1 files changed, 65 insertions, 0 deletions
diff --git a/gnqa/paper2_eval/data/dataset/human/intermediate_files/human_cs_aging_4 b/gnqa/paper2_eval/data/dataset/human/intermediate_files/human_cs_aging_4
new file mode 100644
index 0000000..a42f857
--- /dev/null
+++ b/gnqa/paper2_eval/data/dataset/human/intermediate_files/human_cs_aging_4
@@ -0,0 +1,65 @@
+{
+  "titles": [
+    "2010 - Do different neurons age differently Direct genome-wide analysis of aging in single identified cholinergic neurons.pdf",
+    "2020 - Whole-genome sequencing of Chinese.pdf",
+    "2011 - EXPLOITING NATURAL AND INDUCED GENETIC VARIATION TO STUDY HEMATOPOIESIS.pdf",
+    "2000 - Genome-wide study of aging and oxidative stress.pdf",
+    "2009 - The Human Ageing Genomic Resources online.pdf",
+    "2020 - A multidimensional systems biology.pdf",
+    "2008 - Combining transcriptional profiling and genetic linkage analysis to uncover gene networks operating in hematopoietic stem cells and their progeny.pdf",
+    "2012 - Genome-Environment Interactions That Modulate.pdf",
+    "2012 - Genome-Environment Interactions That Modulate.pdf",
+    "2012 - Genome-Environment Interactions That Modulate.pdf"
+  ],
+  "extraction_id": [
+    "81c68113-aa96-5af3-b4fc-5898fa20e379",
+    "0d3deffe-1f4d-5a6b-9acb-56d56141ad60",
+    "2b1a11ea-1574-5df6-b73a-a34052098751",
+    "ac5d00c0-f445-5c6a-b248-12c82c985d9a",
+    "52c67b46-63f2-54ae-a78e-e9d54a55f6e4",
+    "9d1656aa-32d2-5094-8232-4817655b1cbd",
+    "bf7b1e3c-bb4f-5a88-9167-a8c3b90cd68a",
+    "d59d7882-333d-5576-86ab-3cfa6354b946",
+    "d59d7882-333d-5576-86ab-3cfa6354b946",
+    "a01ca925-4ccf-5863-a162-7bd4c754fe89"
+  ],
+  "document_id": [
+    "153b070f-0291-5ed4-ad33-edea5e3fa8f7",
+    "9ac921c7-3991-579b-bd53-7966b91e3aae",
+    "6f250b15-61b3-57ed-8900-5aa4a173fa8c",
+    "3fc2266c-d677-54f9-b3a2-5129eedf214a",
+    "e43cd3b6-ad8e-5422-ba7c-ceb6e66cc529",
+    "d040bfe3-e409-5b5c-b8f8-f3dd4fc060e3",
+    "af6e0103-849d-542f-bca7-0251082bc0b3",
+    "b1a1997c-e9df-5dc0-9d12-a3977d0c64ec",
+    "b1a1997c-e9df-5dc0-9d12-a3977d0c64ec",
+    "b1a1997c-e9df-5dc0-9d12-a3977d0c64ec"
+  ],
+  "id": [
+    "chatcmpl-ADZVSukRfQ2bwSsJtuTxllhMDtRvP",
+    "6f04401a-b938-5a60-8b69-d37f9086748c",
+    "02b405a4-71d7-5b85-9138-8a97c537601c",
+    "8f8848f4-d5fb-5f8c-a6b1-0f965f2abbc6",
+    "b58deffd-3cd3-5b7b-893d-b9cfc880830b",
+    "8fd5ab85-67ed-55e6-bbfa-09436c4fdbfb",
+    "61baeaa5-d65a-54b5-bfee-9bab8bbf1985",
+    "2eb33321-d0fe-5fc4-aab0-7184f2b397e0",
+    "b719fbc0-94e4-5df0-abb7-0d13fc36214c",
+    "413f8f54-b5cc-5089-9f5c-d9e3b8bcf594",
+    "3c369292-4b9c-5156-a80f-4b3301026f30"
+  ],
+  "contexts": [
+    "OTHER AGING RELATED GENES",
+    "ation of the process of aging. Studies revealed from 300 to 750 genes related to longev- ity that are critically involved in a variety of life activities, such as growth and developme nt, energy metabolism, oxi- dative stress, genomic stability maintenance, and neurocog- nition [ 4]. These candidate genes include mainly APOE, a gene involved in lipoprotein metabolism [ 5,6]. Others are those involved in cell cycle regulation, cell growth and signal transduction, the maintenance of genome stability,",
+    "down-regulated during aging were genes involved in DNA repair and chromatin remodelling. 55 While these studies revealed thousands of age-regulated genes,  the ultimate causes of these expression perturbations remain unknown. Analyzing age-dependent gene expression changes using multi-dimensional genetical genomics could bring the identification of genes causing the age-induced alterations  and thereby future therapeutic intervention strategies  one step  closer.  Adding the dimension of epigenetics",
+    "dam-age, as well as genes involved in inducing apoptosis (10, 11). Theaging process is also accompanied by changes in the expressionpatterns of a number of genes (1214). How the regulation ofgene expression in aging correlates with that in response tooxidative stress, however, is understood poorly.",
+    "www.ncbi.nlm.nih.gov/homologene)  of genes strongly asso-ciated with aging in model organisms. Also included are genesin which mutations result in segmental progeroid syndromes,such as the Werners syndrome gene, as well as genes criticalin pathways previously related to aging, such as the insulin/insulin-like signalling pathway (de Magalhes   et     al  ., 2005a). The",
+    "genes driving cellular senescence, and perform various integrative analyses. Genes inducing cellular senescence tend to be overexpressed with age in human tissues and are significantly overrepresented in anti-longevity and tumor-suppressor genes, while genes inhibiting cellular senescence overlap with pro-longevity and oncogenes. Furthermore, cellular senescence genes are strongly conserved in mammals but not in invertebrates. We also build",
+    "those down-regulated during aging were genes involved in DNA repair and chromatin remodelling (Chambers et al. 2007b ). While these studies revealed thousands of age- regulated genes, the ultimate causes of these expressionperturbations remain unknown. Analyzing age-dependent gene expression changes using multidimensional genetical genomics could bring the identification of genes causingthe age-induced alterations and thereby future therapeutic intervention strategies one step closer.",
+    "lar signatures of mammalian aging. Some of the genes",
+    "overexpressed with age seem to be a response to aging,in that they have been previously found to have protec-tive functions (de Magalha es et al., 2009b). As such,these genes may help organisms manage aging andcould be targets for manipulation. Likewise, gene ex-pression analysis of CR has been conducted to identifyassociated genes (Lee et al., 1999, 2000). A number ofmolecular signatures have emerged from such studiesthat could be useful to identify candidate processes andpathways that affect aging,",
+    "al., 2009; Stanfel et al., 2009). Many of these genesmodulate the response to environmental signals, such asfood availability, and act in signaling pathways that ifunderstood can be targeted (Fig. 1). The genetic regula-tion of aging is therefore an emerging field with multipleapplications in the human nutrition, cosmetic, and phar-maceutical industries. AGING GENES AS TARGETS FOR DRUG DISCOVERY 91"
+  ],
+  "answer": "Several genes are involved in the aging process, as identified in the provided context:  1. **APOE**: This gene is involved in lipoprotein metabolism and is one of the candidate genes related to longevity [2]. 2. **Genes involved in cell cycle regulation, cell growth, and signal transduction**: These genes play a role in maintaining genome stability and are implicated in the aging process [2]. 3. **Genes involved in DNA repair and chromatin remodeling**: These genes are down-regulated during aging, indicating their involvement in the aging process [3], [7]. 4. **Genes inducing apoptosis**: These genes are also associated with the aging process [4]. 5. **Werners syndrome gene**: Mutations in this gene result in segmental progeroid syndromes, which are related to aging [5]. 6. **Genes in the insulin/insulin-like signaling pathway**: These genes are critical in pathways previously related to aging [5]. 7. **Genes driving cellular senescence**: These genes tend to be overexpressed with age in human tissues and are significantly overrepresented in anti-longevity and tumor-suppressor genes [6].  These genes collectively contribute to various aspects of the aging process, including genomic stability, cellular senescence, and response to oxidative stress.",
+  "question": "which genes are involved in the aging process"
+}
+\ No newline at end of file