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Res."},{"key":"10.1016\/j.xgen.2025.101108_bib69","doi-asserted-by":"crossref","first-page":"1078","DOI":"10.1016\/S0022-5347(05)65925-3","article-title":"The influence of sex hormones on renal osteopontin expression and urinary constituents in experimental urolithiasis","volume":"166","author":"Yagisawa","year":"2001","journal-title":"J. Urol."},{"key":"10.1016\/j.xgen.2025.101108_bib70","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1186\/s12920-023-01519-6","article-title":"Identification and validation of immune-related biomarkers and potential regulators and therapeutic targets for diabetic kidney disease","volume":"16","author":"Chen","year":"2023","journal-title":"BMC Med. 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Alzheimers Dis."},{"key":"10.1016\/j.xgen.2025.101108_bib87","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1101\/gad.13.5.523","article-title":"Mouse MutS-like protein Msh5 is required for proper chromosome synapsis in male and female meiosis","volume":"13","author":"de Vries","year":"1999","journal-title":"Genes Dev."},{"key":"10.1016\/j.xgen.2025.101108_bib88","doi-asserted-by":"crossref","first-page":"1728","DOI":"10.1101\/gad.9.14.1728","article-title":"MSH5, a novel MutS homolog, facilitates meiotic reciprocal recombination between homologs in Saccharomyces cerevisiae but not mismatch repair","volume":"9","author":"Hollingsworth","year":"1995","journal-title":"Genes Dev."},{"key":"10.1016\/j.xgen.2025.101108_bib89","doi-asserted-by":"crossref","first-page":"7193","DOI":"10.1073\/pnas.0700815104","article-title":"Role for Msh5 in the regulation of Ig class switch recombination","volume":"104","author":"Sekine","year":"2007","journal-title":"Proc. Natl. Acad. Sci. 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(NY)"},{"key":"10.1016\/j.xgen.2025.101108_bib123","doi-asserted-by":"crossref","first-page":"399","DOI":"10.1677\/joe.0.0130399","article-title":"Modification of the mouse estrous cycle by external male-associated stimuli","volume":"13","author":"Whitten","year":"1956","journal-title":"J. Endocrinol."},{"key":"10.1016\/j.xgen.2025.101108_bib124","doi-asserted-by":"crossref","first-page":"4576","DOI":"10.1073\/pnas.83.12.4576","article-title":"Promotion of the Whitten effect in female mice by synthetic analogs of male urinary constituents","volume":"83","author":"Jemiolo","year":"1986","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.xgen.2025.101108_bib125","doi-asserted-by":"crossref","first-page":"16219","DOI":"10.1073\/pnas.1408886111","article-title":"A circadian gene expression atlas in mammals: Implications for biology and medicine","volume":"111","author":"Zhang","year":"2014","journal-title":"Proc. Natl. Acad. Sci. 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