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diff --git a/gnqa/paper2_eval/data/dataset/human/intermediate_files/human_cs_gn_13 b/gnqa/paper2_eval/data/dataset/human/intermediate_files/human_cs_gn_13 new file mode 100644 index 0000000..4263d86 --- /dev/null +++ b/gnqa/paper2_eval/data/dataset/human/intermediate_files/human_cs_gn_13 @@ -0,0 +1,65 @@ +{ + "titles": [ + "2009 - eQTL analysis in mice and rats.pdf", + "2015 - Genetic Control of Survival and Weight Loss during Pneumonic Burk.pdf", + "2015 -Emery- Genetic Control of Survival and Weight Loss during Pneumonic Burk.pdf", + "2005 - quantitative-trait-locus-analysis-of-aggressive-behaviours-in-mi.pdf", + "2005 -Broadkin- quantitative-trait-locus-analysis-of-aggressive-behaviours-in-mi.pdf", + "2006 - From_gene_to_behavior_and_back_again_new.pdf", + "2009 - Experimental_Evolution.pdf", + "2009 - Garland_and_Rose_Experimental_Evolution.pdf", + "2005 - quantitative-trait-analysis-in-the-investigation-of-function-and.pdf", + "2012 - Systems genetic analysis of the effects of iron deficiency in mouse brain.pdf" + ], + "extraction_id": [ + "71981bfb-284e-50ad-854e-2055c07f77a7", + "615ee0cd-5960-57e5-b4e6-56e4b8020a1b", + "268a23e8-f528-5b59-89f2-188331e0a03c", + "9de93371-6239-53c2-b42c-71f615a0614b", + "0a5c759e-8dab-55f1-ac59-e8211ec683b8", + "64c0287d-aeea-52eb-a074-e9591c5593ae", + "8ee78018-b998-590c-99ab-788a447ede81", + "cbce50ea-be78-5d54-beb1-849222c5bfdd", + "0a895880-91c0-5079-b258-73926b38430f", + "6ab990b0-4f9c-5be3-ab79-9ca6835271fa" + ], + "document_id": [ + "8d67ea90-f7b1-5bb8-937c-4a9eceddff43", + "ae1025b0-1410-51ae-9be2-26fa2e9d5808", + "a9aceace-bf48-5472-b54c-59a458a84c62", + "0dc730ba-4ff4-52aa-a988-71075113c416", + "e6027e7f-aec0-5e76-8aff-96b36389e701", + "7a088b36-11b7-5379-bfe5-ce571e11de07", + "34821353-1b74-5ee2-ac39-66dd46f145bf", + "496faa7f-9623-5ab7-9816-7c3755abb3aa", + "dac1c73c-0b5f-5a54-bb12-7e8b654009c0", + "99fc80f0-f3c3-5766-a604-921552bb3298" + ], + "id": [ + "chatcmpl-ADZKK0KDNVDBm3vRB6dGuJYB5JlVa", + "73540700-b5cf-5838-852b-b281ca086140", + "374c456a-d1db-5b4a-8713-97abe4162d77", + "b9d52798-0235-5018-bccd-560565d16cc3", + "c8f17022-aeae-5242-9082-d6d1eee4c4bf", + "1b2de424-be9f-572d-bd62-dc2ecd92192b", + "fef212bc-631b-591d-b8e3-d1523da0507d", + "f72795a1-66c3-5a98-84bc-b085e8008073", + "31a32dc5-81ac-52ba-a463-c61e293f21e5", + "b660d882-1cb0-5150-ae76-8eb3ccb88a58", + "7ef9df1d-b21a-597a-9e74-6eace5d0c33c" + ], + "contexts": [ + "While most of the Y chromosome does not undergo recombination, the recombination rate of the X chromosomeis slower than that of the autosomes. This has important consequences on the detection of significant QTLs. For a comprehensive view of these issues, see(43). 9.Probe hybridization artifacts When several probes are available for the same gene, it is not uncommon to observe a difference in the mapping results", + "8 QTL Mapping Allelic variation exists among natural populations and inbred strains, and this is reflective of the segregation of quantitative tr ait loci (QTLs) [96]. QTLs are stretches of DNA that are closely linked to genes that underlie a phenotype of interest. QTL analysis has been proven to be an invaluable tool to help unravel heritable traits, by enabling researchers to map different quantitative traits back to the genomic location involved in the regulation of these phenotypes.", + "8 QTL Mapping Allelic variation exists among natural populations and inbred strains, and this is reflective of the segregation of quantitative tr ait loci (QTLs) [96]. QTLs are stretches of DNA that are closely linked to genes that underlie a phenotype of interest. QTL analysis has been proven to be an invaluable tool to help unravel heritable traits, by enabling researchers to map different quantitative traits back to the genomic location involved in the regulation of these phenotypes.", + "genes underlying QTLs in animals and plants (see for example Shirley et al 2004,Korstanje & Paigen 2002, Fridman et al 2004). I should also point out, though, that even in a single QTL region isolated in a congenic strain, it is possible that there is more than one allele that aects the phenotype. So, you have a fair pointabout the challenges and complexities of QTL analysis. Koolhaas: There are dierent questions underlying both approaches. The QTL", + "genes underlying QTLs in animals and plants (see for example Shirley et al 2004,Korstanje & Paigen 2002, Fridman et al 2004). I should also point out, though, that even in a single QTL region isolated in a congenic strain, it is possible that there is more than one allele that aects the phenotype. So, you have a fair pointabout the challenges and complexities of QTL analysis. Koolhaas: There are dierent questions underlying both approaches. The QTL", + "The basic pr emise of QTL an alysis is simple (Ph illips and Belknap, 2002 ) . First, one must meas ure a speci c phen otype within a popul ation. Next, the population must be genotyped at a hundred or more marker loci186 Boehm II et al.", + "through analysis of line crosses, quantitative trait loci (QTL) mapping, and verification of candidate genes with quantitative complementation tests or genetic engineering (e.g.,McGuire and Tully 1987; Chandra et al. 2001; Dierick and Greenspan 2006; Edwardset al. 2006). They can also be used to study the underlying physiological, neural, andmolecular mechanisms of the differences in behavior between selected and controllines, or between divergently selected lines.", + "through analysis of line crosses, quantitative trait loci (QTL) mapping, and verification of candidate genes with quantitative complementation tests or genetic engineering (e.g.,McGuire and Tully 1987; Chandra et al. 2001; Dierick and Greenspan 2006; Edwardset al. 2006). They can also be used to study the underlying physiological, neural, andmolecular mechanisms of the differences in behavior between selected and controllines, or between divergently selected lines.", + "genetic background. Gene identification of QTL should be distinguished from identification of the quanti- tative trait nucleotide (QTN). The latter is a daunting task, since SNPs are so frequent. Final proof for a QTN in mice would require placing a genomic segment containing theputative QTN from a donor mouse strain on the background of another strain using homologous recombination and reproducing the phenotype of the donor strain.", + "because these strains have been genotyped at more than 14,000 markers, including single nucleotide polymorphisms (SNP). Hundreds of genes may lie within a QTL interval, so identifying the underlying genes requires complementary methods. One method is to use BXD gene expression data (a public resource at www.genenetwork.org) to screen for genes within the QTL interval whose expression correlates with the trait of interest [23]." + ], + "answer": "To differentiate between X and Y DNA with respect to DNA tracing and determining quantitative trait loci (QTLs), one must consider the unique characteristics of each chromosome: 1. **Recombination Rates**: - The Y chromosome largely does not undergo recombination, which means it is passed down relatively unchanged from father to son. This makes it easier to trace paternal lineage but limits its utility in QTL mapping due to the lack of recombination [1]. - The X chromosome, on the other hand, does undergo recombination, although at a slower rate compared to autosomes. This recombination can complicate tracing but is crucial for detecting significant QTLs [1]. 2. **QTL Mapping**: - QTLs are stretches of DNA closely linked to genes that influence a phenotype of interest. The detection and mapping of QTLs on the X chromosome can be more complex due to its recombination, but this recombination is necessary for identifying the genomic locations involved in regulating phenotypes [2]. - The Y chromosome's lack of recombination means it is less useful for QTL mapping, as the identification of QTLs relies on the recombination events that help pinpoint the genomic regions associated with specific traits [1]. In summary, the primary difference lies in the recombination behavior of the X and Y chromosomes, which affects their utility in DNA tracing and QTL determination. The X chromosome's recombination, although slower, is essential for QTL mapping, whereas the Y chromosome's lack of recombination makes it more suitable for tracing paternal lineage but less useful for QTL analysis.", + "question": "How does one tell the difference between X and Y DNA, with respect to DNA tracing and determining QTLs?" +}
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