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What is the primary effect of severe gibberellin deficiency, as seen in the ga1-3 mutant, on the flowering of Arabidopsis thaliana under short-day conditions? | HORMONES | [
"Arabidopsis thaliana"
] | [
"It causes significantly earlier flowering.",
"It prevents flowering.",
"It induces flowering independently of photoperiod."
] | 10.1105/tpc.10.5.791 | Model Organisms | HORMONES | 10.1105/tpc.10.5.791 | 1,998 | 430 | 1 | Plant Cell | false |
How do gibberellins primarily promote the transition to flowering in Arabidopsis thaliana? | GENE REGULATION | [
"Arabidopsis thaliana"
] | [
"By directly activating the CONSTANS (CO) protein.",
"By activating the promoter of the floral meristem identity gene LEAFY (LFY).",
"By repressing the promoter of the SPINDLY (SPY) gene."
] | 10.1105/tpc.10.5.791 | Model Organisms | GENE REGULATION | 10.1105/tpc.10.5.791 | 1,998 | 430 | 1 | Plant Cell | false |
What is the consequence of the ga1-3 mutation on LEAFY (LFY) promoter activity in Arabidopsis thaliana grown under short days? | GENE REGULATION | [
"Arabidopsis thaliana"
] | [
"LFY promoter activity is delayed but eventually reaches wild-type levels.",
"LFY promoter activity is constitutively high.",
"The induction of LFY promoter activity is absent."
] | 10.1105/tpc.10.5.791 | Model Organisms | GENE REGULATION | 10.1105/tpc.10.5.791 | 1,998 | 430 | 2 | Plant Cell | false |
Can the flowering defect of the gibberellin-deficient ga1-3 mutant Arabidopsis thaliana under short days be overcome? | GROWTH AND DEVELOPMENT | [
"Arabidopsis thaliana"
] | [
"No, the defect is absolute and cannot be rescued genetically.",
"Yes, by increasing the expression of the CONSTANS (CO) gene.",
"Yes, by constitutively expressing the LEAFY (LFY) gene."
] | 10.1105/tpc.10.5.791 | Model Organisms | GROWTH AND DEVELOPMENT | 10.1105/tpc.10.5.791 | 1,998 | 430 | 2 | Plant Cell | false |
In Arabidopsis thaliana, what effect does constitutive gibberellin signal transduction, caused by mutations in the SPINDLY (SPY) gene, have on LEAFY (LFY) expression? | CELL BIOLOGY AND CELL SIGNALING | [
"Arabidopsis thaliana"
] | [
"It decreases LFY promoter activity.",
"It abolishes LFY promoter activity.",
"It increases LFY promoter activity."
] | 10.1105/tpc.10.5.791 | Model Organisms | CELL BIOLOGY AND CELL SIGNALING | 10.1105/tpc.10.5.791 | 1,998 | 430 | 2 | Plant Cell | false |
What is the general interaction preference observed among Arabidopsis MADS box transcription factors identified through yeast two-hybrid assays? | GENE REGULATION | [
"Arabidopsis thaliana"
] | [
"Type I proteins readily form homodimers, while type II proteins exclusively interact with type I proteins.",
"Both type I and type II proteins show equal preference for homodimerization and heterodimerization within and between types.",
"Type II (MIKC) proteins predominantly interact with other type II proteins, while type I proteins often require a Mα type protein to form stable dimers with Mβ or Mγ types."
] | 10.1105/tpc.105.031831 | Model Organisms | GENE REGULATION | 10.1105/tpc.105.031831 | 2,005 | 470 | 2 | Plant Cell | false |
What type of interactions link the flowering time regulation network and the floral organ formation network in Arabidopsis? | GROWTH AND DEVELOPMENT | [
"Arabidopsis thaliana"
] | [
"Flowering time regulators exclusively interact amongst themselves and do not form complexes with floral organ identity proteins.",
"Floral organ identity proteins (like AG, SEP, SHP) interact with both positive (SOC1, AGL24) and negative (SVP) regulators of flowering time.",
"Floral organ identity proteins only interact with positive regulators of flowering time, activating downstream pathways."
] | 10.1105/tpc.105.031831 | Model Organisms | GROWTH AND DEVELOPMENT | 10.1105/tpc.105.031831 | 2,005 | 470 | 1 | Plant Cell | false |
What molecular mechanism is proposed to explain the altered floral phenotypes observed upon ectopic overexpression of flowering time regulators like SVP or AGL24 in Arabidopsis? | GENE REGULATION | [
"Arabidopsis thaliana"
] | [
"These regulators directly bind to floral organ identity gene promoters, causing transcriptional silencing.",
"These ectopically expressed proteins form dominant-negative complexes with floral organ identity proteins (like AP1, SEP3), disrupting their normal function.",
"Overexpression leads to depletion of shared interaction partners, preventing the formation of any functional MADS box complexes."
] | 10.1105/tpc.105.031831 | Model Organisms | GENE REGULATION | 10.1105/tpc.105.031831 | 2,005 | 470 | 1 | Plant Cell | false |
How are higher-order complexes of MIKC-type MADS box proteins typically formed in Arabidopsis? | CELL BIOLOGY AND CELL SIGNALING | [
"Arabidopsis thaliana"
] | [
"They form stable homodimers that do not associate further into higher-order structures.",
"They are often formed as tetramers, hypothesized to consist of two dimers interacting via their C-terminal domains.",
"They primarily form large aggregates through non-specific interactions involving the MADS domain."
] | 10.1105/tpc.105.031831 | Model Organisms | CELL BIOLOGY AND CELL SIGNALING | 10.1105/tpc.105.031831 | 2,005 | 470 | 1 | Plant Cell | false |
What does the comparison of MADS box protein interactions across different plant species, such as Arabidopsis, petunia, and rice, suggest? | EVOLUTION | [
"non-specific"
] | [
"Interactions are conserved only for floral organ identity proteins, but not for flowering time regulators.",
"Many protein-protein interactions among orthologous MADS box proteins are conserved, indicating evolutionary preservation of regulatory networks.",
"MADS box protein interactions are highly species-specific, showing little conservation even between closely related plants."
] | 10.1105/tpc.105.031831 | Non-specific | EVOLUTION | 10.1105/tpc.105.031831 | 2,005 | 470 | 1 | Plant Cell | false |
In rice (Oryza sativa), how do the epigenetic marks DNA methylation and H3K4me3 generally correlate with gene transcription levels in genic regions? | GENE REGULATION | [
"Oryza sativa"
] | [
"Both DNA methylation and H3K4me3 correlate positively with transcription levels.",
"High levels of H3K4me3 correlate positively with transcription, while high levels of DNA methylation correlate negatively.",
"High levels of DNA methylation correlate positively with transcription, while high levels of H3K4me3 correlate negatively."
] | 10.1105/tpc.109.072041 | Model Organisms | GENE REGULATION | 10.1105/tpc.109.072041 | 2,010 | 468 | 1 | Plant Cell | false |
When comparing the rice subspecies Nipponbare and 93-11, what correlation is typically observed between differential DNA methylation in genic regions and differential gene expression? | GENOME AND GENOMICS | [
"Oryza sativa"
] | [
"A strong positive correlation, where higher methylation is associated with higher expression.",
"A weak negative correlation, where higher methylation tends to be associated with lower expression.",
"No significant correlation between differential methylation and differential expression."
] | 10.1105/tpc.109.072041 | Model Organisms | GENOME AND GENOMICS | 10.1105/tpc.109.072041 | 2,010 | 468 | 1 | Plant Cell | false |
In reciprocal hybrids of Oryza sativa subspecies, genes consistently showing nonadditive expression (upregulation relative to mid-parent) are significantly enriched for which biological function? | PHYSIOLOGY AND METABOLISM | [
"Oryza sativa"
] | [
"Energy metabolic processes, including the Calvin cycle.",
"Flowering time regulation.",
"Stress response pathways."
] | 10.1105/tpc.109.072041 | Model Organisms | PHYSIOLOGY AND METABOLISM | 10.1105/tpc.109.072041 | 2,010 | 468 | 0 | Plant Cell | false |
What is the relationship between the difference in expression levels of a gene between two parental rice lines and the allelic expression bias of that gene in their F1 hybrid? | GENE REGULATION | [
"Oryza sativa"
] | [
"There is a strong negative correlation; the allele from the lower-expressing parent tends to be more highly expressed in the hybrid.",
"There is no consistent correlation between parental expression differences and allelic bias in the hybrid.",
"There is a strong positive correlation; the allele from the higher-expressing parent tends to be more highly expressed in the hybrid."
] | 10.1105/tpc.109.072041 | Model Organisms | GENE REGULATION | 10.1105/tpc.109.072041 | 2,010 | 468 | 2 | Plant Cell | false |
What general trend is observed for the expression of small interfering RNA (siRNA) clusters in reciprocal rice hybrids compared to the mid-parent value? | GENE REGULATION | [
"Oryza sativa"
] | [
"More siRNA clusters are upregulated than downregulated, suggesting a general activation in hybrids.",
"siRNA cluster expression generally shows an additive pattern, matching the mid-parent value.",
"More siRNA clusters are downregulated than upregulated, suggesting a general suppression in hybrids."
] | 10.1105/tpc.109.072041 | Model Organisms | GENE REGULATION | 10.1105/tpc.109.072041 | 2,010 | 468 | 2 | Plant Cell | false |
How does the activity level of miR156 influence the relative accumulation of anthocyanins and flavonols in Arabidopsis thaliana stems? | GENE REGULATION | [
"Arabidopsis thaliana"
] | [
"Increased miR156 activity favors flavonol accumulation, while decreased activity favors anthocyanin accumulation.",
"miR156 activity levels affect total flavonoid content but not the ratio between anthocyanins and flavonols.",
"Increased miR156 activity favors anthocyanin accumulation, while decreased activity favors flavonol accumulation."
] | 10.1105/tpc.111.084525 | Model Organisms | GENE REGULATION | 10.1105/tpc.111.084525 | 2,011 | 781 | 2 | Plant Cell | false |
What is the primary regulatory role of the SPL9 transcription factor, a target of miR156, concerning anthocyanin biosynthesis in Arabidopsis thaliana? | GENE REGULATION | [
"Arabidopsis thaliana"
] | [
"SPL9 acts as a negative regulator, suppressing anthocyanin accumulation.",
"SPL9 primarily regulates flavonol biosynthesis, with no direct effect on anthocyanins.",
"SPL9 acts as a positive regulator, promoting anthocyanin accumulation."
] | 10.1105/tpc.111.084525 | Model Organisms | GENE REGULATION | 10.1105/tpc.111.084525 | 2,011 | 781 | 0 | Plant Cell | false |
By what molecular mechanism does the SPL9 transcription factor repress anthocyanin biosynthetic genes like DFR in Arabidopsis thaliana? | GENE REGULATION | [
"Arabidopsis thaliana"
] | [
"SPL9 directly binds to the DFR promoter's core cis-regulatory elements, acting as a transcriptional repressor.",
"SPL9 enhances the degradation of DFR mRNA transcripts post-transcriptionally.",
"SPL9 interacts with the MYB protein PAP1, disrupting the MYB-bHLH-WD40 activation complex."
] | 10.1105/tpc.111.084525 | Model Organisms | GENE REGULATION | 10.1105/tpc.111.084525 | 2,011 | 781 | 2 | Plant Cell | false |
What is the spatial relationship between the expression levels of the anthocyanin biosynthetic gene DFR and the miR156-targeted genes SPL9/SPL15 along the Arabidopsis thaliana stem axis? | GENE REGULATION | [
"Arabidopsis thaliana"
] | [
"DFR expression is highest apically and decreases basally, while SPL9/SPL15 expression shows the inverse pattern.",
"DFR expression is highest basally and decreases apically, while SPL9/SPL15 expression shows the inverse pattern.",
"Both DFR and SPL9/SPL15 expression levels decrease from the base to the apex of the stem."
] | 10.1105/tpc.111.084525 | Model Organisms | GENE REGULATION | 10.1105/tpc.111.084525 | 2,011 | 781 | 1 | Plant Cell | false |
Is the MYB-bHLH-WD40 transcriptional activation complex required for the miR156/SPL pathway to modulate DFR gene expression in Arabidopsis thaliana? | GENE REGULATION | [
"Arabidopsis thaliana"
] | [
"Yes, the complex (including components like PAP1, TT8, TTG1) is necessary for the observed upregulation of DFR when SPL activity is low.",
"No, the miR156/SPL pathway regulates DFR independently of the MYB-bHLH-WD40 complex.",
"The MYB-bHLH-WD40 complex is only required for suppressing DFR expression when SPL activity is high."
] | 10.1105/tpc.111.084525 | Model Organisms | GENE REGULATION | 10.1105/tpc.111.084525 | 2,011 | 781 | 0 | Plant Cell | false |
How do artificial microRNAs (amiRNAs) primarily achieve gene silencing in plants? | BIOTECHNOLOGY | [
"non-specific"
] | [
"By introducing long double-stranded RNA that triggers non-specific degradation.",
"By directly interfering with DNA replication in the nucleus.",
"By utilizing endogenous miRNA precursor processing pathways to produce specific silencing RNAs."
] | 10.1111/j.1365-313X.2007.03328.x | Non-specific | BIOTECHNOLOGY | 10.1111/j.1365-313X.2007.03328.x | 2,008 | 549 | 2 | Plant Journal | false |
What is the predominant mechanism by which most plant miRNAs regulate their target genes? | GENE REGULATION | [
"non-specific"
] | [
"Cleavage of the target mRNA transcript.",
"Inhibition of target mRNA translation initiation.",
"Modification of chromatin structure at the target gene locus."
] | 10.1111/j.1365-313X.2007.03328.x | Non-specific | GENE REGULATION | 10.1111/j.1365-313X.2007.03328.x | 2,008 | 549 | 0 | Plant Journal | false |
Which family of enzymes is responsible for processing long RNA precursors into functional silencing RNAs (miRNAs and siRNAs) in plants like Arabidopsis thaliana? | CELL BIOLOGY AND CELL SIGNALING | [
"Arabidopsis thaliana"
] | [
"RNA-dependent RNA Polymerases (RDRs).",
"Dicer-like (DCL) enzymes.",
"Argonaute (AGO) proteins."
] | 10.1111/j.1365-313X.2007.03328.x | Model Organisms | CELL BIOLOGY AND CELL SIGNALING | 10.1111/j.1365-313X.2007.03328.x | 2,008 | 549 | 1 | Plant Journal | false |
What is the fundamental principle behind Virus-Induced Gene Silencing (VIGS) in plants? | BIOTECHNOLOGY | [
"non-specific"
] | [
"Using viral proteins to directly bind and inhibit plant gene promoters.",
"Exploiting the plant's antiviral defense system by using modified viruses to express sequences homologous to target plant genes, leading to their silencing.",
"Introducing viral RNA that enhances the expression of specific plant genes."
] | 10.1111/j.1365-313X.2007.03328.x | Non-specific | BIOTECHNOLOGY | 10.1111/j.1365-313X.2007.03328.x | 2,008 | 549 | 1 | Plant Journal | false |
According to design principles for effective siRNAs/miRNAs, what characteristic often correlates with efficient incorporation into the silencing complex (RISC)? | GENE REGULATION | [
"non-specific"
] | [
"High GC content throughout the small RNA sequence.",
"Perfect complementarity along the entire length of the target mRNA.",
"Thermodynamic instability at the 5' end of the guide strand."
] | 10.1111/j.1365-313X.2007.03328.x | Non-specific | GENE REGULATION | 10.1111/j.1365-313X.2007.03328.x | 2,008 | 549 | 2 | Plant Journal | false |
What primarily characterizes quantitative disease resistance (QDR) in plants compared to qualitative resistance? | GENE REGULATION | [
"non-specific"
] | [
"It always provides complete and durable immunity against all pathogen races.",
"It is controlled by a single major R-gene providing complete immunity.",
"It is typically controlled by multiple genetic loci, each contributing a small effect towards resistance."
] | 10.1016/j.tplants.2008.10.006 | Non-specific | GENE REGULATION | 10.1016/j.tplants.2008.10.006 | 2,009 | 562 | 2 | TIPS | false |
What is a major limitation of relying solely on single R-gene mediated resistance for crop protection? | EVOLUTION | [
"non-specific"
] | [
"Resistance conferred by single R-genes can often be overcome by pathogen evolution, leading to resistance breakdown.",
"R-genes only provide quantitative resistance, never complete immunity.",
"R-genes are only effective against bacterial pathogens, not fungal ones."
] | 10.1016/j.tplants.2008.10.006 | Non-specific | EVOLUTION | 10.1016/j.tplants.2008.10.006 | 2,009 | 562 | 0 | TIPS | false |
Which type of genes, involved in recognizing conserved microbial patterns, are hypothesized to contribute to quantitative disease resistance (QDR) through allelic variation? | CELL BIOLOGY AND CELL SIGNALING | [
"non-specific"
] | [
"Genes controlling plant flowering time exclusively.",
"Major R-genes that recognize specific pathogen effectors.",
"Pattern-recognition receptors (PRRs) like FLS2 or CERK1 involved in basal defense."
] | 10.1016/j.tplants.2008.10.006 | Non-specific | CELL BIOLOGY AND CELL SIGNALING | 10.1016/j.tplants.2008.10.006 | 2,009 | 562 | 2 | TIPS | false |
How might some Quantitative Resistance Loci (QRLs) be related to classical Resistance (R) genes? | GENOME AND GENOMICS | [
"non-specific"
] | [
"Some QRLs may represent weaker alleles or 'defeated' versions of R-genes, sometimes retaining residual or race-specific effects.",
"QRLs exclusively encode detoxification enzymes, while R-genes encode receptors.",
"QRLs and R-genes always operate through completely independent molecular pathways."
] | 10.1016/j.tplants.2008.10.006 | Non-specific | GENOME AND GENOMICS | 10.1016/j.tplants.2008.10.006 | 2,009 | 562 | 0 | TIPS | false |
What does the characterization of the rice QRL pi21 suggest about the genetic basis of quantitative disease resistance? | GENOME AND GENOMICS | [
"Oryza sativa"
] | [
"The pi21 gene encodes a typical NB-LRR resistance protein.",
"QDR can be mediated by genes with novel functions, not necessarily related to known R-genes or defense signaling pathways.",
"All QRLs are allelic variants of classical R-genes."
] | 10.1016/j.tplants.2008.10.006 | Model Organisms | GENOME AND GENOMICS | 10.1016/j.tplants.2008.10.006 | 2,009 | 562 | 1 | TIPS | false |
How do non-essential heavy metals like Cadmium (Cd) primarily enter plant cells? | PHYSIOLOGY AND METABOLISM | [
"non-specific"
] | [
"Exclusively by binding to cell wall pectins and polysaccharides.",
"By utilizing transporters intended for essential inorganic ions with similar properties.",
"Through passive diffusion across the plasma membrane only."
] | 10.1016/j.tplants.2008.10.007 | Non-specific | PHYSIOLOGY AND METABOLISM | 10.1016/j.tplants.2008.10.007 | 2,009 | 912 | 1 | TIPS | false |
Which key subcellular locations are predominant sources of Reactive Oxygen Species (ROS) generation in plant cells under metal stress? | CELL BIOLOGY AND CELL SIGNALING | [
"non-specific"
] | [
"Vacuoles, cell wall, and cytosol.",
"Nucleus, endoplasmic reticulum, and Golgi apparatus.",
"Chloroplasts, mitochondria, and peroxisomes."
] | 10.1016/j.tplants.2008.10.007 | Non-specific | CELL BIOLOGY AND CELL SIGNALING | 10.1016/j.tplants.2008.10.007 | 2,009 | 912 | 2 | TIPS | false |
What are some major enzymatic and non-enzymatic components of the plant cellular antioxidant defense system? | PHYSIOLOGY AND METABOLISM | [
"non-specific"
] | [
"Heavy metal transporters and storage lipids.",
"Phytohormones like Auxin and Cytokinin, and structural proteins.",
"Enzymes like Superoxide Dismutase (SOD), Ascorbate Peroxidase (APX), Catalase (CAT), and molecules like Glutathione (GSH) and Ascorbate."
] | 10.1016/j.tplants.2008.10.007 | Non-specific | PHYSIOLOGY AND METABOLISM | 10.1016/j.tplants.2008.10.007 | 2,009 | 912 | 2 | TIPS | false |
In Arabidopsis thaliana, what was the effect of overproducing Serine Acetyl Transferase (SAT) from the hyperaccumulator Thlaspi goesingense? | BIOTECHNOLOGY | [
"Arabidopsis thaliana"
] | [
"It enhanced resistance to Ni-induced growth inhibition and oxidative stress, coinciding with increased levels of OAS, Cys, and GSH.",
"It decreased tolerance to Nickel (Ni) due to excessive cysteine production.",
"It specifically increased phytochelatin levels without altering glutathione (GSH) concentration."
] | 10.1016/j.tplants.2008.10.007 | Model Organisms | BIOTECHNOLOGY | 10.1016/j.tplants.2008.10.007 | 2,009 | 912 | 0 | TIPS | false |
What specific protective role does α-tocopherol (Vitamin E) play in Arabidopsis thaliana when exposed to copper (Cu) or cadmium (Cd)? | PHYSIOLOGY AND METABOLISM | [
"Arabidopsis thaliana"
] | [
"It acts as an antioxidant, protecting against metal-induced oxidative stress and lipid peroxidation.",
"It functions as a signaling molecule to directly activate heavy metal efflux pumps.",
"It serves as the primary chelator, directly binding and sequestering Cu and Cd ions."
] | 10.1016/j.tplants.2008.10.007 | Model Organisms | PHYSIOLOGY AND METABOLISM | 10.1016/j.tplants.2008.10.007 | 2,009 | 912 | 0 | TIPS | false |
How does stomatal conductance typically respond to sustained high Vapor Pressure Deficit (VPD) in most plant species? | PHYSIOLOGY AND METABOLISM | [
"non-specific"
] | [
"It remains unchanged.",
"It increases.",
"It declines."
] | 10.1111/nph.16485 | Non-specific | PHYSIOLOGY AND METABOLISM | 10.1111/nph.16485 | 2,020 | 1,262 | 2 | New Phy | false |
How does the stomatal sensitivity to increasing leaf-to-air Vapor Pressure Deficit (VPDL) generally compare between mesic plant species and desert plant species, relative to their stomatal conductance at low VPDL (gsref)? | PHYSIOLOGY AND METABOLISM | [
"non-specific"
] | [
"Desert species generally exhibit higher sensitivity compared to mesic species.",
"Mesic species generally exhibit higher sensitivity (e.g., sensitivity parameter m ≈ 0.6 × gsref) compared to desert species (e.g., m ≈ 0.4 × gsref).",
"Both mesic and desert species exhibit equally low sensitivity relative to their gsref."
] | 10.1111/nph.16485 | Non-specific | PHYSIOLOGY AND METABOLISM | 10.1111/nph.16485 | 2,020 | 1,262 | 1 | New Phy | false |
What significant role has elevated Vapor Pressure Deficit (VPD) been identified to play in recent drought-associated events affecting conifers in regions like southwestern USA? | ENVIRONMENT | [
"non-specific"
] | [
"It primarily enhances tree growth and resilience against drought.",
"It has a negligible impact on tree mortality compared to pathogen attacks or soil nutrient depletion.",
"It is a major contributor to tree mortality, sometimes more strongly correlated with mortality than temperature or precipitation anomalies."
] | 10.1111/nph.16485 | Non-specific | ENVIRONMENT | 10.1111/nph.16485 | 2,020 | 1,262 | 2 | New Phy | false |
What fundamental trade-off do recent goal-oriented stomatal models, like the gain-risk algorithm, propose that stomata balance? | PHYSIOLOGY AND METABOLISM | [
"non-specific"
] | [
"The rate of water uptake from soil against the rate of nutrient absorption from leaves.",
"The risk of hydraulic stress (e.g., cavitation) against the opportunity for photosynthetic gain.",
"The energy cost of stomatal movement against the energy gained from root respiration."
] | 10.1111/nph.16485 | Non-specific | PHYSIOLOGY AND METABOLISM | 10.1111/nph.16485 | 2,020 | 1,262 | 1 | New Phy | false |
In seed plants, what transient stomatal response is often observed immediately before the steady-state decrease in stomatal conductance following exposure to increased leaf-to-air Vapor Pressure Deficit (VPDL)? | PHYSIOLOGY AND METABOLISM | [
"non-specific"
] | [
"Stomata temporarily 'pop open' to a wider aperture.",
"Stomata immediately close to their minimum possible aperture.",
"Stomata exhibit a rapid and sustained oscillation between fully open and fully closed states."
] | 10.1111/nph.16485 | Non-specific | PHYSIOLOGY AND METABOLISM | 10.1111/nph.16485 | 2,020 | 1,262 | 0 | New Phy | false |
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