Docker image built to run code, all evals run using R2RHEADmaster

1 files changed, 65 insertions, 0 deletions

diff --git a/gnqa/paper2_eval/data/dataset/human/intermediate_files/human_de_gn_11 b/gnqa/paper2_eval/data/dataset/human/intermediate_files/human_de_gn_11
new file mode 100644
index 0000000..8dcfd54
--- /dev/null
+++ b/gnqa/paper2_eval/data/dataset/human/intermediate_files/human_de_gn_11
@@ -0,0 +1,65 @@
+{
+  "titles": [
+    "2009 - Opening Up the Conversation on Genetics.pdf",
+    "2008 -  Study Design and Statistical Issues.pdf",
+    "2015 - Constraint and divergence of global gene expression in the mammalian embryo.pdf",
+    "2015 - Constraint and divergence of global gene expression in the mammalian embryo.pdf",
+    "2015 - Basic Concepts and Potential Applications of Genetics and Genomics for Cardiovascular and Stroke Clinicians.pdf",
+    "2019 - Sexual Dimorphism in the Age of Genomics How, When, Where.pdf",
+    "2008 - Genotype-phenotype relationships and the patterning of complex traits as exemplified in the mammalian dentition.pdf",
+    "2007 - Promoting_Student_Scientific_Literacy_of_Molecular Genetics and Genomics.pdf",
+    "2015 - Basic Concepts and Potential Applications of Genetics and Genomics for Cardiovascular and Stroke Clinicians.pdf",
+    "2019 - The influence of paternal diet on sncRNA-mediated epigenetic.pdf"
+  ],
+  "extraction_id": [
+    "51dbd5e2-fde6-5097-aa05-fcf57d3ca6b1",
+    "06bf0605-388a-592c-96ad-3a53bb36362c",
+    "261c4af7-f63d-51ac-b164-0d9e7a64bff9",
+    "261c4af7-f63d-51ac-b164-0d9e7a64bff9",
+    "8a1ce8fa-b5f4-5942-b7b1-14a8a7887710",
+    "e22bb6fb-bec4-5c4c-8690-c96d0b8d13d4",
+    "5aab3e60-b8b0-52ad-b4d3-817cf012cfa5",
+    "67369433-749b-5d6a-b5ef-3f0afe78b767",
+    "206b8810-b7c1-5195-a10f-4e291864b77c",
+    "84335575-34d7-56b6-aa06-5a8ac13d637a"
+  ],
+  "document_id": [
+    "b62a8f54-c2f5-5bbb-9324-af80f7537167",
+    "c3bd9cf0-f768-55c4-be94-96590d7acc21",
+    "3d9005f1-8f71-5d39-8749-4ebeab962cab",
+    "3d9005f1-8f71-5d39-8749-4ebeab962cab",
+    "8610e699-218a-50e6-8d1d-ef689623266f",
+    "3f8c03b0-4235-5774-9d26-e43d55c1001b",
+    "f6e866b8-b233-5862-bfb8-9949d0dabb97",
+    "755f34c4-cc06-5275-a744-16d48162b012",
+    "8610e699-218a-50e6-8d1d-ef689623266f",
+    "dfcbd6e6-f60d-5eb7-867b-34ec78415e82"
+  ],
+  "id": [
+    "chatcmpl-ADZAJ4XRzNSAEiekxHtxfyNvHLw8G",
+    "60ad1512-b0c0-59cd-ace4-c146e2c04b52",
+    "1e151ad5-59d9-598d-97ba-90ba0e64c4cb",
+    "a66b8b00-d51c-575b-b6ac-fa445c4ca715",
+    "df4c6108-740d-5bcf-99e6-dbda74f7e41a",
+    "4472740a-d22d-5bb1-98e3-e91332cbb303",
+    "0158f264-120f-5942-ad55-ef5fde1f188a",
+    "47b9142f-98a3-5a45-8eaa-d327c9cc055d",
+    "8e3fdc2c-0962-5854-83e7-a60ab05cf6de",
+    "6c8dfaa1-a96f-5f1c-8b5a-870acfd46f5f",
+    "be93ee68-72ae-5015-a3f0-19e7bf24827a"
+  ],
+  "contexts": [
+    "the egg and the sperm. Such a process would result in genetic changes that will be copied into every cell of the future adult, including reproductive cells (Stock & Campbell, 2000), opening the door to irreversibly alter the human species. Inevitably, signifi  cant self-disclosure and discussion challenges await families",
+    "phenomena such as mutations and gene conversion events) occur in relevant meioses  leading up to the formation of the gametes (i.e., egg and sperm) which are combined  during fertilization and the formation of zygotes. Thus, individuals inherit a patch- work of chromosomal segments from maternal and paternal chromosomes.",
+    "a fertilized egg is a complicated process that relies on controlling: which genes are active; whenthese genes activate; and for how long they are active. In broad terms, there are four ways that thiscontrol can be achieved: First, inside the sperm or egg, genes can be marked with small chemical tags that flag these genes",
+    "to be activated (or remain inactive) after fertilization, depending on whether the modification wasmade by the father (in the sperm) or the mother (in the egg); this process is known as imprinting. Second, the mother can alter the gene activity in her offspring via the placenta; this process is known as maternal effect. Third, instructions encoded within the embryos DNA can directly control if, andwhen, a nearby gene becomes activated; this is known as  cis-regulation. Finally, similar instructions",
+    "(Figures 8 and 9). Two gametes (egg and sperm) ultimately  join into a single cell, the zygote, which has the full comple-ment of 23 chromosome pairs restored. If all goes well, the zygote gives rise to a live offspring. The Mendel Laws: Segregation and Independent  Assortment Both of the Mendel laws pertain directly to the process of  meiosis. The first Mendel law, the law of segregation, states  that each parent passes a randomly selected allele for a given",
+    "sex chromosome effects. (B)Soon after fertilization, male and female cells have sex-specic transcriptomes, epigenomes, and phenotypes (for example, male embryos grow faster than female embryos). At implantation, lineage determination begins and gene expression differences are reduced. Epigenetic marks, however, are less constrained and some are maintained, affecting gene expression, and phenotype later in development. Once specic lineages are established, differences in",
+    "the subset of that genetic information that is active.  But how does the differentiation process  begin?  The key insight in resolving this conundrum came from fly genetics and was the  realization that the egg is not a homogenous sack of protoplasm.  The maternally-derived genes  active in the fertilized egg are asymmetrically distributed such that at the first cell division each  daughter cell receives a different complement of factors.  Development continues as a",
+    "genes.  An altered gene may be passed on to every cell that develops from it.  The resulting features my help, harm, or have little or no effect on the offsprings success in its environment. (AAAS, pg. 109, 5B:9-12#4 ) 6. Heritable material: The information passed from parents to offspring is coded in DNA molecules (AAAS, pg 108, 5B:9-12#3) 7. Mutagens: Gene mutations can be caused by such things as radiation and chemicals.  When they occur in sex cells, the mutations can be passed onto offspring; if they",
+    "or father (sperm cell). Each gamete has a set of 23 unpaired chromosomes. Two human gametes (egg and sperm) combine  to create a cell (zygote) that contains the full human genome  of 23 paired chromosomes.Genetic Information Nondiscrimination Act (GINA) US federal legislation that makes it unlawful to discriminate  against individuals on the basis of their genetic profiles in regard to health insurance and employment. These protections  are intended to encourage Americans to take advantage of",
+    "spermatozoa: more than the sum of its parts? DNA, histones, pro - tamines and epigenetics. Reproduction 139:287301 Nilsson EE, Sadler-Riggleman I, Skinner MK (2018) Environmentally  induced epigenetic transgenerational inheritance of disease. Envi-ron Epigenet 4:dvy016Pembrey M, Saffery R, Bygren LO, Network in Epigenetic Epide-"
+  ],
+  "answer": "Once a sperm combines with an egg, the traits passed onto the resulting lifeform are determined by several genetic and epigenetic factors:  1. **Chromosomal Segments**: Individuals inherit a patchwork of chromosomal segments from maternal and paternal chromosomes, which are combined during fertilization to form the zygote [2].     2. **Mendelian Laws**: The Mendel laws of segregation and independent assortment play a crucial role. Each parent passes a randomly selected allele for a given trait to the offspring, ensuring genetic diversity [5].  3. **Gene Activation and Regulation**: The process of gene activation and regulation is complex and involves several mechanisms:    - **Imprinting**: Genes can be marked with small chemical tags that determine whether they are activated or remain inactive after fertilization, depending on whether the modification was made by the father (in the sperm) or the mother (in the egg) [3], [4].    - **Maternal Effect**: The mother can alter gene activity in her offspring via the placenta [4].    - **Cis-regulation**: Instructions encoded within the embryo's DNA can directly control if and when a nearby gene becomes activated [4].  4. **Epigenetic Marks**: Epigenetic marks, which are less constrained and can be maintained, affect gene expression and phenotype later in development [6].  These factors collectively determine how traits are passed onto the resulting lifeform after the sperm combines with the egg.",
+  "question": "Once a sperm combines with an egg, what determines how traits are passed onto the resulting lifeform?"
+}
\ No newline at end of file