and represent key targets in drug discovery, garnering significant experimental and computational attention. Recent advances in computational screening techniques have enabled th…
View article: Performance Tuning of Polarizable Gaussian Multipole Model in Molecular Dynamics Simulations
Performance Tuning of Polarizable Gaussian Multipole Model in Molecular Dynamics Simulations Open
Molecular dynamics (MD) simulations are essential for understanding molecular phenomena at the atomic level, with their accuracy largely dependent on both the employed force field and sampling. Polarizable force fields, which incorporate a…
View article: A Stepwise Decision Tree Model for Differential Diagnosis of Kimura's Disease in the Head and Neck
A Stepwise Decision Tree Model for Differential Diagnosis of Kimura's Disease in the Head and Neck Open
Objectives:This study aims to differentiate Kimura's disease (KD) from Sjogren's syndrome with mucosa-associated lymphoid tissue lymphoma (SS with MALT lymphoma), neurofibromatosis (NF), and lymphoma in the head and neck using a stepwise d…
View article: Study on the Selection of Takeaway Operating Modes from a Restaurant Perspective
Study on the Selection of Takeaway Operating Modes from a Restaurant Perspective Open
There are three operational modes for restaurant takeaway services: a takeaway platform combined with restaurant delivery (mode A), a takeaway platform paired with platform delivery (mode B), and a self-established platform with delivery (…
View article: Functional annotation of the Hippo pathway somatic mutations in human cancers
Functional annotation of the Hippo pathway somatic mutations in human cancers Open
The Hippo pathway is commonly altered in cancer initiation and progression; however, exactly how this pathway becomes dysregulated to promote human cancer development remains unclear. Here we analyze the Hippo somatic mutations in the huma…
View article: End-to-End Reaction Field Energy Modeling via Deep Learning based Voxel-to-voxel Transform
End-to-End Reaction Field Energy Modeling via Deep Learning based Voxel-to-voxel Transform Open
In computational biochemistry and biophysics, understanding the role of electrostatic interactions is crucial for elucidating the structure, dynamics, and function of biomolecules. The Poisson-Boltzmann (PB) equation is a foundational tool…
View article: Conformal Thresholded Intervals for Efficient Regression
Conformal Thresholded Intervals for Efficient Regression Open
This paper introduces Conformal Thresholded Intervals (CTI), a novel conformal regression method that aims to produce the smallest possible prediction set with guaranteed coverage. Unlike existing methods that rely on nested conformal fram…
View article: Targeting SHP2 Cryptic Allosteric Sites for Effective Cancer Therapy
Targeting SHP2 Cryptic Allosteric Sites for Effective Cancer Therapy Open
SHP2, a pivotal component downstream of both receptor and non-receptor tyrosine kinases, has been underscored in the progression of various human cancers and neurodevelopmental disorders. Allosteric inhibitors have been proposed to regulat…
View article: Role of artificial intelligence in revolutionizing drug discovery
Role of artificial intelligence in revolutionizing drug discovery Open
The application of artificial intelligence (AI) in medicine, particularly through machine learning (ML), marked a significant progression in drug discovery. AI acts as a powerful catalyst in narrowing the gap between disease understanding …
View article: PCMRESP: A Method for Polarizable Force Field Parameter Development and Transferability of the Polarizable Gaussian Multipole Models Across Multiple Solvents
PCMRESP: A Method for Polarizable Force Field Parameter Development and Transferability of the Polarizable Gaussian Multipole Models Across Multiple Solvents Open
The transferability of force field parameters is a crucial aspect of high-quality force fields. Previous investigations have affirmed the transferability of electrostatic parameters derived from polarizable Gaussian multipole models (pGMs)…
View article: Assessment of Amino Acid Electrostatic Parametrizations of the Polarizable Gaussian Multipole Model
Assessment of Amino Acid Electrostatic Parametrizations of the Polarizable Gaussian Multipole Model Open
Accurate parametrization of amino acids is pivotal for the development of reliable force fields for molecular modeling of biomolecules such as proteins. This study aims to assess amino acid electrostatic parametrizations with the polarizab…
View article: Targeting SHP2 Cryptic Allosteric Sites for Effective Cancer Therapy
Targeting SHP2 Cryptic Allosteric Sites for Effective Cancer Therapy Open
SHP2, a pivotal component downstream of both receptor and non-receptor tyrosine kinases, has been underscored in the progression of various human cancers and neurodevelopmental disorders. Allosteric inhibitors have been proposed to regulat…
View article: Targeting SHP2 Cryptic Allosteric Sites for Effective Cancer Therapy
Targeting SHP2 Cryptic Allosteric Sites for Effective Cancer Therapy Open
SHP2, a pivotal component downstream of both receptor and non-receptor tyrosine kinases, has been underscored in the progression of various human cancers and neurodevelopmental disorders. Allosteric inhibitors have been proposed to regulat…