% Bibliography for hypothesis h-b0cda336
% Title: Digital Twin-Guided Metabolic Reprogramming
% Generated: 2026-04-28T13:52:26Z

@article{pmid39577614,
  title = {Polystyrene microplastics induced spermatogenesis disorder via disrupting mitochondrial function through the regulation of the Sirt1-Pgc1α signaling pathway in male mice.},
  author = {["Jin H", "Xue B", "Chen X", "Ma T", "Ma Y", "Zou H", "Zhu J", "Tong X", "Song R", "Meng W"]},
  journal = {Environmental pollution (Barking, Essex : 1987)},
  year = {2025},
  pmid = {39577614},
  doi = {10.1016/j.envpol.2024.125364},
}

@article{pmid39987285,
  title = {Glucose Metabolic Reprogramming in Microglia: Implications for Neurodegenerative Diseases and Targeted Therapy.},
  author = {Fang M, Zhou Y, He K, Lu Y, Tao F, Huang H},
  journal = {Mol Neurobiol},
  year = {2025},
  pmid = {39987285},
  doi = {10.1007/s12035-025-04775-y},
  url = {https://pubmed.ncbi.nlm.nih.gov/39987285},
}

@article{pmid40327990,
  title = {Metformin restores mitochondrial bioenergetics and redox homeostasis through modulation of mitochondrial biogenesis and dynamics in patient derived cultured fibroblasts and an animal model of molybdenum cofactor deficiency.},
  author = {Brondani M, Ribeiro RT, Pinheiro CV, Hoffmann CIH, Marcuzzo MB, Mohsen AW, Wajner M, Seminotti B, Vockley J, Leipnitz G},
  journal = {Biomed Pharmacother},
  year = {2025},
  pmid = {40327990},
  doi = {10.1016/j.biopha.2025.118123},
  url = {https://pubmed.ncbi.nlm.nih.gov/40327990},
}

@article{pmid40664965,
  title = {System biology-based assessment of the molecular mechanism of epigallocatechin gallate in Parkinson's disease: via network pharmacology, in-silico evaluation & in-vitro studies.},
  author = {Fanai HL, Chand J, Ahmad SF, Attia SM, Emran TB},
  journal = {Sci Rep},
  year = {2025},
  pmid = {40664965},
  doi = {10.1038/s41598-025-11592-9},
  url = {https://pubmed.ncbi.nlm.nih.gov/40664965},
}

@article{pmid40914506,
  title = {Lipid metabolism and immune crosstalk in fish gut-liver axis: Insights from SOCS8 knockout and dietary stress models.},
  author = {Altaf F, Wu N, Shi M, Li J, Shan J, Su L, Wang G, Zhu Q, Hu Y, Cheng Y, Zhang W, Unger BH, Xia XQ},
  journal = {Fish & shellfish immunology},
  year = {2025},
  pmid = {40914506},
  doi = {10.1016/j.fsi.2025.110705},
  url = {https://pubmed.ncbi.nlm.nih.gov/40914506/},
}

@article{pmid41045381,
  title = {p75NTR Modulation by LM11A-31 Counteracts Oxidative Stress and Cholesterol Dysmetabolism in a Rotenone-Induced Cell Model of Parkinson's Disease.},
  author = {["Pensabene D", "Martella N", "Scavo G", "Bisesto E", "Cavicchia F", "Colardo M", "Varone M", "Moreno S", "Segatto M"]},
  journal = {Neurochemical research},
  year = {2025},
  pmid = {41045381},
  doi = {10.1007/s11064-025-04569-7},
}

@article{pmid41269417,
  title = {PSMD4 Alleviates Aβ₁₋₄₂-Induced Mitochondrial Dysfunction and Oxidative Stress via the PGC-1α/Nrf Axis in Alzheimer's Disease Models.},
  author = {["Yuan M", "Han X", "Luo C", "Pan H", "Zhou H"]},
  journal = {Molecular neurobiology},
  year = {2025},
  pmid = {41269417},
  doi = {10.1007/s12035-025-05445-9},
}

@article{pmid41269417,
  title = {PSMD4 Alleviates Aβ₁₋₄₂-Induced Mitochondrial Dysfunction and Oxidative Stress via the PGC-1α/Nrf Axis in Alzheimer's Disease Models.},
  author = {Yuan M, Han XJ, Luo CQ, Pan HL, Zhou HY},
  journal = {Mol Neurobiol},
  year = {2025},
  pmid = {41269417},
  doi = {doi: 10.1007/s12035-025-05445-9},
  url = {https://pubmed.ncbi.nlm.nih.gov/41269417/},
}

@article{pmid38501315,
  title = {Glymphatic system dysfunction predicts amyloid deposition, neurodegeneration, and clinical progression in Alzheimer's disease.},
  author = {Huang SY, Zhang YR, Guo Y, Du J, Ren P, Wu BS, Feng JF, Alzheimer's Disease Neuroimaging Initiative, Cheng W, Yu JT},
  journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association},
  year = {2024},
  pmid = {38501315},
  doi = {10.1002/alz.13789},
  url = {https://pubmed.ncbi.nlm.nih.gov/38501315/},
}

@article{pmid38889331,
  title = {Cordycepin Modulates Microglial M2 Polarization Coupled with Mitochondrial Metabolic Reprogramming by Targeting HKII and PDK2.},
  author = {["Zhong X", "Gong S", "Meng L", "Yao W", "Du K", "Jiao L", "Ma G", "Liang J", "Wei B", "Jin X"]},
  journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
  year = {2024},
  pmid = {38889331},
  doi = {10.1002/advs.202304687},
}

@article{pmid39528464,
  title = {Inflammation in atherosclerosis: pathophysiology and mechanisms.},
  author = {Ajoolabady A, Pratico D, Lin L, Mantzoros CS, Bahijri S, Tuomilehto J, Ren J},
  journal = {Cell death & disease},
  year = {2024},
  pmid = {39528464},
  doi = {10.1038/s41419-024-07166-8},
  url = {https://pubmed.ncbi.nlm.nih.gov/39528464/},
}

@article{pmid37586250,
  title = {Metabolic reprogramming in inflammatory microglia indicates a potential way of targeting inflammation in Alzheimer's disease.},
  author = {["Sangineto M", "Ciarnelli M", "Cassano T", "Radesco A", "Moola A", "Bukke V", "Romano A", "Villani R", "Kanwal H", "Capitanio N"]},
  journal = {Redox biology},
  year = {2023},
  pmid = {37586250},
  doi = {10.1016/j.redox.2023.102846},
}

@article{pmid34822940,
  title = {Effect of DEHP and DnOP on mitochondrial damage and related pathways of Nrf2 and SIRT1/PGC-1α in HepG2 cells.},
  author = {["Liu H", "Han W", "Zhu S", "Li Z", "Liu C"]},
  journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association},
  year = {2021},
  pmid = {34822940},
  doi = {10.1016/j.fct.2021.112696},
}

@article{pmid35011673,
  title = {Covering the Role of PGC-1α in the Nervous System.},
  author = {Kuczynska Z, Metin E, Liput M, Buzanska L},
  journal = {Cells},
  year = {2021},
  pmid = {35011673},
  doi = {10.3390/cells11010111},
  url = {https://pubmed.ncbi.nlm.nih.gov/35011673/},
}

@article{pmid32758586,
  title = {Minutes of PPAR-γ agonism and neuroprotection.},
  author = {Prashantha Kumar BR, Kumar AP, Jose JA, Prabitha P, Yuvaraj S, Chipurupalli S, Jeyarani V, Manisha C, Banerjee S, Jeyabalan JB},
  journal = {Neurochem Int},
  year = {2020},
  pmid = {32758586},
  doi = {10.1016/j.neuint.2020.104814},
  url = {https://pubmed.ncbi.nlm.nih.gov/32758586},
}

@article{pmid31257151,
  title = {A Breakdown in Metabolic Reprogramming Causes Microglia Dysfunction in Alzheimer's Disease.},
  author = {["Baik S", "Kang S", "Lee W", "Choi H", "Chung S", "Kim J", "Mook-Jung I"]},
  journal = {Cell metabolism},
  year = {2019},
  pmid = {31257151},
  doi = {10.1016/j.cmet.2019.06.005},
}

@article{pmid30201263,
  title = {Ropivacaine impairs mitochondrial biogenesis by reducing PGC-1α.},
  author = {["Niu Z", "Tang J", "Ren Y", "Feng W"]},
  journal = {Biochemical and biophysical research communications},
  year = {2018},
  pmid = {30201263},
  doi = {10.1016/j.bbrc.2018.08.186},
}

@article{pmid30249643,
  title = {Stimulation of AMPK prevents degeneration of photoreceptors and the retinal pigment epithelium.},
  author = {["Xu L", "Kong L", "Wang J", "Ash J"]},
  journal = {Proceedings of the National Academy of Sciences of the United States of America},
  year = {2018},
  pmid = {30249643},
  doi = {10.1073/pnas.1802724115},
}

@article{pmid26971449,
  title = {Promotion of mitochondrial biogenesis by necdin protects neurons against mitochondrial insults.},
  author = {["Hasegawa K", "Yasuda T", "Shiraishi C", "Fujiwara K", "Przedborski S", "Mochizuki H", "Yoshikawa K"]},
  journal = {Nature communications},
  year = {2016},
  pmid = {26971449},
  doi = {10.1038/ncomms10943},
}

@article{pmid27188934,
  title = {Alzheimer's disease.},
  author = {["Masters C", "Bateman R", "Blennow K", "Rowe C", "Sperling R", "Cummings J"]},
  journal = {Nature reviews. Disease primers},
  year = {2015},
  pmid = {27188934},
  doi = {10.1038/nrdp.2015.56},
}

@article{pmid24558078,
  title = {The pharmacogenetics of type 2 diabetes: a systematic review.},
  author = {Nisa M Maruthur, Matthew O Gribble, Wendy L Bennett, Shari Bolen, Lisa M Wilson et al.},
  journal = {Diabetes care},
  year = {2014},
  pmid = {24558078},
  doi = {10.2337/dc13-1276},
  url = {https://pubmed.ncbi.nlm.nih.gov/24558078},
}

@article{pmid23602910,
  title = {PGC-1α, mitochondrial dysfunction, and Huntington's disease.},
  author = {Johri A, Chandra A, Flint Beal M},
  journal = {Free radical biology & medicine},
  year = {2013},
  pmid = {23602910},
  doi = {10.1016/j.freeradbiomed.2013.04.016},
  url = {https://pubmed.ncbi.nlm.nih.gov/23602910/},
}

@article{pmid23145024,
  title = {Pgc-1α overexpression downregulates Pitx3 and increases susceptibility to MPTP toxicity associated with decreased Bdnf.},
  author = {["Clark J", "Silvaggi J", "Kiselak T", "Zheng K", "Clore E", "Dai Y", "Bass C", "Simon D"]},
  journal = {PloS one},
  year = {2012},
  pmid = {23145024},
  doi = {10.1371/journal.pone.0048925},
}