Dan Lü

Deep Learning and Spectrum Analysis for Timbre Evaluation in Guzheng Performances

Dan Lü

Guzheng, a representative of Chinese traditional instrumental music, has long relied on subjective timbre evaluation without systematic modeling. This study integrates spectrum analysis and deep learning to construct an automatic sound quality evaluation framework. Audio samples across multiple playing styles were collected …

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Abstract 4053: Dynamic combinatorial p53 post-translational modifications regulate temporal transcription program and cell fates

Dan Lü

Abstract The tumor suppressor p53 is activated by a range of cellular stresses including DNA damage, oncogenic signals, and nutrient deprivation. Upon activation, p53 transcriptionally upregulates an extensive repertoire of genes including those affecting cell fates such as cell cycle arrest, senescence, …

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Identification, characterization, and expression of Oryza sativa tryptophan decarboxylase genes associated with fluroxypyr‐meptyl metabolism

Hao Wen Wang, Xu Zhen Shi, Gan Ai, Yan Hui Wang et autres

Abstract Tryptophan decarboxylase (TDC) belongs to a family of aromatic amino acid decarboxylases and catalyzes the conversion of tryptophan to tryptamine. It is the enzyme involved in the first step of melatonin (MT) biosynthesis and mediates several key functions in abiotic stress …

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Identification and characterization of a human MORC2 DNA binding region that is required for gene silencing

Nikole L. Fendler, Jimmy Ly, Luisa M. Welp, Dan Lü et autres

The eukaryotic microrchidia (MORC) protein family are DNA gyrase, Hsp90, histidine kinase, MutL (GHKL)-type ATPases involved in gene expression regulation and chromatin compaction. The molecular mechanisms underlying these activities are incompletely understood. Here, we studied the full-length human MORC2 protein biochemically. We …

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SubCell: Proteome-aware vision foundation models for microscopy capture single-cell biology

Zoe Wefers, Konstantin Kahnert, Jan N. Hansen, Anthony J. Cesnik et autres

Cell morphology and subcellular protein organization provide important insights into cellular function and behavior. These features of cells can be studied using large-scale protein fluorescence microscopy, and machine learning has become a powerful tool to interpret the resulting images for biological insights. …

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Temporal regulation of gene expression through integration of p53 dynamics and modifications

Dan Lü, Marjan Faizi, Bryon Drown, Alina Simerzin et autres

The master regulator of the DNA damage response, the transcription factor p53, orchestrates multiple downstream responses and coordinates repair processes. In response to double-strand DNA breaks, p53 exhibits pulses of expression, but how it achieves temporal coordination of downstream responses remains unclear. …

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Genome-wide identification and expression of Oryza sativa haloacid dehalogenase genes associated with oxadiazon metabolism

Zhao Jie Chen, Ya Nan Qu, Jun Jin Lu, Si Ying Li et autres

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Comprehensive analyses show the enhancement effect of exogenous melatonin on fluroxypyr-meptyl multiple phase metabolisms in Oryza sativa for reducing environmental risks

Zhao Jie Chen, Si Ying Li, Ya Nan Qu, Gan Ai et autres

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MSModDetector: a tool for detecting mass shifts and post-translational modifications in individual ion mass spectrometry data

Marjan Faizi, Ryan T. Fellers, Dan Lü, Bryon Drown et autres

MOTIVATION: Post-translational modifications (PTMs) on proteins regulate protein structures and functions. A single protein molecule can possess multiple modification sites that can accommodate various PTM types, leading to a variety of different patterns, or combinations of PTMs, on that protein. Different PTM …

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MSModDetector: A Tool for Detecting Mass Shifts and Post-Translational Modifications in Individual Ion Mass Spectrometry Data

Marjan Faizi, Ryan T. Fellers, Dan Lü, Bryon Drown et autres

Motivation: Post-translational modifications (PTMs) on proteins regulate protein structures and functions. A single protein molecule can possess multiple modification sites that can accommodate various PTM types, leading to a variety of different patterns, or combinations of PTMs, on that protein. Different PTM …

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Binding selectivity-dependent molecular mechanism of inhibitors towards CDK2 and CDK6 investigated by multiple short molecular dynamics and free energy landscapes

Lifei Wang, Dan Lü, Yan Wang, Xiaoyan Xu et autres

Understanding selectivity-dependent molecular mechanism of inhibitors towards CDK2 over CDK6 is prominent for improving drug design towards the CDK family. Multiple short molecular dynamics (MD) simulations combined with MM-GBSA approach are adopted to investigate molecular mechanism on binding selectivity of inhibitors X64, …

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Network pharmacology-based strategy for predicting therapy targets of Sanqi and Huangjing in diabetes mellitus

Xiaoyan Cui, Xiao Wu, Dan Lü, Dan Michelle Wang

BACKGROUND: , respectively. However, the combined effects of SQHJ on diabetes mellitus (DM) are still unclear. AIM: To explore the potential mechanism of Panax notoginseng (Sanqi in Chinese) and Polygonati Rhizoma (Huangjing in Chinese) for the treatment of DM using network pharmacology. …

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