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| author | SoloDShelby | 2024-07-19 14:41:40 +0300 |
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| committer | SoloDShelby | 2024-07-19 14:41:40 +0300 |
| commit | 3fa31b50af2861382fbe2c76406f5a04c3fefc93 (patch) | |
| tree | 34d581648b0e0d3fc8dbe6577752a4fd433a3258 /gnqa/paper1_eval/src/data/ratings/2024_05_21-gnqa_responses.json | |
| parent | 74616897e30c7daafe5e74d34073466464921316 (diff) | |
| download | gn-ai-3fa31b50af2861382fbe2c76406f5a04c3fefc93.tar.gz | |
Evaluation code for paper 1
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diff --git a/gnqa/paper1_eval/src/data/ratings/2024_05_21-gnqa_responses.json b/gnqa/paper1_eval/src/data/ratings/2024_05_21-gnqa_responses.json new file mode 100644 index 0000000..c90818f --- /dev/null +++ b/gnqa/paper1_eval/src/data/ratings/2024_05_21-gnqa_responses.json @@ -0,0 +1,513 @@ +[ +{ + "user_id": "b4601142-3b57-4d5b-9b55-80bdf0ea4599", + "query": "List as many studies as you can that include rapamycin.", + "answer": "1. Study by Kaeberlein (2013b) on the use of Rapamycin in preventing organ transplant rejection, some forms of cancer, and restenosis in cardiac stents.\n2. Study by Mannick et al. (2014) on the use of Rapamycin derivative RAD001 in improving age-associated decline in immune function in elderly people.\n3. Study by Yi et al. (2014) on the use of Rapamycin in improving outcomes in a glycogen storage disease model.\n4. Study by Paoloni et al. (2010) on the use of Rapamycin in veterinary clinical trials for osteosarcoma.\n5. Study by Kaeberlein (2015) on the use of Rapamycin in assessing side effects and effects on age-associated cardiac function in elderly dogs.\n6. Study by Meric-Bernstam and Gonzalez-Angulo (2009) on the use of Rapamycin in the context of cancer.\n7. Study by Larson et al. (2016) on the use of Rapamycin in determining initial dosing regimens in healthy dogs.\n8. Study by Dai et al. (2014) and Flynn et al. (2013) on the use of Rapamycin in improving cardiac function in laboratory mice.\n9. Study by Johnson et al. (2015) on the use of Rapamycin in improving health and reducing mortality in middle-aged companion dogs.\n10. Study by Chen et al. (2009) on the use of Rapamycin in delaying aging in mice.\n11. Study by Augustine et al. (2007) and de Oliveira et al. (2011) on the side effects of Rapamycin.\n12. Study by Lamming et al. (2012) on the possible side effects of Rapamycin on glucose homeostasis.\n13. Study on the use of Rapamycin as a CRM due to its modulating properties over proteostasis.\n14. Study by Johnson et al. (2013) on the use of Rapamycin in extending lifespan and delaying age-related functional declines in rodents.", + "weight": 1, + "task_id": "2D8205C79915FF9CEB8DECCE51E6E473" +}, +{ + "user_id": "e031ac19-fec1-4d97-a037-cd39d3817c54", + "query": "What are the genetic bases for the varying efficacy of diabetes treatments among individuals?", + "answer": "The varying efficacy of diabetes treatments among individuals can be attributed to genetic variants present in drug receptors or drug metabolizers, such as OCT genes, KCNJ11, ABCC8, and CYP2C9. These genetic variants can influence the metabolism, transportation, and therapeutic mechanisms of antidiabetic drugs, leading to differences in drug disposition, glycemic response, tolerability, and incidence of adverse effects. Additionally, gene-gene, gene-environment, and gene-treatment interactions may also contribute to the variation in disease progression and response to therapy.", + "weight": 1, + "task_id": "849E78D8214245F8E8167E78C01BEE60" +}, +{ + "user_id": "e031ac19-fec1-4d97-a037-cd39d3817c54", + "query": "List as many studies as you can that include rapamycin.", + "answer": "1. A study by Kaeberlein in 2013b on the use of rapamycin to prevent organ transplant rejection, some forms of cancer, and restenosis in cardiac stents.\n2. A study by Mannick et al. in 2014 on the use of rapamycin derivative RAD001 to improve age-associated decline in immune function in healthy elderly people.\n3. A study by Yi et al. in 2014 on the use of rapamycin in dogs to improve outcomes in a glycogen storage disease model.\n4. A study by Paoloni et al. in 2010 on the use of rapamycin in veterinary clinical trials as a treatment for osteosarcoma.\n5. A study by Kaeberlein in 2015 on the use of rapamycin in a veterinary clinical trial to assess side effects and effects on age-associated cardiac function in healthy elderly dogs.\n6. A study by Johnson et al. in 2013 on the use of rapamycin as a pharmacological intervention for extending lifespan and delaying age-related functional declines in rodents.\n7. A study by Augustine et al. in 2007 and de Oliveira et al. in 2011 on the side effects of rapamycin.\n8. A study by Lamming et al. in 2012 on the possible exception of impaired glucose homeostasis as a side effect of rapamycin.\n9. A study by Larson et al. in 2016 on the pharmacokinetic analysis of rapamycin treatment in healthy dogs.\n10. A study by Dai et al. in 2014 and Flynn et al. in 2013 on the improvements in cardiac function in aged dogs and mice after rapamycin treatment.\n11. A study by Johnson et al. in 2015 on the beneficial impacts of rapamycin on multiple age-related phenotypes in aging mice.\n12. A study by Chen et al. in 2009 on the effects of rapamycin on the aged immune system in elderly mice.\n13. A study by Mannick et al. in 2014 on the use of rapamycin derivative RAD001 to enhance the function of the aged immune system in humans.", + "weight": -1, + "task_id": "2C477A3C76794C27A1FBBF437CFF75EE" +}, +{ + "user_id": "e031ac19-fec1-4d97-a037-cd39d3817c54", + "query": "Why is it so diffuclut to map gene loci that control aging in humans?", + "answer": "Mapping gene loci that control aging in humans is difficult due to several reasons. Firstly, aging is a complex phenotype influenced by multiple genes and numerous different pathophysiological processes and diseases. Secondly, any common variation in genes associated with aging probably has a small effect, requiring large studies for identification. Thirdly, human studies face issues like environmental heterogeneity, genetic diversity, and lack of birth matched controls. Lastly, the influence of environmental factors and human-specific confounders like psychosocial, economic, and cultural factors can potentially mask purely biological aging mechanisms, making the analysis more difficult.", + "weight": 1, + "task_id": "CAD6C6C2AB42AA66BFDD65F0F11932B2" +}, +{ + "user_id": "6365589e-a47b-4fa8-a53c-88cb5ee1a991", + "query": "What are the potential benefits and risk associated with gene editing technologies like CRISPRR-Cas9?", + "answer": "The potential benefits of gene editing technologies like CRISPR-Cas9 include precise modification of DNA sequences, which can be used to alter gene function, treat genetic diseases, improve crop species, and advance biomedical research. It can also be used for functional screening in drug development and personalized medicine. However, there are risks and limitations associated with this technology. These include off-target effects or unintended modifications, which could potentially lead to harmful consequences. There's also the risk of triggering an immune response, and the potential for wide-ranging deletions or recombination events. Ethical concerns also arise, particularly in the context of editing human genomes.", + "weight": 1, + "task_id": "EC2BFCD8E06079A3E595114822D2A44D" +}, +{ + "user_id": "6365589e-a47b-4fa8-a53c-88cb5ee1a991", + "query": "How does epigenetics inluence gene expression without changing the underlying DNA sequence?", + "answer": "Epigenetics influences gene expression without changing the underlying DNA sequence through mechanisms such as DNA methylation, histone modifications, and chromatin remodeling. These processes can alter the structure of the DNA and its accessibility to transcription factors, thereby regulating gene expression. For instance, DNA methylation typically represses gene expression, while histone modifications can either enhance or repress gene expression depending on the specific modification. These changes can be heritable and are influenced by environmental and lifestyle factors.", + "weight": -1, + "task_id": "59AA8E8D7A97CFF47C6CFD65629F29F9" +}, +{ + "user_id": "6365589e-a47b-4fa8-a53c-88cb5ee1a991", + "query": "Describe the role of mitochondrial DNA in heredity and how it differs from nuclear DNA.", + "answer": "Mitochondrial DNA (mtDNA) is inherited solely from the maternal lineage, unlike nuclear DNA which requires both paternal and maternal contributions. This uniparental transmission of mtDNA is ensured by complex mechanisms that eliminate paternal mitochondria from sperm during fertilization. mtDNA also exhibits a higher mutation rate than nuclear DNA, leading to significant population-level mtDNA polymorphisms. These polymorphisms can be clustered into distinct haplogroups that represent major branch points on the mitochondrial phylogenetic tree. In contrast, nuclear DNA undergoes bi-parental recombination.", + "weight": 1, + "task_id": "C58CFF41F7422B321DF88A110E278FD5" +}, +{ + "user_id": "6365589e-a47b-4fa8-a53c-88cb5ee1a991", + "query": "What are the ethical considerations surrounding prenatal genetic testing and the selective termination of pregnancies based on genetic factors?", + "answer": "The ethical considerations surrounding prenatal genetic testing and selective termination of pregnancies based on genetic factors include the potential for implicit pressure on individuals to violate personal ethics to reduce financial burden on society, the risk of routinization of testing leading to social or medical expectations of testing in all eligible individuals, and the potential compromise of values of informed consent and individual autonomy. There are also cultural and religious beliefs to consider, as well as the potential psychological impact on parents who may feel guilt if they are carriers of genetic conditions. Furthermore, the decision to terminate a pregnancy based on genetic factors is a joint decision between parents, and the involvement of extended family members in this process varies greatly across different cultures.", + "weight": 1, + "task_id": "BCD1175CCB27FBA1E6F9D7670B17E527" +}, +{ + "user_id": "6365589e-a47b-4fa8-a53c-88cb5ee1a991", + "query": "Create a how-to guide for genetic sequencing.", + "answer": "1. Start with an initial linkage or association: This is the first step in a genetic study where a trait or disease is linked to a specific region of the genome.\n\n2. Perform Laboratory Genotyping: This involves determining the genetic variation of an individual by examining their DNA sequence using biological assays and comparing it to a standard sequence.\n\n3. Use Genomic Sequence: The role of genomic sequence is crucial at every stage. It serves as a common thread that ties all the stages together.\n\n4. Establish True Orthology: Determine the true orthology between genes in different species. If two genes are truly orthologous, their evolution closely follows patterns of speciation.\n\n5. Apply Bioinformatics: Use bioinformatics tools and techniques to analyze the data. This can be applied to sequence data from any collection of organisms.\n\n6. Understand Genome Structure and Content: Provide an overview of genome structure and content to provide a context for subsequent discussions.\n\n7. Improve DNA Sequencing Methods: Constantly work on improving DNA sequencing methods with the ultimate goal of sequencing a human genome in a single day for a cost of about US $1,000.\n\n8. Interpret the Information: The major challenge ahead is the interpretation of this information. Understand how our genes interact with each other, and how the environment contributes to the development of health and disease.\n\n9. Consider the Implications: Understand the individual and societal implications of knowing our genome sequence.\n\n10. Keep Up with Technological Advances: With further technological advances, other previously unimaginable research approaches will become real.", + "weight": 1, + "task_id": "5341FE6588C6175BC8A688A483928BC0" +}, +{ + "user_id": "6365589e-a47b-4fa8-a53c-88cb5ee1a991", + "query": "What is the significance of the length of telomeres?", + "answer": "The length of telomeres is significant as it is associated with aging, disease, and mortality. Longer telomeres are generally associated with better health outcomes, including protection from age-related diseases, better cognitive function, and healthier lipid profiles. Shorter telomeres, on the other hand, have been linked to higher risks of heart disease, infection-related death, and other diseases. Telomere length can also be influenced by factors such as stress, with high-stress situations potentially leading to faster telomere shortening and premature aging.", + "weight": 1, + "task_id": "42847DE50D50E6A9B26ED0B03CFD160E" +}, +{ + "user_id": "6365589e-a47b-4fa8-a53c-88cb5ee1a991", + "query": "Once a sperm combines with an egg, what determines how traits are passed onto the resulting lifeform?", + "answer": "The traits are determined by the combination of genes from both the sperm and the egg. This process involves meiosis, where each gamete (sperm and egg) contributes one chromosome to each pair, resulting in a zygote with a full complement of 23 chromosome pairs. The process of recombination or crossing over, where similar DNA sequences from the paired chromosomes swap genetic material, also plays a crucial role in determining the traits of the offspring. This results in a shuffling of genetic material and contributes to the genetic variation seen among offspring.", + "weight": 1, + "task_id": "12BEAFA9366519672FC8B06959FB2DAF" +}, +{ + "user_id": "6365589e-a47b-4fa8-a53c-88cb5ee1a991", + "query": "Why is genetic tracing matrilineal rather than patrilineal?", + "answer": "Genetic tracing is matrilineal due to the inheritance of mitochondrial DNA (mtDNA), which is passed from mother to all her children without any admixture from the father. This allows for a clear lineage tracing through the maternal line. In contrast, Y-DNA is passed from father to son, allowing for patrilineal tracing, but it does not provide information about the genetic contributions of other ancestors in a family tree.", + "weight": 1, + "task_id": "64FEC152131BC6502E15EA6A6348D70B" +}, +{ + "user_id": "e031ac19-fec1-4d97-a037-cd39d3817c54", + "query": "What is apoptosis?", + "answer": "Apoptosis, also known as cell suicide or programmed cell death, is a biological process in multicellular organisms that allows specific cells to be removed during the development of complex tissues, or potentially dangerous damaged cells to be destroyed for the benefit of the whole organism. It is characterized by a sequence of well-defined events resulting in cell destruction and is necessary for normal cell turnover. It is also essential to various other biological processes.", + "weight": 1, + "task_id": "78A0CD7E12AFEF6865583142603EE039" +}, +{ + "user_id": "e031ac19-fec1-4d97-a037-cd39d3817c54", + "query": "What is the most cited environmental factor for the onset of asthma?", + "answer": "The most cited environmental factor for the onset of asthma is living in an urban area, particularly in low-income settings. Other factors include exposure to air pollution, toxins in food and drink, and aerosols, especially during the rainy season.", + "weight": 1, + "task_id": "33FC2CC0F61BA22E4D095586B95703BD" +}, +{ + "user_id": "b4601142-3b57-4d5b-9b55-80bdf0ea4599", + "query": "genetics", + "answer": "Genetics plays a significant role in various aspects of human life and health, including aging, weight loss, bone traits, physical activity levels, and susceptibility to diseases. Genetic factors can influence lifespan, with certain genes linked to conditions like Alzheimer's disease, heart disease, and cancer. Studies have also shown that genetics can affect the magnitude of weight loss and physical activity levels. In addition, genetics can impact bone traits and the response to different diets. Research on animal models has further demonstrated the influence of genetics on exercise capacity and responses to training regimens.", + "weight": 1, + "task_id": "370380F3A38AC4A788463D14E0EC673A" +}, +{ + "user_id": "b4601142-3b57-4d5b-9b55-80bdf0ea4599", + "query": "what is bioinformatics", + "answer": "Bioinformatics is a field that deals with the application of computer systems to the understanding and organization of biological data. It involves the use of computational tools to gather, store, analyze and integrate biological and genetic information. This can then be used for gene-based drug discovery and development, prediction of protein function from sequence and structural information, and analysis of genomic data.", + "weight": 1, + "task_id": "1E0DA0931F4E3A8C2893353CCA114B10" +}, +{ + "user_id": "e031ac19-fec1-4d97-a037-cd39d3817c54", + "query": "How would one extract the DNA, from say, flora or fauna?", + "answer": "DNA extraction from flora or fauna involves several steps. For flora, a common method is the mixed alkyl trimethyl ammonium bromide (MATAB) procedure. Plant material is ground and incubated in a pre-warmed extraction buffer, then purified with chloroform:isoamylalcohol, and DNA extracts are precipitated with isopropanol. For fauna, DNA can be extracted from various samples such as blood, tissue, or even stool. A common method involves cell rupture in the presence of EDTA to prevent DNA fragmentation, followed by enzymatic digestion of cell walls, solubilization of the cell membrane, and purification using phenol-chloroform extraction and ethanol precipitation. In both cases, the extracted DNA is usually stored at -20 C until use.", + "weight": 1, + "task_id": "59E2406798D265A3CB466B766683E63C" +}, +{ + "user_id": "6365589e-a47b-4fa8-a53c-88cb5ee1a991", + "query": "Explain the process of DNA replication and how it ensures accurate copying of genetic information during cell division.", + "answer": "DNA replication is a process where the DNA molecule creates two identical copies of itself. This process begins with the separation of the two strands of the mother cell DNA. New nucleotides are then assembled to form two double helices identical to the original one. This is facilitated by the base pairing rules where adenine (A) pairs with thymine (T) and cytosine (C) pairs with guanine (G). This ensures that each daughter cell receives an exact copy of the DNA. The replication process is crucial during cell division as it allows for the accurate transmission of genetic information from one generation of cells to the next.", + "weight": -1, + "task_id": "3F9EDFE9A0222EA70459EC8985F134C4" +}, +{ + "user_id": "6365589e-a47b-4fa8-a53c-88cb5ee1a991", + "query": "What are the potential benefits and risks associated with gene editing technologies like CRISPR-Cas9?", + "answer": "The potential benefits of gene editing technologies like CRISPR-Cas9 include the ability to modify genes for the treatment of diseases, improvement of crop species, and the development of personalized drug or cell therapies. It can also be used for functional screening in the development of therapies and for the study of molecular causes of ageing. However, there are risks associated with these technologies. These include off-target effects, which can lead to unwanted mutations, and the potential for wide-ranging deletions or recombination events. There's also a risk of triggering a P53 response leading to apoptosis in cycling cells, and the potential for subjects to generate antibodies to Cas9, which could limit gene therapies. Furthermore, the long-term safety of CRISPR genome editing in humans is yet to be determined.", + "weight": 1, + "task_id": "A010490B55F739DF95BB82DF2B0F5AA3" +}, +{ + "user_id": "d8abfb12-9a11-400a-8cd0-0a436602581c", + "query": "Explain the process of finding a genetic marker followed by a quantitative trait loci.", + "answer": "The process of finding a genetic marker followed by a quantitative trait loci (QTL) involves several steps. First, a population is developed for genetic mapping. This population can be a segregating population or a permanent population. The population is then genotyped using molecular markers. Next, the population is phenotyped for an interested trait. QTL analysis is then conducted using statistical procedures to find markers linked to the QTL. This involves single-marker regression across all chromosomes, where a hypothetical QTL is evaluated at the location of each marker locus. The significance of that QTL is estimated from a likelihood ratio statistic. A permutation test is then conducted to establish genome-wide significance criteria for the trait. The result is a list of marker loci that show a significant association with the trait. These loci are most likely to be near QTLs. The goal of QTL mapping is to identify regions of the genome that harbor genes relevant to a specified trait.", + "weight": 1, + "task_id": "02A94D1056FDA77BDA9AC6CFDE0D5FC6" +}, +{ + "user_id": "d8abfb12-9a11-400a-8cd0-0a436602581c", + "query": "Describe the genotypes related to Alzheimers and dementia which have commonalities with those for aging.", + "answer": "The genotypes related to Alzheimer's and dementia that have commonalities with those for aging include a locus on chromosome 17 associated with the age at onset of Alzheimer's. A specific variant in the CCL11 gene is likely responsible for this association. Additionally, the APOE gene is a strong genetic risk factor for late-onset Alzheimer's, which typically occurs in individuals aged 65 and older. Other genes associated with Alzheimer's include APP, PSEN1, and PSEN2 for early-onset Alzheimer's, and CR1, BIN1, CLU for late-onset Alzheimer's. These genetic factors are believed to interact with environmental components and contribute to the complex etiology of these aging-associated neurodegenerative diseases.", + "weight": 1, + "task_id": "96B873A13E3B386E38940EF6ECA90D4A" +}, +{ + "user_id": "b4601142-3b57-4d5b-9b55-80bdf0ea4599", + "query": "genetics", + "answer": "Genetics plays a significant role in various aspects of human life and health, including aging, weight loss, bone traits, physical activity levels, and susceptibility to diseases. Genetic factors can influence lifespan, with certain genes linked to conditions like Alzheimer's disease, heart disease, and cancer. Studies have also shown that genetics can affect the magnitude of weight loss and physical activity levels. In addition, genetics can impact bone traits and the response to different diets. Research on animal models has further demonstrated the influence of genetics on exercise capacity and responses to training regimens.", + "weight": 1, + "task_id": "A55310A1C19732792B5894A2DB5E8596" +}, +{ + "user_id": "d2f71149-a0d5-4666-95d8-15c82543243b", + "query": "genetics", + "answer": "Genetics plays a significant role in aging, lifespan, and various age-related conditions such as type 2 diabetes, cardiovascular disease, and Alzheimer's disease. Genetic factors also influence weight loss, physical activity levels, and bone traits. Research has identified specific genes and DNA regions that affect lifespan and susceptibility to certain diseases. Studies on animal models have further demonstrated the impact of genetics on aging and metabolic traits.", + "weight": 1, + "task_id": "7CA65F6B192BE7896422284B962CF5C3" +}, +{ + "user_id": "b4601142-3b57-4d5b-9b55-80bdf0ea4599", + "query": "genetics", + "answer": "Genetics plays a significant role in aging, lifespan, and various age-related conditions such as type 2 diabetes, cardiovascular disease, and Alzheimer's disease. Genetic factors also influence weight loss, physical activity levels, and bone traits. Research has identified specific genes and DNA regions that affect lifespan and susceptibility to certain diseases. Studies on animal models have further demonstrated the impact of genetics on aging and metabolic traits.", + "weight": -1, + "task_id": "2EDD65822CDA4669FCAD678288C2E3E9" +}, +{ + "user_id": "b4601142-3b57-4d5b-9b55-80bdf0ea4599", + "query": "which genes are involved in the aging process", + "answer": "The genes involved in the aging process include daf-16, daf-2, BAZ2B, HMGB4, NOC2L, RAI1, SIK1, SMARCA2, SPZ1, TBP, TRIP13, ZKSCAN1, DBH, TPO, LSS, GPER, HCRTR2, ATG2A, NEDD4L, PSMB1, UBXN4, USP6, EEF1A2, ITGB2, TUBB2C, WRN, ABCA7, AZGP1, CD36, DEGS2, PI4KA, SOAT2, APOE, LDLR, CDKN2B, RBM38, IGF1R, FOXO3, SNCA, NAP1L4, GAB2, QKI, and many others.", + "weight": 1, + "task_id": "DA98AC2EA5D1F776D3F04FCBC7F01339" +}, +{ + "user_id": "b4601142-3b57-4d5b-9b55-80bdf0ea4599", + "query": "what causes the aging process", + "answer": "The aging process is caused by a combination of factors including genetic influences, environmental conditions, and stochastic processes. It involves the accumulation of molecular damage, mutations, incomplete repair, and genetic programs. Other factors include wear and tear on cells, decreased immune defenses, oxidation and inefficient mitochondria, toxins and radiation, glycosylation, caloric intake and sirtuin production, neurotransmitter imbalance, hormone mechanisms, reduced nitric oxide, and stem cell slowdown. Aging is also associated with changes in dynamic biological, physiological, environmental, psychological, behavioral, and social processes.", + "weight": 1, + "task_id": "117299AD06C2B147F49E9C9BC036CEA4" +}, +{ + "user_id": "d8abfb12-9a11-400a-8cd0-0a436602581c", + "query": "Describe the genotypes related to Alzheimer's and dementia which have commonalities with those for aging.", + "answer": "The genotypes related to Alzheimer's and dementia that have commonalities with those for aging include a locus on chromosome 17 associated with the age at onset of Alzheimer's. A specific variant in CCL11 is probably responsible for this association. Other genes associated with Alzheimer's include APP, PSEN1, PSEN2, and APOE. These genes are also associated with early-onset and late-onset forms of Alzheimer's, which are more common in older individuals. The APOE gene, specifically the 4 allele, is a significant genetic risk factor for late-onset Alzheimer's. Genome-wide studies have also identified several genetic susceptibility factors for age-related macular degeneration (AMD), another aging-associated neurodegenerative disease.", + "weight": 1, + "task_id": "F4DA6C97230E89C0226B1433532A16D9" +}, +{ + "user_id": "b4601142-3b57-4d5b-9b55-80bdf0ea4599", + "query": "which genes are involved in the aging process", + "answer": "The genes involved in the aging process include daf-16, daf-2, BAZ2B, HMGB4, NOC2L, RAI1, SIK1, SMARCA2, SPZ1, TBP, TRIP13, ZKSCAN1, DBH, TPO, LSS, GPER, HCRTR2, ATG2A, NEDD4L, PSMB1, UBXN4, USP6, EEF1A2, ITGB2, TUBB2C, WRN, ABCA7, AZGP1, CD36, DEGS2, PI4KA, SOAT2, APOE, LDLR, CDKN2B, RBM38, IGF1R, FOXO3, SNCA, NAP1L4, GAB2, QKI, and many others.", + "weight": 0, + "task_id": "FBBFB0D391778CDE9536F742300C1809" +}, +{ + "user_id": "6365589e-a47b-4fa8-a53c-88cb5ee1a991", + "query": "Create a how-to guide for genetic sequencing.", + "answer": "1. Start with an initial linkage or association: This is the first step in a genetic study where a trait or disease is linked to a specific region of the genome.\n\n2. Perform Laboratory Genotyping: This involves determining the genetic variation of an individual by examining their DNA sequence using biological assays and comparing it to a standard sequence.\n\n3. Use Genomic Sequence: The role of genomic sequence is crucial at every stage. It serves as a common thread that ties all the stages together.\n\n4. Establish True Orthology: Determine the true orthology between genes in different species. If two genes are truly orthologous, their evolution closely follows patterns of speciation.\n\n5. Apply Bioinformatics: Use bioinformatics tools and techniques to analyze the data. This can be applied to sequence data from any collection of organisms.\n\n6. Understand Genome Structure and Content: Provide an overview of genome structure and content to provide a context for subsequent discussions.\n\n7. Improve DNA Sequencing Methods: Constantly work on improving DNA sequencing methods with the ultimate goal of sequencing a human genome in a single day for a cost of about US $1,000.\n\n8. Interpret the Information: The major challenge ahead is the interpretation of this information. Understand how our genes interact with each other, and how the environment contributes to the development of health and disease.\n\n9. Consider the Implications: Understand the individual and societal implications of knowing our genome sequence.\n\n10. Keep Up with Technological Advances: With further technological advances, other previously unimaginable research approaches will become real.", + "weight": 1, + "task_id": "32CE1E54032485B73B5968395B3D3538" +}, +{ + "user_id": "6365589e-a47b-4fa8-a53c-88cb5ee1a991", + "query": "What is the significance of the length of telomeres?", + "answer": "The length of telomeres is significant as it is associated with aging, disease, and mortality. Longer telomeres are generally associated with better health outcomes, including protection from age-related diseases, better cognitive function, and healthier lipid profiles. Shorter telomeres, on the other hand, have been linked to higher risks of heart disease, infection-related death, and other diseases. Telomere length can also be influenced by factors such as stress, with high-stress situations potentially leading to faster telomere shortening and premature aging.", + "weight": 1, + "task_id": "59CCE2D70104154865218876DD53D049" +}, +{ + "user_id": "6365589e-a47b-4fa8-a53c-88cb5ee1a991", + "query": "Once a sperm combines with an egg, what determines how traits are passed onto the resulting lifeform?", + "answer": "The traits are determined by the combination of genes from both the sperm and the egg. This process involves meiosis, where each gamete (sperm and egg) contributes one chromosome to each pair, resulting in a zygote with a full complement of 23 chromosome pairs. The process of recombination or crossing over, where similar DNA sequences from the paired chromosomes swap genetic material, also plays a crucial role in determining the traits of the offspring. This results in a shuffling of genetic material and contributes to the genetic variation seen among offspring.", + "weight": 1, + "task_id": "0AE973110158192E0D1F50E1D79764FB" +}, +{ + "user_id": "6365589e-a47b-4fa8-a53c-88cb5ee1a991", + "query": "Why is genetic tracing matrilineal rather than patrilineal?", + "answer": "Genetic tracing is matrilineal due to the inheritance of mitochondrial DNA (mtDNA), which is passed from mother to all her children without any admixture from the father. This allows for a clear lineage tracing through the maternal line. In contrast, Y-DNA is passed from father to son, allowing for patrilineal tracing, but it does not provide information about the genetic contributions of other ancestors in a family tree.", + "weight": 1, + "task_id": "33749EB09AAC7AD0404C8E3E584B98D2" +}, +{ + "user_id": "6365589e-a47b-4fa8-a53c-88cb5ee1a991", + "query": "How does one tell the difference between X and Y DNA, with repsect to DNA tracing and determining QTLs?", + "answer": "The text does not provide specific information on how to differentiate between X and Y DNA in the context of DNA tracing and determining QTLs.", + "weight": 1, + "task_id": "471A145E9CA1E517E462499ABCA8EA2D" +}, +{ + "user_id": "6365589e-a47b-4fa8-a53c-88cb5ee1a991", + "query": "For text and biological resources, do you mean add some books (on biology stuff) or/and web resources (as ensembl) on your system?", + "answer": "The text suggests using online bioinformatics resources such as Ensembl, UCSC Human Genome Browser, and others for research and data analysis. It doesn't specifically mention adding books or web resources to a system, but refers to utilizing these online tools and databases for information retrieval and bioinformatic analysis.", + "weight": 1, + "task_id": "19EBC6CA7E425D0C1279475BD0B411B6" +}, +{ + "user_id": "6365589e-a47b-4fa8-a53c-88cb5ee1a991", + "query": "what is ensembl?", + "answer": "Ensembl is a joint project between the EBI and the Wellcome Trust Sanger Institute that provides a database for genome data. Launched in 1999, it was the first to provide a window on the draft genome, curating the results of computational analyses. It contains automatically annotated genomes and integrates data from a wide range of biological research sources. Ensembl also provides tools for data retrieval and analysis, and it includes quality checks for genetic variants in its variation pipeline.", + "weight": -1, + "task_id": "9CFE932D7898C83E473E590BC77B4FCB" +}, +{ + "user_id": "6ee46240-38bf-4035-b9a8-0d72e29401b5", + "query": "Create a how to guide for genetic sequencing ", + "answer": "1. Start with an initial linkage or association in a genetic study.\n2. Use bioinformatics to analyze the genomic sequence, which is a common thread through every stage.\n3. Establish true orthology between genes in different species, especially if one is identified to play a role in a disease model.\n4. Apply the approaches to sequence data from any collection of organisms, with an emphasis on human genetics.\n5. Understand the genome structure and content to provide context for subsequent discussions.\n6. Utilize genotyping and sequencing technologies to produce, store, and analyze the sequence data.\n7. Use the genome sequence as a framework for integration of genetic and biological data.\n8. Analyze short-read, whole genome, DNA sequences.\n9. Perform comparative analysis of the genome sequences from members of a family to define sequencing errors and genetic heterozygosity.\n10. Track sequence changes/inconsistencies in inheritance from parent to offspring.", + "weight": -1, + "task_id": "C52A9690417093A861C669A0753689BD" +}, +{ + "user_id": "6ee46240-38bf-4035-b9a8-0d72e29401b5", + "query": "What is the significance of the length of telomeres? ", + "answer": "The length of telomeres is significant as it is associated with aging and disease. Shorter telomeres are considered a sign of advanced age and have been linked to age-related diseases, mortality, and higher risk of heart disease and infection-related death. Longer telomeres, on the other hand, are associated with protection from age-related diseases, better cognitive function, and healthier aging. Telomere length can also be influenced by factors such as stress, with high-stress situations potentially leading to faster telomere shortening and thus, accelerated aging.", + "weight": 1, + "task_id": "93DE2EF005059DFEA5A7FBBA3BD17D03" +}, +{ + "user_id": "6ee46240-38bf-4035-b9a8-0d72e29401b5", + "query": "Once a sperm combines with an egg, what determines how traits are passed on to the resulting lifeform? ", + "answer": "The traits are determined by the combination of chromosomes from the sperm and egg during fertilization. Each parent contributes one set of 23 chromosomes, which include both dominant and recessive genes. These genes interact with each other and the environment, and sometimes by chance, to determine the traits of the offspring. The process of meiosis and recombination, or crossing over, also plays a crucial role in shuffling genetic material and creating genetic variation.", + "weight": 1, + "task_id": "477FC54178046FE98BF97FAAC5FE167F" +}, +{ + "user_id": "6ee46240-38bf-4035-b9a8-0d72e29401b5", + "query": "Why is genetic tracing matrilineal rather than patrilineal? ", + "answer": "Genetic tracing is both matrilineal and patrilineal. Matrilineal tracing is done through mitochondrial DNA (mtDNA), which is passed from mother to all her children without any contribution from the father. Patrilineal tracing, on the other hand, is done through Y-DNA, which is passed from father to son. Both types of tracing provide different insights into an individual's ancestry.", + "weight": 1, + "task_id": "6B80ECC5F657EB7CBDE69D411A30D3EA" +}, +{ + "user_id": "6ee46240-38bf-4035-b9a8-0d72e29401b5", + "query": "How does one tell the difference between X and Y DNA, with respect to DNA tracing and determining QTLs?", + "answer": "The difference between X and Y DNA is not explicitly discussed in the context of determining QTLs in the provided text. However, in general, X and Y chromosomes are different in size and gene content, which can be identified through genetic sequencing. In the context of QTL studies, these differences could potentially influence the traits being studied. However, the specific process of how this is done in QTL mapping is not detailed in the provided text.", + "weight": 1, + "task_id": "2DE25ABD7E487B80D0C489319640EACC" +}, +{ + "user_id": "6ee46240-38bf-4035-b9a8-0d72e29401b5", + "query": "what type of dataset is useful for qtl mapping analysis in genenetwork2? ", + "answer": "GeneNetwork2 utilizes datasets containing legacy SNP and transcriptome data for QTL mapping analysis. It also uses gene expression datasets from multiple brain regions and the entirety of > 7,000 BXD Published Phenotypes deposited in GeneNetwork2.", + "weight": 1, + "task_id": "6498ED71891B79908B2E383D9AA5BAC5" +}, +{ + "user_id": "6ee46240-38bf-4035-b9a8-0d72e29401b5", + "query": "What genetic factors influence aging in humans? ", + "answer": "Several genetic factors influence aging in humans. These include genes such as the apolipoprotein E gene (APOE), the forkhead box O3A (FOXO3A) gene, and the exonuclease 1 (EXO1) gene. Other factors include the insulin-IGF1 signaling pathway, the growth hormone or insulinlike growth factor and insulin (GH, IGF, INS) axis, and the heatshock proteins and heat-shock factors. Additionally, genetic variants within genes involved in pathways associated with aging identified in animal models, such as insulin-like growth factor (IGF)-insulin signaling, regulation of lipoprotein metabolism, the mTOR pathway, and the oxidative stress response may also influence survival to old age in humans.", + "weight": 1, + "task_id": "B2F5CB7BCD9A827D3A6E0152C030C4B4" +}, +{ + "user_id": "6ee46240-38bf-4035-b9a8-0d72e29401b5", + "query": "Is there a direct association between aging and susceptibility to having diabetes?", + "answer": "Yes, there is a direct association between aging and susceptibility to having diabetes. The risk of onset of type 2 diabetes increases with age, and most diabetic patients in certain regions are 40 years old or more. Additionally, aging is associated with changes in body composition and glucose tolerance, which can contribute to the development of diabetes.", + "weight": 1, + "task_id": "72FBC4F382B6502EAF41BD6682E63A2D" +}, +{ + "user_id": "6ee46240-38bf-4035-b9a8-0d72e29401b5", + "query": "How does genetics influence the emergency of diabetes? ", + "answer": "Genetics plays a significant role in the emergence of diabetes. Certain forms of the disease result from mutations in a single gene, while others are multifactorial in origin. For example, monogenic forms of diabetes, which account for approximately 5% of cases, are caused by mutations in genes encoding insulin, the insulin receptor, and other factors. In type 1 diabetes, gene variants in the human leukocyte antigen (HLA) locus and about 50 other genes contribute to the genetic risk. These genes modulate immune regulation, viral responses, and responses to environmental signals. Genetic susceptibility to type 1 diabetes is also determined by genes related to immune function. Both type 1 and type 2 diabetes are polygenic diseases where many common variants contribute to overall disease risk.", + "weight": 1, + "task_id": "02C953165B9CA94E273DD4A04301C89F" +}, +{ + "user_id": "e8855be7-59fd-4224-90ad-575e7158c34c", + "query": "Create a how-to guide for genetic sequencing.", + "answer": "1. Start with an initial linkage or association: This is the first step in a genetic study where a trait or disease is linked to a specific region of the genome.\n\n2. Perform Laboratory Genotyping: This involves determining the genetic variation of an individual by examining their DNA sequence using biological assays and comparing it to a standard sequence.\n\n3. Use Genomic Sequence: The role of genomic sequence is crucial at every stage. It serves as a common thread that ties all the stages together.\n\n4. Establish True Orthology: Determine the true orthology between genes in different species. If two genes are truly orthologous, their evolution closely follows patterns of speciation.\n\n5. Apply Bioinformatics: Use bioinformatics tools and techniques to analyze the data. This can be applied to sequence data from any collection of organisms.\n\n6. Understand Genome Structure and Content: Provide an overview of genome structure and content to provide a context for subsequent discussions.\n\n7. Improve DNA Sequencing Methods: Constantly work on improving DNA sequencing methods with the ultimate goal of sequencing a human genome in a single day for a cost of about US $1,000.\n\n8. Interpret the Information: The major challenge ahead is the interpretation of this information. Understand how our genes interact with each other, and how the environment contributes to the development of health and disease.\n\n9. Consider the Implications: Understand the individual and societal implications of knowing our genome sequence.\n\n10. Keep Up with Technological Advances: With further technological advances, other previously unimaginable research approaches will become real.", + "weight": -1, + "task_id": "19DC9E909DDE6D9CDB3E86D1069F5A69" +}, +{ + "user_id": "e8855be7-59fd-4224-90ad-575e7158c34c", + "query": "What is the significance of the length of telomeres?", + "answer": "The length of telomeres is significant as it is associated with aging, disease, and mortality. Longer telomeres are generally associated with better health outcomes, including protection from age-related diseases, better cognitive function, and healthier lipid profiles. Shorter telomeres, on the other hand, have been linked to higher risks of heart disease, infection-related death, and other diseases. Telomere length can also be influenced by factors such as stress, with high-stress situations potentially leading to faster telomere shortening and premature aging.", + "weight": 1, + "task_id": "F2843EA2D5A239D022186329C8D5D8EF" +}, +{ + "user_id": "e8855be7-59fd-4224-90ad-575e7158c34c", + "query": "Once a sperm combines with an egg, what determines how traits are passed onto the resulting lifeform?", + "answer": "The traits are determined by the combination of genes from both the sperm and the egg. This process involves meiosis, where each gamete (sperm and egg) contributes one chromosome to each pair, resulting in a zygote with a full complement of 23 chromosome pairs. The process of recombination or crossing over, where similar DNA sequences from the paired chromosomes swap genetic material, also plays a crucial role in determining the traits of the offspring. This results in a shuffling of genetic material and contributes to the genetic variation seen among offspring.", + "weight": 1, + "task_id": "4E1F0C2E792BAF0BA349326375D3EE6E" +}, +{ + "user_id": "e8855be7-59fd-4224-90ad-575e7158c34c", + "query": "Why is genetic tracing matrilineal rather than patrilineal?", + "answer": "Genetic tracing is matrilineal due to the inheritance of mitochondrial DNA (mtDNA), which is passed from mother to all her children without any admixture from the father. This allows for a clear lineage tracing through the maternal line. In contrast, Y-DNA is passed from father to son, allowing for patrilineal tracing, but it does not provide information about the genetic contributions of other ancestors in a family tree.", + "weight": -1, + "task_id": "FA8ADB009A499F51B0533FDCB72CB29E" +}, +{ + "user_id": "e8855be7-59fd-4224-90ad-575e7158c34c", + "query": "How does one tell the difference between X and Y DNA, with respect to DNA tracing and determining QTLs?", + "answer": "The difference between X and Y DNA is not explicitly discussed in the context of QTLs in the provided text. However, in general, X and Y chromosomes can be differentiated based on their size, gene content, and specific sequences. In the context of QTL mapping, the process would involve identifying the genomic regions affecting a trait, which could be located on any chromosome, including X or Y. The specific methods for tracing and determining QTLs would be the same for all chromosomes.", + "weight": -1, + "task_id": "38BD5864A7928C6DBCA1D844327F3A19" +}, +{ + "user_id": "e8855be7-59fd-4224-90ad-575e7158c34c", + "query": "what genes are associated with diabetes?", + "answer": "The genes associated with diabetes include PPARG, KCNJ11, TCF7L2, SLC30A8, HHEX, CDKN2A, IGF2BP2, CDKAL1, IRS1, CCR5, FTO, NOTCH2, WFS1, JAZF1, ADIPOQ, AHSG, CAPN10, ENPP1, PPARGC1A, SREBF1, PDX1, PFAS, GCK, GIGYF1, HNF1A, TNRC6B, and G6PC2.", + "weight": 1, + "task_id": "2272C482CC247E746D15C9F55EDD8BCE" +}, +{ + "user_id": "e8855be7-59fd-4224-90ad-575e7158c34c", + "query": "what genes are associated with aging?", + "answer": "Several genes are associated with aging. These include NAP1L4, which is involved in chromatin structure and increases with age in skin tissue. Other genes include GAB2, linked to late-onset Alzheimer's disease, and QKI, linked to coronary heart disease and successful aging. Genes such as Lamp2, Fas, and Ghr also show significant co-expression with aging. Other genes involved in aging include those in the IGF-1 and vitamin D pathways, estrogen metabolism pathway genes, and SIR2 genes. Genes like APOE, LDLR, CDKN2B, and RBM38 influence lifespan in model organisms. Genes involved in DNA damage response, antioxidant properties, and protein misfolding also show age-related changes. The gene Cd63 is highly connected in aging-associated gene sets. In muscle aging, genes involved in proteasomal and mitochondrial functions show altered expression. The insulin/insulin-like growth factor 1 (IGF1) signaling pathway also modulates aging.", + "weight": 1, + "task_id": "C6C7CEF19CE7C27CF4BC6906259CDDF9" +}, +{ + "user_id": "e8855be7-59fd-4224-90ad-575e7158c34c", + "query": "what are the bioinformatics tools for QTLs analysis?", + "answer": "The bioinformatics tools for QTL analysis include R/qtl, QTL cartographer, MapQTL, WebQTL, QTL IciMapping, eQTL Explorer, eQTL Viewer, FastMap, Lirnet, and xQTL workbench. Other tools built into resources include QTL Analyst, Semantic Gene Organizer, and various tools for Gene Ontology overrepresentation and pathway matching.", + "weight": 1, + "task_id": "B4BB83EB5D5C5C042E07173119046A13" +}, +{ + "user_id": "e8855be7-59fd-4224-90ad-575e7158c34c", + "query": "what are the statistical approaches for qtls analysis?", + "answer": "The statistical approaches for QTLs (Quantitative Trait Loci) analysis mentioned in the text include regression analysis, permutation tests, Pearson's correlation, and analysis of variance (ANOVA). QTL mapping analysis was performed using the WebQTL module of GeneNetwork. The GEMMA method was also used for QTL mapping on all chromosomes. Additionally, quantitative trait association for SNPs was performed using a series of ANOVA tests.", + "weight": 1, + "task_id": "D88EF655762CE3D524A7A1EEA3FA16ED" +}, +{ + "user_id": "e8855be7-59fd-4224-90ad-575e7158c34c", + "query": "Create a how-to guide for GWAS analysis?", + "answer": "1. Carefully select the populations for the study, ensuring a large number of cases.\n2. Employ centralized SNP genotyping, data coordination, and control centers for quality control checks and standardized annotation.\n3. Conduct SNP-level association tests using methods like the likelihood ratio test (LRT) to obtain SNP level summary statistics.\n4. Perform a gene-level GWAS on the summary statistics using a hierarchically structured prior that incorporates the SNP-gene hierarchical structure.\n5. Use methods like meta-analysis to combine the results of multiple surveys and replication studies on promising variants.\n6. Incorporate existing information about the SNPs into the analysis, such as prior information about linkage or association evidence.\n7. Use tools like ePheWAS for applications in human cohorts.\n8. Share GWAS results to enable further understanding and analyses by other researchers.\n9. Deposit data in a public repository for wider scientific community access.\n10. Follow up on SNPs that merit further replication analysis.\n11. Use post-GWAS tools to make biological sense of the statistical genetic associations.\n12. Finally, report summarization and visualization of the GWAS results.", + "weight": 1, + "task_id": "245DD8093F5D16F44C2AD7618245086C" +}, +{ + "user_id": "0c4a1c25-539f-453a-b7f6-915ab462cf0b", + "query": "Once a sperm combines with an egg, what determines how traits are passed onto the resulting lifeform?", + "answer": "The traits are determined by the combination of genes from both the sperm and the egg. This process involves meiosis, where each gamete (sperm and egg) contributes one chromosome to each pair, resulting in a zygote with a full complement of 23 chromosome pairs. The process of recombination or crossing over, where similar DNA sequences from the paired chromosomes swap genetic material, also plays a crucial role in determining the traits of the offspring. This results in a shuffling of genetic material and contributes to the genetic variation seen among offspring.", + "weight": 1, + "task_id": "B89A904E71CF7F16126FCA9EAAFBC8A6" +}, +{ + "user_id": "d8abfb12-9a11-400a-8cd0-0a436602581c", + "query": "What about recombination in human centromeres?", + "answer": "Human centromeres contain the CENP-B box, a 17-bp motif that is bound by the centromere protein CENP-B. This motif is present on every chromosome except for the Y chromosome. It is necessary for the formation of de novo centromeres on artificial chromosomes, but it is not essential for the formation of neocentromeres. Mice lacking CENP-B are viable and fertile.", + "weight": 1, + "task_id": "2F8796A8C3DC633F00DB901C9BA396DA" +}, +{ + "user_id": "415d39c0-28b8-4711-8d20-081082660f35", + "query": "Create a how-to guide for genetic sequencing.", + "answer": "1. Start with an initial linkage or association: This is the first step in a genetic study where a trait or disease is linked to a specific region of the genome.\n\n2. Perform Laboratory Genotyping: This involves determining the genetic variation of an individual by examining their DNA sequence using biological assays and comparing it to a standard sequence.\n\n3. Use Genomic Sequence: The role of genomic sequence is crucial at every stage. It serves as a common thread that ties all the stages together.\n\n4. Establish True Orthology: Determine the true orthology between genes in different species. If two genes are truly orthologous, their evolution closely follows patterns of speciation.\n\n5. Apply Bioinformatics: Use bioinformatics tools and techniques to analyze the data. This can be applied to sequence data from any collection of organisms.\n\n6. Understand Genome Structure and Content: Provide an overview of genome structure and content to provide a context for subsequent discussions.\n\n7. Improve DNA Sequencing Methods: Constantly work on improving DNA sequencing methods with the ultimate goal of sequencing a human genome in a single day for a cost of about US $1,000.\n\n8. Interpret the Information: The major challenge ahead is the interpretation of this information. Understand how our genes interact with each other, and how the environment contributes to the development of health and disease.\n\n9. Consider the Implications: Understand the individual and societal implications of knowing our genome sequence.\n\n10. Keep Up with Technological Advances: With further technological advances, other previously unimaginable research approaches will become real.", + "weight": -1, + "task_id": "6188C7826173CD59FD243F98C537AD50" +}, +{ + "user_id": "415d39c0-28b8-4711-8d20-081082660f35", + "query": "What is the significance of the length of telomeres?", + "answer": "The length of telomeres is significant as it is associated with aging, disease, and mortality. Longer telomeres are generally associated with better health outcomes, including protection from age-related diseases, better cognitive function, and healthier lipid profiles. Shorter telomeres, on the other hand, have been linked to higher risks of heart disease, infection-related death, and other diseases. Telomere length can also be influenced by factors such as stress, with high-stress situations potentially leading to faster telomere shortening and premature aging.", + "weight": 1, + "task_id": "2C37A2EC74E4B46F13C6FB23D9547DBB" +}, +{ + "user_id": "415d39c0-28b8-4711-8d20-081082660f35", + "query": "How does one tell the difference between X and Y DNA, with respect to DNA tracing and determining QTLs?", + "answer": "The difference between X and Y DNA is not explicitly discussed in the context of determining QTLs in the provided text. However, in general, X and Y chromosomes are different in size and gene content, which can be identified through genetic sequencing. In the context of QTL studies, these differences could potentially influence the traits being studied. However, the specific process of how this is done in QTL mapping is not detailed in the provided text.", + "weight": 1, + "task_id": "590809C6B2A1504E2AE9A79EFDF3AC9A" +}, +{ + "user_id": "415d39c0-28b8-4711-8d20-081082660f35", + "query": "What is the difference between QTL mapping and GWAS?", + "answer": "QTL mapping is a statistical method used to identify regions in the genome that correlate with variation in a phenotype. It has high power, meaning it can detect a QTL, but it does not precisely identify which of the many genes within the QTL is causal. On the other hand, GWAS (Genome-Wide Association Studies) is a method used to identify genetic variants associated with complex traits. It has low power, requiring large numbers of individuals, but it has high precision, often identifying smaller candidate regions.", + "weight": 1, + "task_id": "6DBC070B2E4DC2FE8036E5BA7480B755" +}, +{ + "user_id": "415d39c0-28b8-4711-8d20-081082660f35", + "query": "How do I determine which gene in my QTL is causal for the trait?", + "answer": "To determine which gene in your QTL is causal for the trait, you can start by narrowing down the list of candidate genes within the QTL. This can be done by performing a strain survey, using genetically engineered mice to alter the expression of a candidate gene, or using comparative genomics to narrow down the QTL to a region containing only a few genes. You can then investigate whether the expression of these genes correlates with the phenotype(s) of interest. If a variant within a gene causes a change in its expression, and the expression of that gene correlates with expression of a phenotypic trait of interest, it is considered a good candidate. Network analyses can also be used to build up more evidence for which gene is causal. Finally, you can confirm the candidate genes by complementation of a QTL, which can be achieved in several ways, including transgenic complementation.", + "weight": 1, + "task_id": "5594EA025D9631328071B6A1A7EF1375" +}, +{ + "user_id": "415d39c0-28b8-4711-8d20-081082660f35", + "query": "Which mouse genes have been associated with longevity?", + "answer": "The mouse genes associated with longevity include the C3H allele at D2Mit58, the BALB allele at D16Mit182, the C57BL/6 allele at D4Mit84, the C3H allele at D9Mit110, and the C57BL/6 and C3H alleles at D12Mit167. Additionally, a locus on chromosome 2 and another on chromosome 6 have been associated with longevity.", + "weight": -1, + "task_id": "AB589D2E046B211A7486A6C4BD4ECFB4" +}, +{ + "user_id": "415d39c0-28b8-4711-8d20-081082660f35", + "query": "How is gene expression in the liver affected by diabetes?", + "answer": "In diabetic conditions, the expression of several key gluconeogenic enzymes in the liver is increased despite higher than normal circulating levels of plasma insulin. Additionally, the activities of insulin-dependent enzymes such as glueokinase, glucose 6-phosphate dehydrogenase, citrate lyase, malic enzyme, and acetyl-CoA synthetase are increased. However, the gene Slc2a2 also shows changes in the liver. Some studies also show that liver cells in diabetic mice are hypertrophied and filled with fat droplets.", + "weight": 1, + "task_id": "8FFF9DCC307B8DBF2C8485637F2ABEF4" +}, +{ + "user_id": "415d39c0-28b8-4711-8d20-081082660f35", + "query": "Why do males have two Y chromosomes and females only one?", + "answer": "Actually, males have one Y chromosome and one X chromosome, while females have two X chromosomes. This combination determines the sex of an individual.", + "weight": 1, + "task_id": "C6B9A982C9283DE065A3371F1264095C" +}, +{ + "user_id": "c5e42006-ddba-4b69-b1d1-61b0dceaec86", + "query": " Create a how-to guide for genetic sequencing", + "answer": "1. Choose the appropriate sequencing method: Depending on the specific requirements of your project, you may choose from various sequencing methods such as whole-genome sequencing, exome sequencing, or targeted sequencing.\n\n2. Prepare the sample: Extract the DNA or RNA from your sample. The quality and quantity of the extracted genetic material are crucial for successful sequencing.\n\n3. Library preparation: Prepare a sequencing library. This involves fragmenting the DNA or RNA into smaller pieces, then attaching specific adapters to the ends of these fragments.\n\n4. Sequencing: Use a sequencing platform to read the genetic information. Platforms like Illumina generate massive amounts of short reads.\n\n5. Data analysis: Analyze the sequencing data. This involves aligning the reads to a reference genome, identifying variants, and interpreting the results. Bioinformatics tools and databases such as UCSC Genome Browser, Ensembl, GenBank, MUSCLE, MAFFT, and PRANK can be used for these steps.\n\n6. Validation: Validate the findings using other techniques such as Sanger sequencing or qPCR.\n\n7. Report: Compile the results into a comprehensive report, including methods, findings, and interpretations.\n\nRemember, each step requires careful planning and execution, and the specific details may vary depending on the sequencing method and the research question.", + "weight": 1, + "task_id": "F9F7EA3DC28534B161ED70DB401C7D11" +}, +{ + "user_id": "c5e42006-ddba-4b69-b1d1-61b0dceaec86", + "query": " Create a how-to guide for genetic sequencing.", + "answer": "1. Start with an initial linkage or association study to identify potential genes of interest.\n2. Use bioinformatics tools to analyze the genomic sequence, which is a common thread through every stage.\n3. Establish true orthology between genes in different species, especially if a gene is identified to play a role in a disease model. If two genes are truly orthologous, their evolution closely follows patterns of speciation.\n4. Apply the approaches to sequence data from any collection of organisms, with an emphasis on human genetics.\n5. Present an overview of genome structure and content to provide a context for subsequent discussions.\n6. Use DNA sequencing and other genome technologies to gather information about the mutations and functional abnormalities found in multiple samples from many major types of diseases.\n7. Analyze the sequence data using advanced technologies and bioinformatics.\n8. Finally, interpret the results of the genetic experiment, which can be a challenge on any level.", + "weight": -1, + "task_id": "4A06F8DF54C82D90E02F81D0E1E8B08A" +}, +{ + "user_id": "c5e42006-ddba-4b69-b1d1-61b0dceaec86", + "query": " What is the significance of the length of telomeres?", + "answer": "The length of telomeres is significant as it is associated with aging, age-related diseases, and mortality. Shorter telomeres are generally considered a sign of advanced age and have been linked to higher risks of heart disease, infection-related death, and other diseases. Longer telomeres, on the other hand, are associated with protection from age-related diseases, better cognitive function, and healthier aging. Telomere length can also potentially influence life expectancy, with some studies suggesting that longer telomeres decrease the risk of dying.", + "weight": 1, + "task_id": "BA6A505E62A0529DB883D036CBC1FD92" +}, +{ + "user_id": "0c4a1c25-539f-453a-b7f6-915ab462cf0b", + "query": "Which genes are associated with aging in human ", + "answer": "The genes associated with aging in humans are APOE, FOXO3A, and to some extent, AKT1.", + "weight": 1, + "task_id": "3EC47C56606B02F00CF2449AB311365C" +}, +{ + "user_id": "0c4a1c25-539f-453a-b7f6-915ab462cf0b", + "query": "Create a how-to guide for genetic sequencing", + "answer": "1. Identify the gene or genome of interest for sequencing.\n2. Choose the appropriate sequencing technology, such as next-generation sequencing.\n3. Prepare the sample by extracting DNA and creating a library for sequencing.\n4. Run the sequencing process using the chosen platform.\n5. Analyze the sequencing data using bioinformatics tools. This may include aligning the sequence reads to a reference genome, identifying variants, and interpreting the results.\n6. Validate the results using additional experiments or databases.\n7. Document and share the findings in a suitable format, such as a scientific paper or a database entry.\n8. For further analysis or research, use online resources like the '1000 genomes' project, the Mouse Genome Database, or the UCSC genome browser tutorial.\n9. Stay updated with best practice guidelines for the use of next-generation sequencing applications in genome diagnostics.", + "weight": 1, + "task_id": "CDFC418BD568E839C09656C57808ADA1" +}, +{ + "user_id": "0c4a1c25-539f-453a-b7f6-915ab462cf0b", + "query": "Create a guide for genetic sequencing", + "answer": "1. Initiate a project for sequencing, like the '1000 genomes' project or the rainbow trout project, involving collaborators from various institutions.\n2. Choose a sequencing platform, such as Illumina, and prepare the sample for sequencing.\n3. Use bioinformatics tools to analyze the sequence data. Tools like Seqnature for RNA-seq or Acembly for predicting gene structures can be used.\n4. Construct an individualized pseudogenome for the sample using prior knowledge of variant sites in the sample's genome.\n5. Use online resources like NCBI Map Viewer for graphical depictions of genetic and physical maps and to locate genes, markers, and SNPs on the assembled sequences.\n6. Use websites offering annotation of the draft genome for various analyses such as gene predictions and similarity searches.\n7. Monitor the progress of sequencing online and aim for a resolution of selective constraint down to a segment length of eight nucleotides.", + "weight": -1, + "task_id": "5DEB102510F48D0BF9C278DC895A8BD1" +}, +{ + "user_id": "0c4a1c25-539f-453a-b7f6-915ab462cf0b", + "query": "Once a sperm combines with an egg, what determines how traits are passed onto the resulting lifeform?", + "answer": "The traits are determined by the combination of genes from both the sperm and the egg. This process involves meiosis, where each gamete (sperm and egg) contributes one chromosome to each pair, resulting in a zygote with a full complement of 23 chromosome pairs. The process of recombination or crossing over, where similar DNA sequences from the paired chromosomes swap genetic material, also plays a crucial role in determining the traits of the offspring. This results in a shuffling of genetic material and contributes to the genetic variation seen among offspring.", + "weight": 1, + "task_id": "5A562D5F7A266BA057B6833F3A83E7A7" +}, +{ + "user_id": "0c4a1c25-539f-453a-b7f6-915ab462cf0b", + "query": "Why is genetic tracing matrilineal rather than patrilineal?", + "answer": "Genetic tracing is matrilineal due to the inheritance of mitochondrial DNA (mtDNA), which is passed from mother to all her children without any admixture from the father. This allows for a clear lineage tracing through the maternal line. In contrast, Y-DNA is passed from father to son, allowing for patrilineal tracing, but it does not provide information about the genetic contributions of other ancestors in a family tree.", + "weight": 1, + "task_id": "53905925B4D6F69CE5706896A3C667CE" +}, +{ + "user_id": "0c4a1c26-539f-453a-b7f6-915ab462cf0b", + "query": "How does one tell the difference between X and Y DNA, with respect to DNA tracing and determining QTLs", + "answer": "The text does not provide specific information on how to differentiate between X and Y DNA in the context of DNA tracing and determining Quantitative Trait Loci (QTLs). However, it discusses the process of identifying QTLs, which involves using mapping data from crosses involving more than two inbred strains and sequence variants in the progenitor strains. The strain distribution pattern in the progenitor strains is tested for consistency with the observed genetic effect of the QTL. This process helps assign a probability that any sequence variant is a Quantitative Trait Nucleotide (QTN). The text does not mention the specific roles of X and Y DNA in this process.", + "weight": -1, + "task_id": "C0015BEE5FE41769A65126B79BB1E40D" +} +]
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