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diff --git a/gnqa/paper2_eval/data/dataset/gpt4o/intermediate_files/gpt4o_cs_aging_20 b/gnqa/paper2_eval/data/dataset/gpt4o/intermediate_files/gpt4o_cs_aging_20 new file mode 100644 index 0000000..3f2af79 --- /dev/null +++ b/gnqa/paper2_eval/data/dataset/gpt4o/intermediate_files/gpt4o_cs_aging_20 @@ -0,0 +1,65 @@ +{ + "titles": [ + "2005 - Rapid and reversible induction of the longevity, anticancer.pdf", + "2009 - Genes and gene expression modules associated with caloric.pdf", + "2017 - Dietary restriction protects from age-associated DNA methylation and induces epigenetic reprogramming of lipid metabolism.pdf", + "2007 - The role of nuclear architecture.pdf", + "2016 - Epigenetics and aging.pdf", + "2012 - Genome-Environment Interactions That Modulate.pdf", + "2005 - Rapid and reversible induction of the longevity, anticancer.pdf", + "2005 - Rapid and reversible induction of the longevity, anticancer.pdf", + "2008 - Longevity mutation in SCH9 prevents recombination.pdf", + "2008 - DNA damage and ageing.pdf" + ], + "extraction_id": [ + "db18d213-92ed-5f3e-a242-60d3ed0ec8c8", + "0b45ae60-562c-5e48-a1c1-9eb29614a63c", + "a29560f5-a9e0-56d0-95f2-138eef516ef5", + "9655c555-838e-5cdf-85cf-13736c3cf028", + "91434549-bda3-5154-b089-28efed9c1089", + "5745c701-a549-51c3-adcc-b19c47436740", + "f4edcf22-ca64-5fe6-9bfa-f97a017d2d08", + "381d5314-5aa1-525f-a2a5-352b70ad86fa", + "bc856edb-7526-5424-a822-47075459a607", + "554b2b00-d006-5b97-aeb1-70ec31482641" + ], + "document_id": [ + "0b1bf178-21e4-5382-97c9-c93cdc1a9e66", + "893ba204-2e69-563f-9046-7246ca61494f", + "fe573bb0-3d37-55e5-93fa-65b3fbc5f532", + "578e2f7d-ddd4-56c8-a5b0-670969f8ff1e", + "71b206ec-81bd-5194-8b21-ae522f8cbc2d", + "b1a1997c-e9df-5dc0-9d12-a3977d0c64ec", + "0b1bf178-21e4-5382-97c9-c93cdc1a9e66", + "0b1bf178-21e4-5382-97c9-c93cdc1a9e66", + "a6b022ba-653f-51d3-845a-dd6b3d61d4a4", + "f170e9cf-dfab-5758-ab23-08daff2af694" + ], + "id": [ + "chatcmpl-AIFlaWmRr9Bl0RbY7T3uxkIANSmkA", + "56e72d29-31c2-5096-b4f8-06c740bce06e", + "2b081115-d36e-57ec-aedc-2fd9691bc5e9", + "bb028469-8295-5657-8061-a715cb314a4a", + "e01c4c58-342d-5369-89e6-98344af55000", + "1e116f55-36fd-525f-9950-9a1354c32f7b", + "b990eb0a-709a-500c-836e-83e202e0d6a6", + "833c9ddc-ec27-5301-9c3b-025eab95e28c", + "8151fbcb-f498-56a7-84ce-8af647fd2245", + "537cff80-380d-5c6a-a25a-04b32e9b1bd7", + "4f28b643-04a4-59e2-8226-ab050e698b64" + ], + "contexts": [ + "caloric restriction. Physiol. Genom. 17, 307 315.Van Remmen, H., Ward, W.F., Sabia, R.V ., Richardson, A., 1995. Gene expression and protein degradation. In: Masoro, E.J. (Ed.), Handbook ofPhysiology. Section 11: Aging. Oxford University Press, New York, pp. 171234. Weindruch, R., Walford, R.L., 1982. Dietary restriction in mice beginning at 1 year of age: effect on life-span and spontaneous cancer incidence.Science 215, 1415 1418.S.R. Spindler / Mechanisms of Ageing and Development 126 (2005) 960 966 966", + "extension by dietary restriction. Annu Rev Biochem 2008, 77:727-54. 8. Harper JM, Leathers CW, Austad SN: Does caloric restriction extend life iin wild mice? Aging Cell 2006, 5:441-9. 9. Forster MJ, Morris P, Sohal RS: Genotype and age influence the effect of caloric intake on mortality in mice. FASEB J 2003, 17:690-2. 10. Spindler SR, Mote PL: Screening candidate longevity therapeu- tics using gene-e xpression arrays. Gerontology 2007, 53:306-21.", + "analysis in calorie-restricted rats implicates epigenetic and post-translational mechanisms in neuroprotection and aging. Genome Biol. 2015;16:285. 21. Gillespie ZE, Pickering J, Eskiw CH. Better living through chemistry: caloric restriction (CR) and CR mimetics alter genome function to promote increased health and lifespan. Front Genet. 2016;7:142. 22. Jiang T, Liebman SE, Lucia MS, Phillips CL, Levi M. Calorie restriction modulates renal expression of sterol regulatory element binding proteins, lipid", + "Calorie restriction, a dietary regimen that extends the lifespan of numerous organisms, also delays the majority of age-related gene-expression changes in mice and, to a certain extent, in flies45,50. It is currently unclear whether the effect of calorie restriction on gene expression underlies its beneficial effect on lifespan or is merely a consequence thereof. Findings in yeast suggest that there may be a causal link: Sir2 not only facilitates heterochromatin and promotes DNA stability, but is", + "Transcriptome analysis in calorie-restricted rats implicates epigenetic and post- translational mechanisms in neuroprotection and aging. Genome Biol. 16,2 8 (2015). 204. M. V. Blagosklonny, Calorie restriction: Decelerating mTOR-driven aging from cells to or- ganisms (including humans). Cell Cycle 9, 683 688 (2010). 205. D. K. Ingram, G. S. Roth, Calorie restriction mimetics: Can you have your cake and eat it, too? Ageing Res. Rev. 20,4 662 (2015).", + "life-span extension by calorie restriction in Saccharomyces cerevisiae. Science 289:21262128. Mair W, Goymer P, Pletcher SD, and Partridge L (2003) Demography of dietary restriction and death in Drosophila. Science 301:17311733. Masoro EJ (2005) Overview of caloric restriction and ageing. Mech Ageing Dev 126:913922. Mathers JC (2006) Nutritional modulation of ageing: genomic and epigenetic ap- proaches. Mech Ageing Dev 127:584589. Meric-Bernstam F and Gonzalez-Angulo AM (2009) Targeting the mTOR signaling", + "Keywords: Caloric restriction; Short-term; Longevity; Cancer; Microarray; Affymetrix Aging is widely assumed to result from the gradual age- related accumulation of essentially irreversible moleculardamage. In this context, CR is often viewed as preventing orslowing the accumulation of such damage, thereby slowingthe process of aging ( Bokov et al., 2004 ). This view is intuitively appealing, as it provides a straightforwardexplanation for the stochastic nature of aging and the onset", + "of short- and long-term caloric restriction effects in the liver of agingmice. Proc. Natl. Acad. Sci. U.S.A. 98, 10630 10635.Capstick, F., Brooks, B.A., Burns, C.M., Zilkens, R.R., Steinbeck, K.S., Yue, D.K., 1997. Very low calorie diet (VLCD): a useful alternative inthe treatment of the obese NIDDM patient. Diab. Res. Clin. Pract. 36, 105111. Chen, H., 2004. Gene expression by the anterior pituitary gland: effects of age and caloric restriction. Mol. Cell. Endocrinol. 222, 21 31.", + "genomic effects of caloric restriction. Mech. Ageing Dev. 126 : 960 966 . Sun , H. , R.J. Bennett , and N. Maizels . 1999 . The Saccharomyces cerevisiae Sgs1 helicase effi ciently unwinds G-G paired DNAs. Nucleic Acids Res. 27 : 1978 1984 . Thompson , L.H. , and D. Schild . 2002 . Recombinational DNA repair and human disease. Mutat. Res. 509 : 49 78 .", + "L. & Spindler, S. R. Genomic profiling of short- and long-term caloric restriction effects in the liver of aging mice. Proc. Natl Acad. Sci. USA 98, 1063010635 (2001). 62. Harman, D. The aging process. Proc. Natl Acad. Sci. USA 78, 71247128 (1981). 63. van der Pluijm I, G. G.et.al. Impaired genome maintenance suppresses the growth hormoneinsulin-like growth factor 1 axis in mice with cockayne syndrome. PLoS Biol. 5, 2338 (2006). 64. Yang, H., Baur, J." + ], + "answer": "Caloric restriction and diet have significant impacts on the genetics of aging through various mechanisms: 1. **Gene Expression and Lifespan Extension**: Caloric restriction (CR) has been shown to delay age-related gene-expression changes in mice and, to some extent, in flies. This suggests that CR may influence the genetic pathways associated with aging, potentially contributing to lifespan extension [4]. 2. **Epigenetic and Post-Translational Mechanisms**: In calorie-restricted rats, transcriptome analysis indicates that CR involves epigenetic and post-translational mechanisms, which are implicated in neuroprotection and aging. These mechanisms may alter genome function to promote increased health and lifespan [3], [5]. 3. **mTOR Pathway**: Caloric restriction is associated with decelerating mTOR-driven aging, which is a significant pathway involved in cellular growth and metabolism. By modulating this pathway, CR may influence the genetic regulation of aging processes [5]. 4. **Genomic and Epigenetic Approaches**: Nutritional modulation, including caloric restriction, can impact aging through genomic and epigenetic approaches. This suggests that diet can influence the genetic and epigenetic landscape, potentially affecting the aging process [6]. Overall, caloric restriction and diet can modulate genetic pathways and mechanisms that are crucial for aging, potentially leading to increased lifespan and improved health during aging.", + "question": "How do caloric restriction and diet impact the genetics of aging?" +}
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